NCBI Conserved Domain Search

The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188816 Cd Length: 56 Bit Score: 128.75 E-value: 1.40e-35

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 929 CTACVKPITGIGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCA 984
Cdd:cd09432    1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDCA 56

The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188805 Cd Length: 59 Bit Score: 127.69 E-value: 3.26e-35

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 744 FANTCEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYD 802
Cdd:cd09421    1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCYD 59

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 118.31 E-value: 5.76e-32

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 744 FANTCEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYD 802
Cdd:cd09343    1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECYS 59

The second LIM domain of protein LIMPETin and related proteins; The second LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188801 Cd Length: 56 Bit Score: 118.02 E-value: 6.61e-32

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 694 LIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYE 741
Cdd:cd09417    9 LIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188814 Cd Length: 52 Bit Score: 117.58 E-value: 1.05e-31

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09430    1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188809 Cd Length: 54 Bit Score: 116.00 E-value: 3.36e-31

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09425    1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 110.50 E-value: 3.30e-29

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09346    1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188733 Cd Length: 56 Bit Score: 109.74 E-value: 6.99e-29

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 929 CTACVKPITGIGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCA 984
Cdd:cd09347    1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPECG 56

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 104.22 E-value: 4.40e-27

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 694 LIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYE 741
Cdd:cd09341    9 LIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188818 Cd Length: 56 Bit Score: 98.29 E-value: 6.24e-25

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 929 CTACVKPITGIGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09434    1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 94.67 E-value: 1.06e-23

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09345    1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188817 Cd Length: 58 Bit Score: 92.75 E-value: 5.38e-23

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 929 CTACVKPITGIGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCAK 985
Cdd:cd09433    1 CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPECGK 57

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 91.98 E-value: 1.16e-22

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECFGELFA 926
Cdd:cd09431    1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 102.32 E-value: 6.12e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 101 KRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEA 180
Cdd:COG1196  240 ELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLE 319

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 181 EENQRKQRENEEKERLENER-RLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAE 259
Cdd:COG1196  320 ELEEELAELEEELEELEEELeELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELA 399

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 260 AAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELspsATESELEEDAAIAEQSRRLISSRTDLEQKQRMIE 339
Cdd:COG1196  400 AQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEE---ALEEAAEEEAELEEEEEALLELLAELLEEAALLE 476

                        250       260       270
                 ....*....|....*....|....*....|..
gi 320545982 340 ENARRFLEAEEEMVMLQQRQLQASHSKEEADE 371
Cdd:COG1196  477 AALAELLEELAEAAARLLLLLEAEADYEGFLE 508

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 88.42 E-value: 1.91e-21

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982 744 FANTCEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYDAQF 805
Cdd:cd09422    1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECYSNEY 62

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 83.71 E-value: 7.71e-20

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09429    1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 91.15 E-value: 1.62e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  50 AAADAEELPRMRERLDKQIKEAAEREALAGTNVMQdgvlYVNGIRvdPAGDKRQALAAELARQQQIEADTRRQLAEAEAK 129
Cdd:COG1196  265 LEAELEELRLELEELELELEEAQAEEYELLAELAR----LEQDIA--RLEERRRELEERLEELEEELAELEEELEELEEE 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 130 LVEERLRVQREKEESEEQQRKLVEAERQRER-EQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRLIDAERE 208
Cdd:COG1196  339 LEELEEELEEAEEELEEAEAELAEAEEALLEaEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLER 418

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 209 REENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALRD 288
Cdd:COG1196  419 LEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAELLEEAALLEAALAELLEELAEAAARLLLLLE 498

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 289 AE----------IVERLLAAERELSPS-----ATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMV 353
Cdd:COG1196  499 AEadyegflegvKAALLLAGLRGLAGAvavliGVEAAYEAALEAALAAALQNIVVEDDEVAAAAIEYLKAAKAGRATFLP 578

                        330
                 ....*....|....*...
gi 320545982 354 MLQQRQLQASHSKEEADE 371
Cdd:COG1196  579 LDKIRARAALAAALARGA 596

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 77.11 E-value: 1.99e-17

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYEEKF 866
Cdd:cd09424    1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188730 Cd Length: 54 Bit Score: 75.95 E-value: 4.69e-17

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNC 800
Cdd:cd09344    1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 74.50 E-value: 1.66e-16

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 806 ASRCDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYE 863
Cdd:cd09427    1 SSKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCYE 58

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 81.91 E-value: 1.15e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 101 KRQALAAELARQQQIEADTRrqlaEAEAKLVE-ERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREaERRQLE 179
Cdd:COG1196  206 ERQAEKAERYRELKEELKEL----EAELLLLKlRELEAELEELEAELEELEAELEELEAELAELEAELEELRL-ELEELE 280

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 180 AEENQRKQRENEEKERLENERRLIDaerereenerrlqeaeeqrereeserrivVAERQREQAEAEKERAEQQRilaeae 259
Cdd:COG1196  281 LELEEAQAEEYELLAELARLEQDIA-----------------------------RLEERRRELEERLEELEEEL------ 325

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 260 aAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSAT------ESELEEDAAIAEQSRRLISSRTDLEQ 333
Cdd:COG1196  326 -AELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAelaeaeEELEELAEELLEALRAAAELAAQLEE 404

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 320545982 334 KQRMIEENARRFLEAEEEMVMLQQRQLQASHSKEEA 369
Cdd:COG1196  405 LEEAEEALLERLERLEEELEELEEALAELEEEEEEE 440

The first LIM domain of Four and a half LIM domains protein 3 (FHL3); The first LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188807 Cd Length: 59 Bit Score: 71.88 E-value: 1.55e-15

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 744 FANTCEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09423    1 FANTCDECKELIGHDSRELYYEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188810 Cd Length: 57 Bit Score: 70.85 E-value: 2.76e-15

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYEEK 865
Cdd:cd09426    1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEKQ 57

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188802 Cd Length: 56 Bit Score: 69.76 E-value: 6.90e-15

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 694 LIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYE 741
Cdd:cd09418    9 IIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188734 Cd Length: 64 Bit Score: 67.87 E-value: 3.94e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982 926 AKRCTACVKPITGIG-GTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCAKQ 986
Cdd:cd09348    2 AKKCSGCQNPITGFGkGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDCAKK 63

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 76.63 E-value: 6.10e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    54 AEELPRMRERLDKQiKEAAEReALAGTNVMQDGVLYVNGIRVDPAGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEE 133
Cdd:TIGR02168  195 LNELERQLKSLERQ-AEKAER-YKELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEEL 272

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   134 RLRVQREKEESEEQQRKLVEAerqrEREQAEKELQEQREAERRqleaeENQRKQRENEEKERLENERRLIDAEREREENE 213
Cdd:TIGR02168  273 RLEVSELEEEIEELQKELYAL----ANEISRLEQQKQILRERL-----ANLERQLEELEAQLEELESKLDELAEELAELE 343

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   214 RRLQEAEEQREREESErrivVAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAeiVE 293
Cdd:TIGR02168  344 EKLEELKEELESLEAE----LEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDR--RE 417

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 320545982   294 RLLAAERELSPSATESELEE--------DAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQ 359
Cdd:TIGR02168  418 RLQQEIEELLKKLEEAELKElqaeleelEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARL 491

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 66.19 E-value: 1.02e-13

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 870 CIKCNKVITSGGV-TYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd08368    1 CAGCGKPIEGRELlRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 63.56 E-value: 8.90e-13

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 320545982   869 RCIKCNKVITSG--GVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:smart00132   1 KCAGCGKPIYGTerVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

The second LIM domain of Testin; The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188800 Cd Length: 56 Bit Score: 63.34 E-value: 1.26e-12

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 320545982 694 LIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09416    9 LIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKPCY 55

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 70.54 E-value: 3.42e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  113 QQIEADTRRQLAEAEAKLVEERLRVQREKEESE-EQQRKLVEAERQRereQAEKELQEQREAERRQLEAEENQRKQRENE 191
Cdd:pfam17380 279 QHQKAVSERQQQEKFEKMEQERLRQEKEEKAREvERRRKLEEAEKAR---QAEMDRQAAIYAEQERMAMERERELERIRQ 355

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  192 EKERLENER---RLIDAEREREENERRLQEAEEQREREESERriVVAERQREQAEAEKERAEQQRILAEAEAAQAERRLF 268
Cdd:pfam17380 356 EERKRELERirqEEIAMEISRMRELERLQMERQQKNERVRQE--LEAARKVKILEEERQRKIQQQKVEMEQIRAEQEEAR 433

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  269 DAEIQRERDQADEEGQALRDAEI-----VERLLAAERELSPSATESELEE-DAAIAEQSRRLISSRTDLEQKQRMIEE-N 341
Cdd:pfam17380 434 QREVRRLEEERAREMERVRLEEQerqqqVERLRQQEEERKRKKLELEKEKrDRKRAEEQRRKILEKELEERKQAMIEEeR 513

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 320545982  342 ARRFLEAEEEMvmlQQRQLQASHSKEEADEYAGMEPVVEE 381
Cdd:pfam17380 514 KRKLLEKEMEE---RQKAIYEEERRREAEEERRKQQEMEE 550

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 61.63 E-value: 4.01e-12

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 320545982   748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNC 800
Cdd:smart00132   2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 61.63 E-value: 5.43e-12

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 320545982   808 RCDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGC 861
Cdd:smart00132   1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 60.41 E-value: 1.27e-11

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320545982 695 IFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd08368    8 IEGRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 59.70 E-value: 2.24e-11

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982   928 RCTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:smart00132   1 KCAGCGKPIYG--TERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 67.84 E-value: 2.60e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  103 QALAAELARQQQIEADTRRQLAEAEAKLveERLRVQREKEESEE--QQRKLVEAERQREREQAEKELQEQREAERRQLEA 180
Cdd:pfam17380 323 KARQAEMDRQAAIYAEQERMAMEREREL--ERIRQEERKRELERirQEEIAMEISRMRELERLQMERQQKNERVRQELEA 400

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  181 --------EENQRK----QRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIV---VAERQREQAEAE 245
Cdd:pfam17380 401 arkvkileEERQRKiqqqKVEMEQIRAEQEEARQREVRRLEEERAREMERVRLEEQERQQQVERLrqqEEERKRKKLELE 480

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  246 KERAEQQRIlaeaeaAQAERRLFDAEIQRERdqadeegQALRDAEIVERLLaaERELSPSATESELEEDAAIAEQSRRL- 324
Cdd:pfam17380 481 KEKRDRKRA------EEQRRKILEKELEERK-------QAMIEEERKRKLL--EKEMEERQKAIYEEERRREAEEERRKq 545

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982  325 --ISSRTDLEQKQRMIEENARRFLEAEEEMVMLqqRQLQASHSKEEadEYAGMEPVVeelCVKKVAPPRFQE--PPE 397
Cdd:pfam17380 546 qeMEERRRIQEQMRKATEERSRLEAMEREREMM--RQIVESEKARA--EYEATTPIT---TIKPIYRPRISEyqPPD 615

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 58.99 E-value: 4.28e-11

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 925 FAKRCTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09343    1 FANTCEECKKKIGC--DSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTEC 57

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 58.11 E-value: 8.42e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982  870 CIKCNKVITSGGVTY-KNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECFGELF 925
Cdd:pfam00412   1 CAGCNRPIYDRELVRaLGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 58.10 E-value: 9.25e-11

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRaGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd08368    1 CAGCGKPIE-GRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 57.71 E-value: 1.00e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIgIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd08368    1 CAGCGKPI-EGRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

The third LIM domain of Testin-like family; The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188728 Cd Length: 57 Bit Score: 57.79 E-value: 1.33e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWH--EACFLCFKCHLSLVDKQFGAKADKIYC 797
Cdd:cd09342    1 CDACGEPIGPDVQRVAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFC 52

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];

Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 64.51 E-value: 1.37e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  55 EELPRMRERLDKQIKEAAER---------EALAGTNVMQDgvlyvNGIrVDPAGDKRQALAAELARQQ--QIEADTRRQL 123
Cdd:COG2268  143 EELNEDREKFAEKVQEVAGTdlaknglelESVAITDLEDE-----NNY-LDALGRRKIAEIIRDARIAeaEAERETEIAI 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 124 AEAEaklveerlrvqREKEESEEQQRKLVEAER--QREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERlenERR 201
Cdd:COG2268  217 AQAN-----------REAEEAELEQEREIETARiaEAEAELAKKKAEERREAETARAEAEAAYEIAEANAEREV---QRQ 282

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 202 LidaerereenerrlqeaeeqrEREESERRIVVAERQREQAEAEKERAEQQRilaeaeaaqaerrlfdAEIQRERDQADE 281
Cdd:COG2268  283 L---------------------EIAEREREIELQEKEAEREEAELEADVRKP----------------AEAEKQAAEAEA 325

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 320545982 282 EGQA-------LRDAEIVERLLAAERELSPSATESEL 311
Cdd:COG2268  326 EAEAeairakgLAEAEGKRALAEAWNKLGDAAILLML 362

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188733 Cd Length: 56 Bit Score: 57.35 E-value: 1.51e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEECNK-IIGI-DSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNC 800
Cdd:cd09347    1 CAACTKpITGLgGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55

The third LIM domain of Testin-like family; The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188728 Cd Length: 57 Bit Score: 57.40 E-value: 1.51e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWH--ENCFCCCVCKTAIGTKSFIPREQEIYCAG 860
Cdd:cd09342    1 CDACGEPIGPDVQRVAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFCSP 54

cell envelope integrity inner membrane protein TolA; Provisional

Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 64.06 E-value: 1.83e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  95 VDPAgdkrqALAAELARQQQIEADTRRQlAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAE 174
Cdd:PRK09510  55 VDPG-----AVVEQYNRQQQQQKSAKRA-EEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAA 128

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 175 RRQLEAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQ 251
Cdd:PRK09510 129 LKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEA 205

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 57.22 E-value: 1.94e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982 805 FASRCDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYEEKF 866
Cdd:cd09422    1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECYSNEY 62

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 64.78 E-value: 2.75e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   98 AGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQqRKLVEAERQREREQAE--KELQEQREAER 175
Cdd:PTZ00121 1466 AEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA-KKAEEAKKADEAKKAEeaKKADEAKKAEE 1544

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  176 RQlEAEENQRKQ--RENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQ---AEAEKERAE 250
Cdd:PTZ00121 1545 KK-KADELKKAEelKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEakkAEEAKIKAE 1623

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  251 QQRILAEAEAAQAERRLFDAEIQRERDQ--ADEEGQALRDAEIVERllAAERELSPSATESELEEDAAIAEQSRRLISSR 328
Cdd:PTZ00121 1624 ELKKAEEEKKKVEQLKKKEAEEKKKAEElkKAEEENKIKAAEEAKK--AEEDKKKAEEAKKAEEDEKKAAEALKKEAEEA 1701

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982  329 TDLEQKQRMIEENARRF--LEAEEEMVMLQQRQLQashSKEEADEYAGMEPVVEELCVKKVAPPRFQEPPEEPMVHKVK 405
Cdd:PTZ00121 1702 KKAEELKKKEAEEKKKAeeLKKAEEENKIKAEEAK---KEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEK 1777

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188818 Cd Length: 56 Bit Score: 56.31 E-value: 3.21e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEECNK-IIGI-DSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNC 800
Cdd:cd09434    1 CAACNKpITGFgGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 64.39 E-value: 3.51e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   49 DAAADAEELPRMRERlDKQIKEAAEREALAGTNVMQDGVLYVNGIRVDPAGDKRQALAAELARQQQIEADTRRQLAEAEA 128
Cdd:PTZ00121 1326 EAKKKADAAKKKAEE-AKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDK 1404

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  129 KLVEERLRVQREKEESEEQQRKlveAERQREREQAEKELQEQREAERRQLEAEEnqrKQRENEEKERLENERRLIDAERE 208
Cdd:PTZ00121 1405 KKADELKKAAAAKKKADEAKKK---AEEKKKADEAKKKAEEAKKADEAKKKAEE---AKKAEEAKKKAEEAKKADEAKKK 1478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  209 REENERRLQEAEEQREREESERRIVVAERQREQAEaEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADE--EGQAL 286
Cdd:PTZ00121 1479 AEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKAD-EAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADElkKAEEL 1557

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  287 RDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEE---------NARRFLEAEEEMVMLQQ 357
Cdd:PTZ00121 1558 KKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEakkaeeakiKAEELKKAEEEKKKVEQ 1637

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  358 RQLQASHSKEEADEYAGMEpvvEELCVKKVAPPRfQEPPEEPMVHKVKTQFGQGSGPEDAYSAKSKTltfpgvSDEGSSL 437
Cdd:PTZ00121 1638 LKKKEAEEKKKAEELKKAE---EENKIKAAEEAK-KAEEDKKKAEEAKKAEEDEKKAAEALKKEAEE------AKKAEEL 1707

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  438 EPKTPFSIQQSSfSTQPSDEGNRIESERPEPEGEDQIQEVQYtedyLRSLDGIKNRPlmredgSGRRRAFKKRRSSGSSN 517
Cdd:PTZ00121 1708 KKKEAEEKKKAE-ELKKAEEENKIKAEEAKKEAEEDKKKAEE----AKKDEEEKKKI------AHLKKEEEKKAEEIRKE 1776

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  518 SSRESRASRDEELKMFTSLEEEELRHGDREDYNPIKYTSEPTLRVKSHRRHKRSPAKDVRPTAEST-TSLEMLGEESTNP 596
Cdd:PTZ00121 1777 KEAVIEEELDEEDEKRRMEVDKKIKDIFDNFANIIEGGKEGNLVINDSKEMEDSAIKEVADSKNMQlEEADAFEKHKFNK 1856

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  597 WGEVVPEHYKDTEFWKREKALSIDEEEIELERPSR---GEDVEEEATNEPKSSSFEEATEAQNEQavaalkqqlsKEQLD 673
Cdd:PTZ00121 1857 NNENGEDGNKEADFNKEKDLKEDDEEEIEEADEIEkidKDDIEREIPNNNMAGKNNDIIDDKLDK----------DEYIK 1926

                         650       660       670
                  ....*....|....*....|....*....|....*...
gi 320545982  674 KEAEKDNPQAVDTSDSNKSNLIFSGEYTKAMDKDWHSG 711
Cdd:PTZ00121 1927 RDAEETREEIIKISKKDMCINDFSSKFCDYMKDNISSG 1964

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188734 Cd Length: 64 Bit Score: 56.31 E-value: 4.19e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 867 ATRCIKCNKVITSGG-----VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09348    2 AKKCSGCQNPITGFGkgtnvVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60

The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188805 Cd Length: 59 Bit Score: 56.04 E-value: 4.46e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 866 FATRCIKCNKVI--TSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09421    1 FANQCEECSKIIgiDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188812 Cd Length: 54 Bit Score: 56.00 E-value: 5.34e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09428    1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPCF 54

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188733 Cd Length: 56 Bit Score: 55.81 E-value: 5.75e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 870 CIKCNKVITSGG----VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09347    1 CAACTKPITGLGgakfISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 55.47 E-value: 5.87e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09336    1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 55.76 E-value: 6.13e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09345    1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 55.42 E-value: 7.03e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 320545982  695 IFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYENVF 744
Cdd:pfam00412   8 IYDRELVRALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

The third LIM domain of Prickle; The third LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188804 Cd Length: 59 Bit Score: 55.14 E-value: 1.09e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWH--ENCFCCCVCKTAIGTKSFIPREQEIYCA 859
Cdd:cd09420    3 CDTCGEHIGVDQGQMTYDGQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYCS 55

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 54.75 E-value: 1.33e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 866 FATRCIKCNKVI--TSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09343    1 FANTCEECKKKIgcDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 54.82 E-value: 1.33e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 929 CTACVKPITGIGgtrfISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCAK 985
Cdd:cd09429    1 CVKCNKPITSGG----VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

The third LIM domain of Prickle; The third LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188804 Cd Length: 59 Bit Score: 54.37 E-value: 1.98e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWH--EACFLCFKCHLSLVDKQFGAKADKIYC 797
Cdd:cd09420    3 CDTCGEHIGVDQGQMTYDGQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYC 54

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 53.87 E-value: 2.26e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIgiDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09346    1 CAKCKKAI--TSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 53.86 E-value: 2.52e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 929 CTACVKPITGiggTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCA 984
Cdd:cd08368    1 CAGCGKPIEG---RELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188805 Cd Length: 59 Bit Score: 53.73 E-value: 2.95e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 925 FAKRCTACVKPItGIGgTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09421    1 FANQCEECSKII-GID-SKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNC 57

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 53.49 E-value: 3.03e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 929 CTACVKPITGiGGtrfISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09346    1 CAKCKKAITS-GG---VTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDC 51

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 53.76 E-value: 3.38e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 925 FAKRCTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09422    1 YSNTCEECKKPIGC--DCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTEC 57

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 53.61 E-value: 3.50e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYDAQF 805
Cdd:cd09424    1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188814 Cd Length: 52 Bit Score: 53.25 E-value: 4.17e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIgiDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09430    1 CSKCNKII--NSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 53.11 E-value: 4.43e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982  748 CEECNKiiGIDSKDLSY-KDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:pfam00412   1 CAGCNR--PIYDRELVRaLGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDY 53

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 60.72 E-value: 4.52e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  49 DAAADAEELPRMRERLDKQIKEAAEREALAGTNVMQDGVLYVNGIRVDPAGDKRQALAAELARQQQIEADT--RRQLAEA 126
Cdd:COG1196  551 IVVEDDEVAAAAIEYLKAAKAGRATFLPLDKIRARAALAAALARGAIGAAVDLVASDLREADARYYVLGDTllGRTLVAA 630

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 127 EAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRLIDAE 206
Cdd:COG1196  631 RLEAALRRAVTLAGRLREVTLEGEGGSAGGSLTGGSRRELLAALLEAEAELEELAERLAEEELELEEALLAEEEEERELA 710

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 207 REREEnerrlqeaeeqrereeserrivvAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQAL 286
Cdd:COG1196  711 EAEEE-----------------------RLEEELEEEALEEQLEAEREELLEELLEEEELLEEEALEELPEPPDLEELER 767

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 287 RDAEIVERL-------LAAERELspsatESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENAR-RFLEA 348
Cdd:COG1196  768 ELERLEREIealgpvnLLAIEEY-----EELEERYDFLSEQREDLEEARETLEEAIEEIDRETReRFLET 832

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 53.23 E-value: 5.08e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECFGELF 925
Cdd:cd09424    1 CKGCYKDILAGDqnVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 52.77 E-value: 5.52e-09

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 320545982   699 EYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKC 739
Cdd:smart00132  14 RVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 52.72 E-value: 7.96e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982  809 CDGCGEVFRAGTKKMEYKTRqWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYEEKF 866
Cdd:pfam00412   1 CAGCNRPIYDRELVRALGKV-WHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188810 Cd Length: 57 Bit Score: 52.74 E-value: 8.04e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYDAQ 804
Cdd:cd09426    1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEKQ 57

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 52.12 E-value: 9.07e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKiiGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09429    1 CVKCNK--PITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52

The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188816 Cd Length: 56 Bit Score: 51.71 E-value: 1.48e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEECNK-IIGID-SKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNC 800
Cdd:cd09432    1 CAACGKpITGIGgTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55

Caldesmon;

Pssm-ID: 460421 [Multi-domain] Cd Length: 495 Bit Score: 58.34 E-value: 1.58e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  107 AELARQQQIEADTRRQLaEAEAKLveERLRVQREKEESEEQQRKlveAERQREREQAEKELQEQREAERRQLEAEENQRK 186
Cdd:pfam02029 228 GGLSQSQEREEEAEVFL-EAEQKL--EELRRRRQEKESEEFEKL---RQKQQEAELELEELKKKREERRKLLEEEEQRRK 301

                          90
                  ....*....|....*
gi 320545982  187 QRENEEKERLENERR 201
Cdd:pfam02029 302 QEEAERKLREEEEKR 316

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 51.45 E-value: 2.17e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 869 RCIKCNKVITSGGVTY-KNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09341    2 RCAACDELIFSGEYTQaEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 58.53 E-value: 2.20e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   155 ERQREREQAEKELQEQrEAERRQLEAEENQ-RKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREReeserriv 233
Cdd:TIGR02168  674 ERRREIEELEEKIEEL-EEKIAELEKALAElRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQ-------- 744

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   234 vAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSpsateselEE 313
Cdd:TIGR02168  745 -LEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELT--------LL 815

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982   314 DAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQLQASHSKEEA 369
Cdd:TIGR02168  816 NEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEEL 871

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 58.16 E-value: 2.95e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    47 SVDAAADAEELPRMRERLdkqikEAAEREalagtnvmqdgvlyvngirvdpagdkRQALAAELARQQQIEADTRRQLAEA 126
Cdd:TIGR02169  666 ILFSRSEPAELQRLRERL-----EGLKRE--------------------------LSSLQSELRRIENRLDELSQELSDA 714

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   127 EAKLVEERLRVQREKEESEEQQRKLVEAER-----QREREQAEKELQE------QREAERRQLEAEENQRKQREN----- 190
Cdd:TIGR02169  715 SRKIGEIEKEIEQLEQEEEKLKERLEELEEdlsslEQEIENVKSELKElearieELEEDLHKLEEALNDLEARLShsrip 794

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   191 ---EEKERLENERRLIDAEREREENERRlqeaeeqrereeserrivvaERQREQAEAEKERAEQQRILAeaeaaqaerrl 267
Cdd:TIGR02169  795 eiqAELSKLEEEVSRIEARLREIEQKLN--------------------RLTLEKEYLEKEIQELQEQRI----------- 843

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   268 fDAEIQR-ERDQADEEGQA-LRD-AEIVERLLAAERELspsatESELEEdaaIAEQSRRLISSRTDLEQKQRMIEEnarr 344
Cdd:TIGR02169  844 -DLKEQIkSIEKEIENLNGkKEElEEELEELEAALRDL-----ESRLGD---LKKERDELEAQLRELERKIEELEA---- 910

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320545982   345 flEAEEEMVMLQQRQLQASHSKEEADEYAGMEPVVEElcvkkvapprfqEPPEEPMVHKVKTQ 407
Cdd:TIGR02169  911 --QIEKKRKRLSELKAKLEALEEELSEIEDPKGEDEE------------IPEEELSLEDVQAE 959

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 56.70 E-value: 3.55e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 101 KRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLveAERQREREQAEKELQEQREAERRQLEA 180
Cdd:COG4942   35 EIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAEL--AELEKEIAELRAELEAQKEELAELLRA 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 181 eeNQRKQRENEEKERLENE------RRLI----------DAEREREENERRLQEAEEQREREESERRIVVAERQREQAEA 244
Cdd:COG4942  113 --LYRLGRQPPLALLLSPEdfldavRRLQylkylaparrEQAEELRADLAELAALRAELEAERAELEALLAELEEERAAL 190

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982 245 EKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALrdaeivERLLAAERELSPSA 306
Cdd:COG4942  191 EALKAERQKLLARLEKELAELAAELAELQQEAEELEALIARL------EAEAAAAAERTPAA 246

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188734 Cd Length: 64 Bit Score: 50.92 E-value: 4.29e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 745 ANTCEECNKII---GIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNC 800
Cdd:cd09348    2 AKKCSGCQNPItgfGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 56.99 E-value: 5.45e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    62 ERLDKQIKEAAEREALAGtnvmqdgvlyvngIRVDPAGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREK 141
Cdd:TIGR02168  680 EELEEKIEELEEKIAELE-------------KALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLE 746

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   142 EESEEQQRKLVEAERQRE-----REQAEKELQEQrEAERRQLEAEENQRKQRENEEKERLE------------------- 197
Cdd:TIGR02168  747 ERIAQLSKELTELEAEIEeleerLEEAEEELAEA-EAEIEELEAQIEQLKEELKALREALDelraeltllneeaanlrer 825

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   198 ---NERRLIDAEREREENERRL-----QEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAAQAERRLFD 269
Cdd:TIGR02168  826 lesLERRIAATERRLEDLEEQIeelseDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRE 905

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   270 AEiqRERDQADEEGQALRD--AEIVERLLAAEREL----SPSATESELEEDAAIAEQSRRLiSSRTDLEQKQRMIEENAR 343
Cdd:TIGR02168  906 LE--SKRSELRRELEELREklAQLELRLEGLEVRIdnlqERLSEEYSLTLEEAEALENKIE-DDEEEARRRLKRLENKIK 982

                          330       340       350
                   ....*....|....*....|....*....|..
gi 320545982   344 RF----LEAEEEMVMLQQRQLQASHSKEEADE 371
Cdd:TIGR02168  983 ELgpvnLAAIEEYEELKERYDFLTAQKEDLTE 1014

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 55.54 E-value: 8.61e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 105 LAAELARQQQIEADTRRQLAEAEAKL--VEERLRVQREKEESEEQQRKLVE---AERQREREQAEKELQEQrEAERRQLE 179
Cdd:COG4942   11 LALAAAAQADAAAEAEAELEQLQQEIaeLEKELAALKKEEKALLKQLAALErriAALARRIRALEQELAAL-EAELAELE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 180 AEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAE 259
Cdd:COG4942   90 KEIAELRAELEAQKEELAELLRALYRLGRQPPLALLLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAEL 169

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 260 AAQAerrlfdAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQR 336
Cdd:COG4942  170 EAER------AELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEELEALIARLEAEAAAAA 240

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 49.60 E-value: 8.62e-08

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 320545982 705 DKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYENVFA 745
Cdd:cd09431   17 DQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 56.08 E-value: 1.03e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  109 LARQQQIEADTRRQLAEAEAKLVEerlrVQREKEESEEQQRKLveaerqrerEQAEKELQEQREAERRQLEAEENQRKQR 188
Cdd:COG4913   598 IRSRYVLGFDNRAKLAALEAELAE----LEEELAEAEERLEAL---------EAELDALQERREALQRLAEYSWDEIDVA 664

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  189 ENEEK-ERLENERRLIDAerereenerrlqeaeeqrereeSERRIVVAERQREQAEAEKERAEQQRILAEAEAAQAERRL 267
Cdd:COG4913   665 SAEREiAELEAELERLDA----------------------SSDDLAALEEQLEELEAELEELEEELDELKGEIGRLEKEL 722

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  268 fdAEIQRERDQA-DEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLissRTDLEQKQRMIEENARRFL 346
Cdd:COG4913   723 --EQAEEELDELqDRLEAAEDLARLELRALLEERFAAALGDAVERELRENLEERIDAL---RARLNRAEEELERAMRAFN 797


                  ..
gi 320545982  347 EA 348
Cdd:COG4913   798 RE 799

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 49.21 E-value: 1.11e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 929 CTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09345    1 CKACGKAIMP--GSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPC 53

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 56.30 E-value: 1.22e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  105 LAAELARQQQIEADTRR---QLAEAEAKLVEERLRVQREKEESEEQQRKlveAERQREREQAEKELQE-QREAERRQLEA 180
Cdd:PTZ00121 1262 MAHFARRQAAIKAEEARkadELKKAEEKKKADEAKKAEEKKKADEAKKK---AEEAKKADEAKKKAEEaKKKADAAKKKA 1338

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  181 EENQR--------------------KQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQRE 240
Cdd:PTZ00121 1339 EEAKKaaeaakaeaeaaadeaeaaeEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKK 1418

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  241 QAEAEKERAEQQRILAEAEAAQAERRLFD-----AEIQRERDQADEEGQALRDAEIVERllAAERELSPSATESELEEDA 315
Cdd:PTZ00121 1419 KADEAKKKAEEKKKADEAKKKAEEAKKADeakkkAEEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAK 1496

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  316 AIAEQSRRLISSRTDLEQKQRmiEENARRFLEAEEEMVMLQQRQLQASHSKEEADEYAGMEPVVEELCVKKVAPPRFQEP 395
Cdd:PTZ00121 1497 KKADEAKKAAEAKKKADEAKK--AEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEE 1574

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  396 PEEPMVHKVKtqfgQGSGPEDAYSAKSKTLTFPGVSDEGSSLEPKTPFSIQQSSFSTQPSDEGNRIESERPEPEGEDQIQ 475
Cdd:PTZ00121 1575 DKNMALRKAE----EAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAE 1650

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  476 EVQYTEDYlrslDGIKNRPLMREDGSGRRRAFKKRRSSGSSNSSRESRASRDEELKmftslEEEELRHGDREDynpiKYT 555
Cdd:PTZ00121 1651 ELKKAEEE----NKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAK-----KAEELKKKEAEE----KKK 1717

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  556 SEPTLRVKSHRRHKRSPAKDVRPTAESTTSLEMLGEESTNPWGEVVPEHYKDTEFWKREKALSIDEeeiELERPSRGEDV 635
Cdd:PTZ00121 1718 AEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEE---ELDEEDEKRRM 1794

                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....
gi 320545982  636 EEEATNEPKSSSFEEATEAQNEqavAALKQQLSKEQLDKEAEkdnpQAVDTSDS 689
Cdd:PTZ00121 1795 EVDKKIKDIFDNFANIIEGGKE---GNLVINDSKEMEDSAIK----EVADSKNM 1841

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188726 Cd Length: 58 Bit Score: 48.75 E-value: 1.53e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEECNKIIGIDS----KDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCG 798
Cdd:cd09340    1 CEKCKEPINPGEvavfAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCG 55

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188818 Cd Length: 56 Bit Score: 48.60 E-value: 1.94e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 809 CDGCGEVFRA--GTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGC 861
Cdd:cd09434    1 CAACNKPITGfgGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 48.60 E-value: 2.10e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 929 CTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCAKQK 987
Cdd:cd09424    1 CKGCYKDILA--GDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKK 57

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 55.31 E-value: 2.14e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   45 DSSVDAAADA-----EELPRMRERLDKqikEAAEREALAgtnvmqdgvlyvngiRVDPAGDKRQALAAELARQQQIEADT 119
Cdd:COG4913   220 EPDTFEAADAlvehfDDLERAHEALED---AREQIELLE---------------PIRELAERYAAARERLAELEYLRAAL 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  120 RRQLAEAEAKLVEERLrvQREKEESEEQQRKLVEAERQRER-EQAEKELQEQ-REAERRQLEAEENQRKQRENEEKERLE 197
Cdd:COG4913   282 RLWFAQRRLELLEAEL--EELRAELARLEAELERLEARLDAlREELDELEAQiRGNGGDRLEQLEREIERLERELEERER 359

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  198 NERRLIDAEREREENERRLQEaeeqrereeserrivVAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAeiQRERD 277
Cdd:COG4913   360 RRARLEALLAALGLPLPASAE---------------EFAALRAEAAALLEALEEELEALEEALAEAEAALRDL--RRELR 422

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 320545982  278 QADEEGQALR------DAEIVERLLAAERELSPSATE 308
Cdd:COG4913   423 ELEAEIASLErrksniPARLLALRDALAEALGLDEAE 459

The first LIM domain of lipoma preferred partner (LPP); The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188737 [Multi-domain] Cd Length: 54 Bit Score: 48.58 E-value: 2.15e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCN-KVITSG-GVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAE 919
Cdd:cd09351    1 CVKCGeKVLGEGsGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEE 52

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.

Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 51.19 E-value: 2.17e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  111 RQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQA-EKELQEQREAERRQLEAEENQRKQRE 189
Cdd:pfam05672  33 ERLEKEEEERLRKEELRRRAEEERARREEEARRLEEERRREEEERQRKAEEEAeEREQREQEEQERLQKQKEEAEAKARE 112

                          90
                  ....*....|...
gi 320545982  190 NEEKERLENERRL 202
Cdd:pfam05672 113 EAERQRQEREKIM 125

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 48.44 E-value: 2.18e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09345    1 CKACGKAIMPGSkkMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

The first LIM domain of Four and a half LIM domains protein 3 (FHL3); The first LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188807 Cd Length: 59 Bit Score: 48.38 E-value: 2.67e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 805 FASRCDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09423    1 FANTCDECKELIGHDSRELYYEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 54.76 E-value: 2.82e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   98 AGDKRQALAAELARQQQIEADTRRQlaeAEAKLVEERLRVQREKEESEEQQRklVEAERQREREQAEKELQEQREAERRQ 177
Cdd:PTZ00121 1196 AEDARKAEAARKAEEERKAEEARKA---EDAKKAEAVKKAEEAKKDAEEAKK--AEEERNNEEIRKFEEARMAHFARRQA 1270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  178 LEAEENQRKQRENEEKErlenERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAE 257
Cdd:PTZ00121 1271 AIKAEEARKADELKKAE----EKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAE 1346

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  258 AEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRM 337
Cdd:PTZ00121 1347 AAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK 1426

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  338 IEE--NARRFLEAEEEMVMLQQRQLQASHSK--EEADEYAGMEPVVEELCVKKVAPPRFQEPPEEPMVHKVKTQFGQGSG 413
Cdd:PTZ00121 1427 AEEkkKADEAKKKAEEAKKADEAKKKAEEAKkaEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAA 1506

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  414 PEDAYSAKSKTLTFPGVSDEGSSLEPKTPFSIQQSSFSTQPSDEGNRIE----------SERPEPEGEDQIQEVQYTEDy 483
Cdd:PTZ00121 1507 EAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEelkkaeekkkAEEAKKAEEDKNMALRKAEE- 1585

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  484 LRSLDGIKNRPLMREDGSGRRRAFKKRRSSGSSNSSRESRASRDEELKMFTSL---EEEELRHGDR----EDYNPIKYTS 556
Cdd:PTZ00121 1586 AKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLkkkEAEEKKKAEElkkaEEENKIKAAE 1665

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  557 EPTLRVKSHRR---------HKRSPAKDVRPTAESTTSLEMLGEESTNPWGEVvpEHYKDTEFWKREKALSIDEEEIELE 627
Cdd:PTZ00121 1666 EAKKAEEDKKKaeeakkaeeDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKA--EELKKAEEENKIKAEEAKKEAEEDK 1743

                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982  628 RPSRGEDVEEEATNEPKSSSFEEATEAQNeqaVAALKQQLSKEQLDKEAEKDNPQAVDTSDSNKSN 693
Cdd:PTZ00121 1744 KKAEEAKKDEEEKKKIAHLKKEEEKKAEE---IRKEKEAVIEEELDEEDEKRRMEVDKKIKDIFDN 1806

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 48.09 E-value: 2.83e-07

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 320545982 705 DKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09346   17 DQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The second LIM domain of protein LIMPETin and related proteins; The second LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188801 Cd Length: 56 Bit Score: 48.30 E-value: 2.85e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 868 TRCIKCNKVITSGGVTYK-NEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09417    1 DRSVQCDELIFSGEYTKAmNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCY 55

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 54.68 E-value: 3.16e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    62 ERLDKQIKEAAEREALAGTNVMQDGVlyvngiRVDPAGDKRQALAAELARQQQieadtrrQLAEAEAKLVEERLRVQREK 141
Cdd:TIGR02168  298 SRLEQQKQILRERLANLERQLEELEA------QLEELESKLDELAEELAELEE-------KLEELKEELESLEAELEELE 364

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   142 EESEEQQRKLVEAERQREREQAE-KELQEQREAERRQLEAEENQrKQRENEEKERLENERR-LIDAEREREENERRLQEA 219
Cdd:TIGR02168  365 AELEELESRLEELEEQLETLRSKvAQLELQIASLNNEIERLEAR-LERLEDRRERLQQEIEeLLKKLEEAELKELQAELE 443

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982   220 EEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAEIQRER 276
Cdd:TIGR02168  444 ELEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARLDSLERLQEN 500

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 54.69 E-value: 3.29e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   120 RRQLAEAEAKLVE-----ERLRVQREK-EESEEQQRKLVEAE----------RQREREQAEKELQEQrEAERRQLEAEEN 183
Cdd:TIGR02169  183 EENIERLDLIIDEkrqqlERLRREREKaERYQALLKEKREYEgyellkekeaLERQKEAIERQLASL-EEELEKLTEEIS 261

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   184 QRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAAQA 263
Cdd:TIGR02169  262 ELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEEL 341

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   264 ERRLfdAEIQRERDQADEEGQALRDaeiVERLLAAERElspsateselEEDAAIAEQSRRLISSRTDLEQKQRMIEENAR 343
Cdd:TIGR02169  342 EREI--EEERKRRDKLTEEYAELKE---ELEDLRAELE----------EVDKEFAETRDELKDYREKLEKLKREINELKR 406

                          250
                   ....*....|....*....
gi 320545982   344 RFLEAEEEMVMLQQRQLQA 362
Cdd:TIGR02169  407 ELDRLQEELQRLSEELADL 425

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188730 Cd Length: 54 Bit Score: 47.83 E-value: 3.36e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09344    1 CAECRKPIGADSkeLHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53

The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188721 [Multi-domain] Cd Length: 54 Bit Score: 47.73 E-value: 3.57e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQ-RFTSRDEKPYCAECF 921
Cdd:cd09335    1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTLKsKFYEFDMKPVCKKCY 53

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 47.98 E-value: 3.58e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 808 RCDGCGEVFRAG--TKKMEyktRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYE 863
Cdd:cd09341    2 RCAACDELIFSGeyTQAEG---KNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188871 [Multi-domain] Cd Length: 54 Bit Score: 47.80 E-value: 4.13e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAGTKKMEyKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09840    1 CSRCGDSVYAAEKIMG-AGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 47.38 E-value: 4.50e-07

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 320545982 698 GEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09336   10 GQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 53.38 E-value: 6.74e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   98 AGDKRQALAAELARQQQ--IEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAER 175
Cdd:COG4913   608 NRAKLAALEAELAELEEelAEAEERLEALEAELDALQERREALQRLAEYSWDEIDVASAEREIAELEAELERLDASSDDL 687

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  176 RQLEAEENQRKQRENEEKERLEnerRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRIl 255
Cdd:COG4913   688 AALEEQLEELEAELEELEEELD---ELKGEIGRLEKELEQAEEELDELQDRLEAAEDLARLELRALLEERFAAALGDAV- 763

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  256 aeaeaaqaeRRLFDAEIQRERDQADEEGQALRDAeiVERLLAAERELSPSATeSELEEDAAIAEQSRRLISS--RTDLEQ 333
Cdd:COG4913   764 ---------ERELRENLEERIDALRARLNRAEEE--LERAMRAFNREWPAET-ADLDADLESLPEYLALLDRleEDGLPE 831

                         250
                  ....*....|....*...
gi 320545982  334 KQ----RMIEENARRFLE 347
Cdd:COG4913   832 YEerfkELLNENSIEFVA 849

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188802 Cd Length: 56 Bit Score: 47.04 E-value: 7.56e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 808 RCDGCGEVFRAgTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYE 863
Cdd:cd09418    2 RCSACDEIIFA-DECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188730 Cd Length: 54 Bit Score: 47.06 E-value: 7.59e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 929 CTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCA 984
Cdd:cd09344    1 CAECRKPIGA--DSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKCT 54

The third LIM domain of Testin-like family; The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188728 Cd Length: 57 Bit Score: 46.62 E-value: 9.20e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 929 CTACVKPItGIGGTRfISFEDRHWH--HDCFVCASCKASLVGRGFITDGPDILC-PDCA 984
Cdd:cd09342    1 CDACGEPI-GPDVQR-VAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFCsPKCK 57

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]

Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 52.16 E-value: 9.67e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  103 QALAAELARQQQIEADTRRQLAEAEAKLveerlrvQREKEESEEQQRKlvEAERQREREQAEKELQEQREAERRQLEAEE 182
Cdd:TIGR02794  46 GAVAQQANRIQQQKKPAAKKEQERQKKL-------EQQAEEAEKQRAA--EQARQKELEQRAAAEKAAKQAEQAAKQAEE 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  183 NQRKQRENEEKERLENerrlidaerereenerrlqeaeeqrereeserrivvaeRQREQAEAE---KERAEQQRILAEAE 259
Cdd:TIGR02794 117 KQKQAEEAKAKQAAEA--------------------------------------KAKAEAEAErkaKEEAAKQAEEEAKA 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  260 AAQaerrlfdAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIE 339
Cdd:TIGR02794 159 KAA-------AEAKKKAEEAKKKAEAEAKAKAEAEAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKADE 231

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 320545982  340 ENARRFLEAEEEMVMLQQRQLQASHSKEEADEYAGM 375
Cdd:TIGR02794 232 AELGDIFGLASGSNAEKQGGARGAAAGSEVDKYAAI 267

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 46.77 E-value: 1.01e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYD 802
Cdd:cd09427    4 CVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCYE 58

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 53.05 E-value: 1.01e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    60 MRERLDKQIKEAAEREALAGTNVMQDGvlyvNGIRVDPAGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQR 139
Cdd:pfam02463  726 RVQEAQDKINEELKLLKQKIDEEEEEE----EKSRLKKEEKEEEKSELSLKEKELAEEREKTEKLKVEEEKEEKLKAQEE 801

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   140 EKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEA 219
Cdd:pfam02463  802 ELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEE 881

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   220 EEQREREESERRIVVAERQREQAEAEKERA---EQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLL 296
Cdd:pfam02463  882 QKLKDELESKEEKEKEEKKELEEESQKLNLleeKENEIEERIKEEAEILLKYEEEPEELLLEEADEKEKEENNKEEEEER 961

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982   297 AAERELSPSATESELEEdaAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEE 351
Cdd:pfam02463  962 NKRLLLAKEELGKVNLM--AIEEFEEKEERYNKDELEKERLEEEKKKLIRAIIEE 1014

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188785 [Multi-domain] Cd Length: 53 Bit Score: 46.56 E-value: 1.04e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 870 CIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09401    1 CPKCGKpVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.

Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 52.26 E-value: 1.18e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  100 DKRQALAAELARQQQIEADTRRQLAEaeaklveERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLE 179
Cdd:pfam15709 333 ASRDRLRAERAEMRRLEVERKRREQE-------EQRRLQQEQLERAEKMREELELEQQRRFEEIRLRKQRLEEERQRQEE 405

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  180 AEENQRKQR--ENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRilae 257
Cdd:pfam15709 406 EERKQRLQLqaAQERARQQQEEFRRKLQELQRKKQQEEAERAEAEKQRQKELEMQLAEEQKRLMEMAEEERLEYQR---- 481

                         170       180       190
                  ....*....|....*....|....*....|....
gi 320545982  258 AEAAQAERRLFDAEiqrERDQADEEGQALRDAEI 291
Cdd:pfam15709 482 QKQEAEEKARLEAE---ERRQKEEEAARLALEEA 512

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 46.52 E-value: 1.21e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKiiGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09431    1 CVQCKK--PITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCF 52

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 52.46 E-value: 1.33e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 100 DKRQALAAELaRQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLE 179
Cdd:COG4717   71 KELKELEEEL-KEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQELEALEAELAELPERLE 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 180 AEENQRKQREN--EEKERLENE----RRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQR 253
Cdd:COG4717  150 ELEERLEELREleEELEELEAElaelQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEEL 229

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188736 Cd Length: 54 Bit Score: 46.24 E-value: 1.41e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKC-NKVITSG-GVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09350    1 CGRCgENVVGEGtGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 46.14 E-value: 1.47e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 929 CTACVKPITGIGgtrfISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09431    1 CVQCKKPITTGG----VTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNC 51

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 52.37 E-value: 1.52e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    79 GTNVMQDGVLYVNGIRVDPAGDKRQALAaeLARQQQIEaDTRRQLAEAEAKLVE---ERLRVQREKEESEEQQRKLVEAE 155
Cdd:TIGR02168  645 YRIVTLDGDLVRPGGVITGGSAKTNSSI--LERRREIE-ELEEKIEELEEKIAElekALAELRKELEELEEELEQLRKEL 721

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   156 RQREREQAEKELQEQREAERRQLEAEENQRKQRENEEkerLENERRLIDAEREReenerrlqeaeeqrereeserrivvA 235
Cdd:TIGR02168  722 EELSRQISALRKDLARLEAEVEQLEERIAQLSKELTE---LEAEIEELEERLEE-------------------------A 773

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   236 ERQREQAEAEKERAEQQrILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATES--ELEE 313
Cdd:TIGR02168  774 EEELAEAEAEIEELEAQ-IEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQieELSE 852

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982   314 DAAIAEQSRRliSSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQLQASHSKEEADE 371
Cdd:TIGR02168  853 DIESLAAEIE--ELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELES 908

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 52.38 E-value: 1.58e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   100 DKRQALAAELA-RQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLV--EAERQREREQAEKELQEQREAERR 176
Cdd:TIGR02169  254 EKLTEEISELEkRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEIASLErsIAEKERELEDAEERLAKLEAEIDK 333

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   177 QLEAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESErrivVAERQREQAEAEKERAEQQRILA 256
Cdd:TIGR02169  334 LLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDE----LKDYREKLEKLKREINELKRELD 409

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   257 EAEAaqaerRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELspSATESELEEDAAIAEQ-SRRLISSRTDLEQKQ 335
Cdd:TIGR02169  410 RLQE-----ELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEI--KKQEWKLEQLAADLSKyEQELYDLKEEYDRVE 482

                          250       260
                   ....*....|....*....|....
gi 320545982   336 RMIEENARRFLEAEEEMVMLQQRQ 359
Cdd:TIGR02169  483 KELSKLQRELAEAEAQARASEERV 506

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188814 Cd Length: 52 Bit Score: 45.93 E-value: 1.68e-06

                         10        20        30
                 ....*....|....*....|....*....|...
gi 320545982 708 WHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09430   20 WHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

The first Lim domain of pollen specific protein SF3; The first Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188824 [Multi-domain] Cd Length: 63 Bit Score: 45.92 E-value: 1.82e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 869 RCIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECFGELF 925
Cdd:cd09440    4 KCKACDKtVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 61

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188818 Cd Length: 56 Bit Score: 45.52 E-value: 2.23e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 870 CIKCNKVITSGG----VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09434    1 CAACNKPITGFGggkyVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188730 Cd Length: 54 Bit Score: 45.52 E-value: 2.28e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGC 861
Cdd:cd09344    1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188802 Cd Length: 56 Bit Score: 45.50 E-value: 2.29e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 869 RCIKCNKVITSGGVT-YKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09418    2 RCSACDEIIFADECTeAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCF 55

The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188816 Cd Length: 56 Bit Score: 45.54 E-value: 2.54e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 809 CDGCGEVFRA--GTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGC 861
Cdd:cd09432    1 CAACGKPITGigGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188817 Cd Length: 58 Bit Score: 45.37 E-value: 2.63e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEEC-NKIIGID-SKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNC 800
Cdd:cd09433    1 CAGCtNPISGLGgTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188789 [Multi-domain] Cd Length: 54 Bit Score: 45.38 E-value: 2.77e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09405    2 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYC 49

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 45.23 E-value: 3.05e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 928 RCTACVKpiTGIGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09427    3 KCVACGK--TVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPC 56

The third LIM domain of Enigma-like family; The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188749 [Multi-domain] Cd Length: 54 Bit Score: 45.12 E-value: 3.57e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09363    1 CHGCDFPIEAGDrfLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 51.30 E-value: 3.94e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  114 QIEADTRRQLAEAEAKLVEERLRVQREK-EESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEE 192
Cdd:PTZ00121 1083 AKEDNRADEATEEAFGKAEEAKKTETGKaEEARKAEEAKKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAED 1162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  193 KERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEK-ERAEQQRILAEAEAAQAERRLFDAE 271
Cdd:PTZ00121 1163 ARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEaRKAEDAKKAEAVKKAEEAKKDAEEA 1242

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  272 IQRERDQADEEGQAL---RDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRmiEENARRFLEA 348
Cdd:PTZ00121 1243 KKAEEERNNEEIRKFeeaRMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKKK--AEEAKKADEA 1320

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  349 EEEMVMLQQRQLQASHSKEEADEYAGMEPVVEELCVKKVAPPRFQEPPEEPMVHKVKTQFGQGSGPED----AYSAKSKT 424
Cdd:PTZ00121 1321 KKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEekkkADEAKKKA 1400

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  425 LTFPGVSDE--GSSLEPKTPFSIQQSSFSTQPSDEG-NRIESERPEPEGEDQIQEVQYTEDYLRSLDGIKNRPLMREDGS 501
Cdd:PTZ00121 1401 EEDKKKADElkKAAAAKKKADEAKKKAEEKKKADEAkKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAE 1480

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  502 GRRRAFKKRRSSGSSNSSRESRASRDEELKMFTSLEE-EELRHGDREDYNPIKYTSEPTLRVKSHRRHKR-SPAKDVRPT 579
Cdd:PTZ00121 1481 EAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKaEEAKKADEAKKAEEAKKADEAKKAEEKKKADElKKAEELKKA 1560

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  580 AESTTSLEMLGEESTNPWG---------------EVVPEHYKDTEFWKREKALSIDEEEIELERPSRGEdvEEEATNEPK 644
Cdd:PTZ00121 1561 EEKKKAEEAKKAEEDKNMAlrkaeeakkaeeariEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAE--EEKKKVEQL 1638

                         570       580       590
                  ....*....|....*....|....*....|....*....
gi 320545982  645 SSSFEEATEAQNEQAVAALKQQLSKEQLDKEAEKDNPQA 683
Cdd:PTZ00121 1639 KKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKA 1677

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]

Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 50.23 E-value: 3.99e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   48 VDAAADAEELPRMRerldKQIKEAAEREALAGTNVMQDgvlyvngirvdpAGDKRQALAAELARQQQIEadtRRQLAEAE 127
Cdd:TIGR02794  43 VDPGAVAQQANRIQ----QQKKPAAKKEQERQKKLEQQ------------AEEAEKQRAAEQARQKELE---QRAAAEKA 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982  128 AKLVEERLRVQREKEESEEQQRKLVEAERQ------REREQAEkELQEQREAERRQLEAEENQRKQRENEEKERLE 197
Cdd:TIGR02794 104 AKQAEQAAKQAEEKQKQAEEAKAKQAAEAKakaeaeAERKAKE-EAAKQAEEEAKAKAAAEAKKKAEEAKKKAEAE 178

LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188783 [Multi-domain] Cd Length: 58 Bit Score: 44.95 E-value: 4.37e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEP----WHRECFTCTHCNITlagqrFTSR------DEKPYCAECF 921
Cdd:cd09397    1 CRKCGLEIEGKSISSKDGElsgqWHRECFVCTTCGCP-----FQFSvpcyvlDDKPYCQQHY 57

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 50.74 E-value: 4.41e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    45 DSSVDAAADAEELPRMRERLDKQIKEAAEREALAGTNVMQDGVLYVNGIRVDPAGDKRQALAAELARQQQIEADTRRQLA 124
Cdd:pfam02463  183 ENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEYLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQEIEK 262

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   125 EAE-AKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRLI 203
Cdd:pfam02463  263 EEEkLAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKEKKKAEKELKKEKEEIEELEK 342

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   204 dAEREREENERRLQEAEEQREREESErrivvAERQREQAEAEKERAEQQRILAEAEAAQAErrlfdAEIQRERDQADEEG 283
Cdd:pfam02463  343 -ELKELEIKREAEEEEEEELEKLQEK-----LEQLEEELLAKKKLESERLSSAAKLKEEEL-----ELKSEEEKEAQLLL 411

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   284 QALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQLQAS 363
Cdd:pfam02463  412 ELARQLEDLLKEEKKEELEILEEEEESIELKQGKLTEEKEELEKQELKLLKDELELKKSEDLLKETQLVKLQEQLELLLS 491


                   ....*..
gi 320545982   364 HSKEEAD 370
Cdd:pfam02463  492 RQKLEER 498

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 44.55 E-value: 4.45e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 858 CAGCYEEKFATRCIKC-NKVitsggvtyknepWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09396    1 CAGCKSEIGHGRFLSAlGAV------------WHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188725 [Multi-domain] Cd Length: 52 Bit Score: 44.64 E-value: 4.59e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09339    1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 50.83 E-value: 4.76e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   118 DTRRQLAEAEAKLVeerlRVQREKEESEEQQRKLveaERQREREQAEKELQEQREAERRQLEAeenQRKQRENEEKERLE 197
Cdd:TIGR02168  176 ETERKLERTRENLD----RLEDILNELERQLKSL---ERQAEKAERYKELKAELRELELALLV---LRLEELREELEELQ 245

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   198 NErrLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAE-----AEKERAEQQRILAEAEAAQAERRLFDAEI 272
Cdd:TIGR02168  246 EE--LKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKElyalaNEISRLEQQKQILRERLANLERQLEELEA 323

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   273 QRERDQADEEGQALRDAEIVERLLAAERELspSATESELEEDAAIAEQSRRLISS--------RTDLEQKQRMIEENARR 344
Cdd:TIGR02168  324 QLEELESKLDELAEELAELEEKLEELKEEL--ESLEAELEELEAELEELESRLEEleeqletlRSKVAQLELQIASLNNE 401

                          250       260
                   ....*....|....*....|....*..
gi 320545982   345 FLEAEEEMVMLQQRQLQASHSKEEADE 371
Cdd:TIGR02168  402 IERLEARLERLEDRRERLQQEIEELLK 428

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 50.71 E-value: 4.84e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  40 FQHPGDSSVDAAADAEELPRMRERLDKQIKEAAEREALAGTNVMQDGVLYVNGIRVDPAGDKRQALAAELARQQQIEADT 119
Cdd:COG1196  614 RYYVLGDTLLGRTLVAARLEAALRRAVTLAGRLREVTLEGEGGSAGGSLTGGSRRELLAALLEAEAELEELAERLAEEEL 693

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 120 RRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEEnQRKQRENEEKERLENE 199
Cdd:COG1196  694 ELEEALLAEEEEERELAEAEEERLEEELEEEALEEQLEAEREELLEELLEEEELLEEEALEEL-PEPPDLEELERELERL 772


                 ....*.
gi 320545982 200 RRLIDA 205
Cdd:COG1196  773 EREIEA 778

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188715 [Multi-domain] Cd Length: 52 Bit Score: 44.62 E-value: 5.09e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 870 CIKCNKVITSGGVTYK-NEPWHRECFTCTHCNITLAGQrFTSRDEKPYCAECF 921
Cdd:cd09329    1 CAGCGQEIKNGQALLAlDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 44.66 E-value: 5.09e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09361    1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188734 Cd Length: 64 Bit Score: 44.75 E-value: 5.23e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 806 ASRCDGCGEV---FRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGC 861
Cdd:cd09348    2 AKKCSGCQNPitgFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188785 [Multi-domain] Cd Length: 53 Bit Score: 44.25 E-value: 5.40e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIGIDSKDLSYKdKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09401    1 CPKCGKPVYFAEKKTSLG-RDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 50.04 E-value: 5.53e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  98 AGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQ 177
Cdd:COG3064   39 AEEERLAELEAKRQAEEEAREAKAEAEQRAAELAAEAAKKLAEAEKAAAEAEKKAAAEKAKAAKEAEAAAAAEKAAAAAE 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 178 LEAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAE 257
Cdd:COG3064  119 KEKAEEAKRKAEEEAKRKAEEERKAAEAEAAAKAEAEAARAAAAAAAAAAAAAARAAAGAAAALVAAAAAAVEAADTAAA 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 258 AEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERL-LAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQR 336
Cdd:COG3064  199 AAAALAAAAAAAAADAALLALAVAARAAAASREAALAAvEATEEAALGGAEEAADLAAVGVLGAALAAAAAGAAALSSGL 278

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 320545982 337 MIEENARRFLEAEEEMVMLQQRQLQASHSKEEADE 371
Cdd:COG3064  279 VVVAAALAGLAAAAAGLVLDDSAALAAELLGAVAA 313

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 49.52 E-value: 5.92e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 103 QALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLveAERQREREQAEKELqEQREAERRQLEAEE 182
Cdd:COG4372   55 EQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEEL--ESLQEEAEELQEEL-EELQKERQDLEQQR 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 183 NQRKQRENE-EKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAA 261
Cdd:COG4372  132 KQLEAQIAElQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEAEQALDELLKEANRNAEKEEELAEAEKLIES 211

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 262 QAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEEN 341
Cdd:COG4372  212 LPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKEELLEEVILKEIEELELAILVEKDTEEEELEIAALELEALEEA 291

                        250       260       270
                 ....*....|....*....|....*....|....
gi 320545982 342 ARRFLEAEEEMVMLQQRQLQASHSKEEADEYAGM 375
Cdd:COG4372  292 ALELKLLALLLNLAALSLIGALEDALLAALLELA 325

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188733 Cd Length: 56 Bit Score: 44.26 E-value: 6.17e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 809 CDGCGEVFRA--GTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGC 861
Cdd:cd09347    1 CAACTKPITGlgGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 49.53 E-value: 6.56e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  101 KRQALAAELARQ---QQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQ 177
Cdd:pfam13868  70 ERKRYRQELEEQieeREQKRQEEYEEKLQEREQMDEIVERIQEEDQAEAEEKLEKQRQLREEIDEFNEEQAEWKELEKEE 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  178 LEAEENQR----KQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQR 253
Cdd:pfam13868 150 EREEDERIleylKEKAEREEEREAEREEIEEEKEREIARLRAQQEKAQDEKAERDELRAKLYQEEQERKERQKEREEAEK 229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  254 ilaeaeaaqaeRRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSAtesELEEDAAIAEQSRRLISSRTDLEQ 333
Cdd:pfam13868 230 -----------KARQRQELQQAREEQIELKERRLAEEAEREEEEFERMLRKQA---EDEEIEQEEAEKRRMKRLEHRREL 295

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 320545982  334 KQRMIEENARRFLEAEEEMVMLQQRQLQASHSKEEADEY 372
Cdd:pfam13868 296 EKQIEEREEQRAAEREEELEEGERLREEEAERRERIEEE 334

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 44.51 E-value: 6.59e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 866 FATRCIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09422    1 YSNTCEECKKPIGCDCkdLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECY 58

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 49.15 E-value: 7.48e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  102 RQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESE---EQQRKLVEAERQREREQAEKELQEQREAERRQL 178
Cdd:pfam13868  54 ERALEEEEEKEEERKEERKRYRQELEEQIEEREQKRQEEYEEKLqerEQMDEIVERIQEEDQAEAEEKLEKQRQLREEID 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  179 EAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQrEQAEAEKERAEQQRILAEA 258
Cdd:pfam13868 134 EFNEEQAEWKELEKEEEREEDERILEYLKEKAEREEEREAEREEIEEEKEREIARLRAQQ-EKAQDEKAERDELRAKLYQ 212

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  259 EAAQAERRLFDAEIQRERDQADEEGQALRDAEIV--ERLLAAEREL------SPSATESELEEDAAIAEQSRRLISSRTD 330
Cdd:pfam13868 213 EEQERKERQKEREEAEKKARQRQELQQAREEQIElkERRLAEEAEReeeefeRMLRKQAEDEEIEQEEAEKRRMKRLEHR 292

                         250       260       270
                  ....*....|....*....|....*....|..
gi 320545982  331 LEQkQRMIEENARRFLEAEEEMVMLQQRQLQA 362
Cdd:pfam13868 293 REL-EKQIEEREEQRAAEREEELEEGERLREE 323

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 49.38 E-value: 7.55e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 154 AERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRLIDAEREREENERRLqeaeeqrereeserriv 233
Cdd:COG4942   23 AEAEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAEL----------------- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 234 vAERQREQAEAEKERAEQQRILaeaeaaqaERRLFDAEIQRERD------QADEEGQALRDAEIVERLLAAERELspsat 307
Cdd:COG4942   86 -AELEKEIAELRAELEAQKEEL--------AELLRALYRLGRQPplalllSPEDFLDAVRRLQYLKYLAPARREQ----- 151

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 320545982 308 ESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEmvmlQQRQLQASHSKEEADE 371
Cdd:COG4942  152 AEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKA----ERQKLLARLEKELAEL 211

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 49.97 E-value: 8.09e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   108 ELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQRERE--QAEKELQEQREAE---RRQLEA-E 181
Cdd:TIGR00618  174 PLDQYTQLALMEFAKKKSLHGKAELLTLRSQLLTLCTPCMPDTYHERKQVLEKElkHLREALQQTQQSHaylTQKREAqE 253

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   182 ENQRKQRENEEKERLENERRLIDAEREREENERRLQ-------EAEEQREREESERRIVVAERQREQAEAEKERAEQQRI 254
Cdd:TIGR00618  254 EQLKKQQLLKQLRARIEELRAQEAVLEETQERINRArkaaplaAHIKAVTQIEQQAQRIHTELQSKMRSRAKLLMKRAAH 333

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   255 LAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELspsateSELEEDAAIAEQSRRLISSRTDL--- 331
Cdd:TIGR00618  334 VKQQSSIEEQRRLLQTLHSQEIHIRDAHEVATSIREISCQQHTLTQHI------HTLQQQKTTLTQKLQSLCKELDIlqr 407

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982   332 EQKQRMIEENARRFLE-----AEEEMVMLQQR-QLQASHSKEEADEYAGMEPVVEEL 382
Cdd:TIGR00618  408 EQATIDTRTSAFRDLQgqlahAKKQQELQQRYaELCAAAITCTAQCEKLEKIHLQES 464

Arginine and glutamate-rich 1; ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes.

Pssm-ID: 405931 [Multi-domain] Cd Length: 151 Bit Score: 46.58 E-value: 8.16e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  110 ARQQQIEADTRRQLAEAEAKLVEERLrvQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEA-EENQRKQR 188
Cdd:pfam15346   3 AESKLLEEETARRVEEAVAKRVEEEL--EKRKDEIEAEVERRVEEARKIMEKQVLEELEREREAELEEERRkEEEERKKR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982  189 ENEEKERLENERRLIDAEREREENERRLQEAEEQREReeserrivvAERQREQAEAEKERAEQQRIL 255
Cdd:pfam15346  81 EELERILEENNRKIEEAQRKEAEERLAMLEEQRRMKE---------ERQRREKEEEEREKREQQKIL 138

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188810 Cd Length: 57 Bit Score: 44.27 E-value: 8.24e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09426    1 CSECKKTIMPGTrkMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCY 54

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188724 [Multi-domain] Cd Length: 53 Bit Score: 43.86 E-value: 8.27e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09338    1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYC 48

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442439 [Multi-domain] Cd Length: 687 Bit Score: 49.63 E-value: 8.40e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 112 QQQIEaDTRRQLAEAEAKLVEERlrvQREKEESEEQQRKLVEAERQREREQAEkELQEQREAERRQLEAEENQRKQRENE 191
Cdd:COG3206  181 EEQLP-ELRKELEEAEAALEEFR---QKNGLVDLSEEAKLLLQQLSELESQLA-EARAELAEAEARLAALRAQLGSGPDA 255

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 192 EKERLEN------ERRLIDAEREREENERRLQeaeeqrereESERRIVVAERQREQAEAEKeRAEQQRILaeaeaaqaer 265
Cdd:COG3206  256 LPELLQSpviqqlRAQLAELEAELAELSARYT---------PNHPDVIALRAQIAALRAQL-QQEAQRIL---------- 315

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 266 rlfdAEIQRERDQADEEGQALRDAeiVERLLAAERELSPSATE-SELEEDAAIAEQS-RRLISSRTDLEQKQRMIEENAR 343
Cdd:COG3206  316 ----ASLEAELEALQAREASLQAQ--LAQLEARLAELPELEAElRRLEREVEVARELyESLLQRLEEARLAEALTVGNVR 389

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188724 [Multi-domain] Cd Length: 53 Bit Score: 43.86 E-value: 9.58e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 320545982 929 CTACVKPITGiggtRFISFEDRHWHHDCFVCASCKASLVGRGF 971
Cdd:cd09338    1 CGGCNKPILE----NYISALNTQWHPECFVCRECHKPFINGSF 39

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 48.76 E-value: 9.92e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  112 QQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQA------EKELQEQREAERRQLEAEENQR 185
Cdd:pfam13868  26 AQIAEKKRIKAEEKEEERRLDEMMEEERERALEEEEEKEEERKEERKRYRQEleeqieEREQKRQEEYEEKLQEREQMDE 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  186 KQRENEEKERLENERRLIDAEREREENERRLQeaeeqrereeserrivvAERQREQAEAEKERAEQQRILAEAEAAQAER 265
Cdd:pfam13868 106 IVERIQEEDQAEAEEKLEKQRQLREEIDEFNE-----------------EQAEWKELEKEEEREEDERILEYLKEKAERE 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  266 RLFDAEIQRERDQADEEGQALRDAEIVERLLAAERElspsatesELEEDAAIAEQSRrlissrtdlEQKQRMIEENARRf 345
Cdd:pfam13868 169 EEREAEREEIEEEKEREIARLRAQQEKAQDEKAERD--------ELRAKLYQEEQER---------KERQKEREEAEKK- 230

                         250       260       270
                  ....*....|....*....|....*....|.
gi 320545982  346 leAEEEMVMLQQRQLQASHSKEEADEYAGME 376
Cdd:pfam13868 231 --ARQRQELQQAREEQIELKERRLAEEAERE 259

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 43.71 E-value: 1.04e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAE 919
Cdd:cd09406    3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEE 52

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 43.65 E-value: 1.21e-05

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 320545982 705 DKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYE 741
Cdd:cd09429   17 DQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

polarized growth protein Scy;

Pssm-ID: 469371 [Multi-domain] Cd Length: 1293 Bit Score: 49.44 E-value: 1.23e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  106 AAELARQQQIEADTRRqlAEAEAKLVEERLRVQREKEESEEQQRKLvEAERQREREQAEKELqEQREAERRQ-LEAEENQ 184
Cdd:NF041483   74 AEQLLRNAQIQADQLR--ADAERELRDARAQTQRILQEHAEHQARL-QAELHTEAVQRRQQL-DQELAERRQtVESHVNE 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  185 RKQRENEEKERLENE-RRLIDAEREreenerrlQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILaEAEAAQA 263
Cdd:NF041483  150 NVAWAEQLRARTESQaRRLLDESRA--------EAEQALAAARAEAERLAEEARQRLGSEAESARAEAEAIL-RRARKDA 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  264 ERRLFDAEIQ----------------RERDQADEEGQAL-RDAEivERLLAAERELSPSATESELEEDAAIAEQSRRLIS 326
Cdd:NF041483  221 ERLLNAASTQaqeatdhaeqlrsstaAESDQARRQAAELsRAAE--QRMQEAEEALREARAEAEKVVAEAKEAAAKQLAS 298

                         250       260
                  ....*....|....*....|....*.
gi 320545982  327 SRTDLEQKQRMI-EENARRFLEAEEE 351
Cdd:NF041483  299 AESANEQRTRTAkEEIARLVGEATKE 324

The third LIM domain of an Enigma subfamily with unknown function; The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188845 Cd Length: 54 Bit Score: 43.31 E-value: 1.24e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09461    1 CVSCGFPIEAGDrwVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFC 50

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188812 Cd Length: 54 Bit Score: 43.29 E-value: 1.26e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09428    1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPCF 54

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 48.88 E-value: 1.26e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  98 AGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERlrvQREKEESEEQQRKLVEAERQREREQAEKELQE-----QRE 172
Cdd:COG3064   20 QAEAEKRAAAEAEQKAKEEAEEERLAELEAKRQAEEE---AREAKAEAEQRAAELAAEAAKKLAEAEKAAAEaekkaAAE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 173 AERRQLEAEENQRKQRENE--EKERLENERRLIDAEREREEnerrlQEAEEQREREESERRIVVAERQREQAEAEKERAE 250
Cdd:COG3064   97 KAKAAKEAEAAAAAEKAAAaaEKEKAEEAKRKAEEEAKRKA-----EEERKAAEAEAAAKAEAEAARAAAAAAAAAAAAA 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 251 QQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTD 330
Cdd:COG3064  172 ARAAAGAAAALVAAAAAAVEAADTAAAAAAALAAAAAAAAADAALLALAVAARAAAASREAALAAVEATEEAALGGAEEA 251

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 320545982 331 LEQKQRMIEENARRFLEAEEEMVMLQQRQLQASHSKEEADEYAGME 376
Cdd:COG3064  252 ADLAAVGVLGAALAAAAAGAAALSSGLVVVAAALAGLAAAAAGLVL 297

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 48.97 E-value: 1.39e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   98 AGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQrerEQAEKELQEQREAERRQ 177
Cdd:pfam17380 400 AARKVKILEEERQRKIQQQKVEMEQIRAEQEEARQREVRRLEEERAREMERVRLEEQERQ---QQVERLRQQEEERKRKK 476

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  178 LEAEENQRKQRENEEKERLENERRLidaerereenerrlqeaeeqrereeserrivvaeRQREQAEAEKERaeqqrilae 257
Cdd:pfam17380 477 LELEKEKRDRKRAEEQRRKILEKEL----------------------------------EERKQAMIEEER--------- 513

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  258 aeaaqaERRLFDAEIQrERDQADEEGQALRDAEIVERllaaerelspsaTESELEEDAAIAEQSRRLISSRTDLEQKQRM 337
Cdd:pfam17380 514 ------KRKLLEKEME-ERQKAIYEEERRREAEEERR------------KQQEMEERRRIQEQMRKATEERSRLEAMERE 574

                         250
                  ....*....|....
gi 320545982  338 iEENARRFLEAEEE 351
Cdd:pfam17380 575 -REMMRQIVESEKA 587

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442439 [Multi-domain] Cd Length: 687 Bit Score: 48.86 E-value: 1.41e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  55 EELPRMRERLDKQIKEAAE-REALAGTNVMQDGVLYVNgiRVDPAGDKRQALAAEL----ARQQQIEA------------ 117
Cdd:COG3206  182 EQLPELRKELEEAEAALEEfRQKNGLVDLSEEAKLLLQ--QLSELESQLAEARAELaeaeARLAALRAqlgsgpdalpel 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 118 -------DTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQaeKELQEQREAERRQLEAEENQRKQREN 190
Cdd:COG3206  260 lqspviqQLRAQLAELEAELAELSARYTPNHPDVIALRAQIAALRAQLQQEA--QRILASLEAELEALQAREASLQAQLA 337

                        170
                 ....*....|....*...
gi 320545982 191 EEKERL----ENERRLID 204
Cdd:COG3206  338 QLEARLaelpELEAELRR 355

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.

Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 48.79 E-value: 1.47e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  109 LARQQQIEADTRRQLAEAEAKLveERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLeaeenqRKQR 188
Cdd:pfam15709 324 LLEKREQEKASRDRLRAERAEM--RRLEVERKRREQEEQRRLQQEQLERAEKMREELELEQQRRFEEIRL------RKQR 395

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  189 ENEEKERL-ENERrlidaerereenerrlqeaeeqrereeserrivvaeRQREQAEAEKERAEQQRilaeaeaAQAERRL 267
Cdd:pfam15709 396 LEEERQRQeEEER------------------------------------KQRLQLQAAQERARQQQ-------EEFRRKL 432

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  268 fdAEIQRERDQ-----ADEEGQalRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRlisSRTDLEQKQRMIEENA 342
Cdd:pfam15709 433 --QELQRKKQQeeaerAEAEKQ--RQKELEMQLAEEQKRLMEMAEEERLEYQRQKQEAEEK---ARLEAEERRQKEEEAA 505

                         250
                  ....*....|....*..
gi 320545982  343 RRFLEAEEEMVMLQQRQ 359
Cdd:pfam15709 506 RLALEEAMKQAQEQARQ 522

The LIM domain of LIM and SH3 Protein (LASP); The LIM domain of LIM and SH3 Protein (LASP): LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains ,but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188831 Cd Length: 53 Bit Score: 43.13 E-value: 1.54e-05

                         10        20        30
                 ....*....|....*....|....*....|
gi 320545982 889 WHRECFTCTHCNITLAGQRFTSRDEKPYCA 918
Cdd:cd09447   21 WHKGCFKCEVCGMTLNMKNYKGYNKKPYCN 50

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188789 [Multi-domain] Cd Length: 54 Bit Score: 43.07 E-value: 1.61e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 320545982 697 SGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09405   10 AGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.

Pssm-ID: 462322 Cd Length: 323 Bit Score: 47.95 E-value: 1.72e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  133 ERLRVQREKEESEEqqRKLVEAERQRER-EQAEKELQEQREAERRQLEAEEnQRKQrenEEKERLENERR 201
Cdd:pfam07946 260 KKAKKTREEEIEKI--KKAAEEERAEEAqEKKEEAKKKEREEKLAKLSPEE-QRKY---EEKERKKEQRK 323

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 48.81 E-value: 1.74e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   100 DKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAerQREREQAEKELQEQREAERRQLE 179
Cdd:TIGR00618  200 TLRSQLLTLCTPCMPDTYHERKQVLEKELKHLREALQQTQQSHAYLTQKREAQEE--QLKKQQLLKQLRARIEELRAQEA 277

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   180 AEENQRKQRENEEKER--LENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQ---------------- 241
Cdd:TIGR00618  278 VLEETQERINRARKAAplAAHIKAVTQIEQQAQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEeqrrllqtlhsqeihi 357

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   242 -----------AEAEKERAEQQRILAEAEAAQAERRLFDA------EIQRERDQADEEGQALRDAEIveRLLAAERELSP 304
Cdd:TIGR00618  358 rdahevatsirEISCQQHTLTQHIHTLQQQKTTLTQKLQSlckeldILQREQATIDTRTSAFRDLQG--QLAHAKKQQEL 435

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982   305 SATESELEEdAAIAEQSRRLISSRTDLEQKQRMIEEnaRRFLEAEEEMVMLQQRQLQASHSKeEADEYAGMEPVVEELC 383
Cdd:TIGR00618  436 QQRYAELCA-AAITCTAQCEKLEKIHLQESAQSLKE--REQQLQTKEQIHLQETRKKAVVLA-RLLELQEEPCPLCGSC 510

The third LIM domain of Enigma-like family; The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188749 [Multi-domain] Cd Length: 54 Bit Score: 42.81 E-value: 1.81e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYC 858
Cdd:cd09363    1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 48.50 E-value: 1.82e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 100 DKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQE-QREAERRQL 178
Cdd:COG3064   63 EAEQRAAELAAEAAKKLAEAEKAAAEAEKKAAAEKAKAAKEAEAAAAAEKAAAAAEKEKAEEAKRKAEEEaKRKAEEERK 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 179 EAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEA 258
Cdd:COG3064  143 AAEAEAAAKAEAEAARAAAAAAAAAAAAAARAAAGAAAALVAAAAAAVEAADTAAAAAAALAAAAAAAAADAALLALAVA 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 259 EAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMI 338
Cdd:COG3064  223 ARAAAASREAALAAVEATEEAALGGAEEAADLAAVGVLGAALAAAAAGAAALSSGLVVVAAALAGLAAAAAGLVLDDSAA 302

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 320545982 339 EENARRFLEAEEEMVMLQQRQLQASHSKEEADEYAGMEPVVEEL 382
Cdd:COG3064  303 LAAELLGAVAAEEAVLAAAAAAGALVVRGGGAASLEAALSLLAA 346

Predicted ATPase [General function prediction only];

Pssm-ID: 443106 [Multi-domain] Cd Length: 1244 Bit Score: 48.70 E-value: 1.84e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   25 ALEFAFVARHLYHWTFQHPGDSSVDAAADAEELPRMRERLDKQIKEAAEREALA---GTNVMQDGVLYVNGIRVDPAGDK 101
Cdd:COG3899   767 LLERALAARALAALAALRHGNPPASARAYANLGLLLLGDYEEAYEFGELALALAerlGDRRLEARALFNLGFILHWLGPL 846

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  102 RQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAE 181
Cdd:COG3899   847 REALELLREALEAGLETGDAALALLALAAAAAAAAAAAALAAAAAAAARLLAAAAAALAAAAAAAALAAAELARLAAAAA 926

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  182 ENQRkqreneekeRLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAA 261
Cdd:COG3899   927 AAAA---------LALAAAAAAAAAAALAAAAAAAALAAALALAAAAAAAAAAALAAAAAAAAAAAAAAAAAALEAAAAA 997

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  262 QAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEEN 341
Cdd:COG3899   998 LLALLAAAAAAAAAAAALAAALLAAALAALAAAAAAAALLAAAAALALLAALAAAAAAAAAAAALAAAAALLAAAAAAAA 1077

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 320545982  342 ARRFLEAEEEMVMLQQRQLQASHSKEEADEYAGMEPVVEEL 382
Cdd:COG3899  1078 AAAAAAAAAALAAALAAAALAAAAAAALALAAALAALALAA 1118

NIMA-related protein kinase; Provisional

Pssm-ID: 173502 [Multi-domain] Cd Length: 1021 Bit Score: 48.58 E-value: 1.99e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982  133 ERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENER 200
Cdd:PTZ00266  436 ERARIEKENAHRKALEMKILEKKRIERLEREERERLERERMERIERERLERERLERERLERDRLERDR 503

The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188840 [Multi-domain] Cd Length: 52 Bit Score: 42.68 E-value: 2.20e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09456    1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYC 48

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 48.11 E-value: 2.31e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  98 AGDKRQALAAELARQQQIEADTRRQLAEAEAKLvEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQ 177
Cdd:COG3064    1 AQEALEEKAAEAAAQERLEQAEAEKRAAAEAEQ-KAKEEAEEERLAELEAKRQAEEEAREAKAEAEQRAAELAAEAAKKL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 178 LEAEenqRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESErrivvAERQ-REQAEAEKERAEQQRILA 256
Cdd:COG3064   80 AEAE---KAAAEAEKKAAAEKAKAAKEAEAAAAAEKAAAAAEKEKAEEAKRK-----AEEEaKRKAEEERKAAEAEAAAK 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 257 EAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQR 336
Cdd:COG3064  152 AEAEAARAAAAAAAAAAAAAARAAAGAAAALVAAAAAAVEAADTAAAAAAALAAAAAAAAADAALLALAVAARAAAASRE 231

                        250       260
                 ....*....|....*....|....*....
gi 320545982 337 MIEENARRFLEAEEEMVMLQQRQLQASHS 365
Cdd:COG3064  232 AALAAVEATEEAALGGAEEAADLAAVGVL 260

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188779 Cd Length: 56 Bit Score: 42.69 E-value: 2.53e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHC----NITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09393    1 CASCGKSIEDECIKFEDKRWHLKCFTCSRChreiSSELSDAAFNNKDQRILCSNC 55

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 48.43 E-value: 2.73e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   120 RRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAErrqLEAEENQRKQRENEEKERLENE 199
Cdd:pfam02463  155 RLEIEEEAAGSRLKRKKKEALKKLIEETENLAELIIDLEELKLQELKLKEQAKKA---LEYYQLKEKLELEEEYLLYLDY 231

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   200 RRLIdaerereenerrlqeaeeqrereeseRRIVVAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQA 279
Cdd:pfam02463  232 LKLN--------------------------EERIDLLQELLRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKEKKLQE 285

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   280 DEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQ 359
Cdd:pfam02463  286 EELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKEKKKAEKELKKEKEEIEELEKELKELEIKREAEEEEEEELEKLQ 365

                          250
                   ....*....|....*..
gi 320545982   360 LQASHSKEEADEYAGME 376
Cdd:pfam02463  366 EKLEQLEEELLAKKKLE 382

The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188745 Cd Length: 53 Bit Score: 42.64 E-value: 2.81e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 320545982 870 CIKCNKVI-TSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09359    1 CARCGKIVyPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYC 49

The LIM domain of Mical (molecule interacting with CasL) like family; The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188744 [Multi-domain] Cd Length: 53 Bit Score: 42.26 E-value: 2.93e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 870 CIKCNKVItsggvtYKNE-------PWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09358    1 CAVCGKTV------YPMErlvadgkLFHKSCFRCSHCNKTLRLGNYASLEGKLYC 49

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 42.38 E-value: 2.94e-05

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 320545982 828 RQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09336   18 KTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase

Pssm-ID: 440475 [Multi-domain] Cd Length: 152 Bit Score: 45.16 E-value: 3.05e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 100 DKRQAL------AAELARQ--QQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQR 171
Cdd:COG0711   30 DERQEKiadglaEAERAKEeaEAALAEYEEKLAEARAEAAEIIAEARKEAEAIAEEAKAEAEAEAERIIAQAEAEIEQER 109

                         90
                 ....*....|
gi 320545982 172 EAERRQLEAE 181
Cdd:COG0711  110 AKALAELRAE 119

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442439 [Multi-domain] Cd Length: 687 Bit Score: 48.09 E-value: 3.05e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  53 DAEELPRMRERLDKQIKEAAEREALAGTNVMQdgvlyvngIRVDpagDKRQALAAELA-------RQQQIEAdtRRQLAE 125
Cdd:COG3206  108 DPLGEEASREAAIERLRKNLTVEPVKGSNVIE--------ISYT---SPDPELAAAVAnalaeayLEQNLEL--RREEAR 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 126 AEAKLVEERLRVQREK-EESEE------QQRKLVEAERQREREQAE-KELQEQREAERRQLEAEENQRKQRENEEKERLE 197
Cdd:COG3206  175 KALEFLEEQLPELRKElEEAEAaleefrQKNGLVDLSEEAKLLLQQlSELESQLAEARAELAEAEARLAALRAQLGSGPD 254

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 198 NERRLIDAErereenerrlqeaeeqrereeserriVVAERQREQAEAEKERAEQQRILAEAeaaqaerrlfDAEIQRERD 277
Cdd:COG3206  255 ALPELLQSP--------------------------VIQQLRAQLAELEAELAELSARYTPN----------HPDVIALRA 298

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 278 QADEegqalrdaeiVERLLAAERELSPSATESELEedaAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQ 357
Cdd:COG3206  299 QIAA----------LRAQLQQEAQRILASLEAELE---ALQAREASLQAQLAQLEARLAELPELEAELRRLEREVEVARE 365

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|..
gi 320545982 358 RQLQASHSKEEADEYAGMEPVVeelcVKKVAPPrfqEPPEEP 399
Cdd:COG3206  366 LYESLLQRLEEARLAEALTVGN----VRVIDPA---VVPLKP 400

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188787 Cd Length: 54 Bit Score: 42.18 E-value: 3.19e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAGTKKMEyKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09403    1 CPRCGKSVYAAEKIIG-AGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

chromosome partition protein MukB;

Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 48.03 E-value: 3.31e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  108 ELARQQQIEADTRRQLAEAeAKLV---------EERLRVQREKEESEEQQRKLVEAERQREREQAEKE--LQEQREAERR 176
Cdd:PRK04863  460 SLEQKLSVAQAAHSQFEQA-YQLVrkiagevsrSEAWDVARELLRRLREQRHLAEQLQQLRMRLSELEqrLRQQQRAERL 538

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  177 QLEAEENQRKQRENEEK-ERLENERrlidaerereenerrlqeaeeqrereeserrivvaERQREQAEAEKERAEQQRIl 255
Cdd:PRK04863  539 LAEFCKRLGKNLDDEDElEQLQEEL-----------------------------------EARLESLSESVSEARERRM- 582

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  256 aeaeAAQAERRLFDAEIQRERDQAdEEGQALRDAeiVERLlaaeRELSPSATESELEEDAAI---AEQSRRLISSRTDLE 332
Cdd:PRK04863  583 ----ALRQQLEQLQARIQRLAARA-PAWLAAQDA--LARL----REQSGEEFEDSQDVTEYMqqlLERERELTVERDELA 651

                         250
                  ....*....|....*..
gi 320545982  333 QKQRMIEENARRFLEAE 349
Cdd:PRK04863  652 ARKQALDEEIERLSQPG 668

The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188852 Cd Length: 52 Bit Score: 42.27 E-value: 3.31e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 748 CEECNKIIgIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFgAKADKIYC 797
Cdd:cd09468    1 CAGCNQHI-LDKFILKVLDRHWHSSCLKCADCQMQLAERCF-SRAGNVYC 48

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 42.24 E-value: 3.33e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 320545982 929 CTACVKPItgiGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDG 975
Cdd:cd09396    1 CAGCKSEI---GHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSG 44

The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188792 [Multi-domain] Cd Length: 52 Bit Score: 42.11 E-value: 3.33e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09408    1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188795 [Multi-domain] Cd Length: 52 Bit Score: 42.24 E-value: 3.53e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09411    1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52

LIM domain; This family represents two copies of the LIM structural domain.

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 42.32 E-value: 3.63e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982  929 CTACVKPITGIGGTRFisfEDRHWHHDCFVCASCKASLVGRG-FITDGpDILCPDC 983
Cdd:pfam00412   1 CAGCNRPIYDRELVRA---LGKVWHPECFRCAVCGKPLTTGDfYEKDG-KLYCKHD 52

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188712 Cd Length: 53 Bit Score: 42.20 E-value: 3.67e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09326    1 CPRCGKsVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSC 52

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 42.11 E-value: 3.90e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 809 CDGCGEVFRAGtkKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYE 863
Cdd:cd09429    1 CVKCNKPITSG--GVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006

Pssm-ID: 425677 [Multi-domain] Cd Length: 132 Bit Score: 44.23 E-value: 4.02e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   99 GDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKL-----VEAERQRER--EQAEKELQEQR 171
Cdd:pfam00430  29 DKRRELIADEIAEAEERRKDAAAALAEAEQQLKEARAEAQEIIENAKKRAEKLkeeivAAAEAEAERiiEQAAAEIEQEK 108

                          90
                  ....*....|
gi 320545982  172 EAERRQLEAE 181
Cdd:pfam00430 109 DRALAELRQQ 118

The second LIM domain of Testin; The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188800 Cd Length: 56 Bit Score: 42.15 E-value: 4.04e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 869 RCIKCNKVITSGGVTY-KNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09416    2 RCAGCDELIFSNEYTQaENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKPCY 55

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.

Pssm-ID: 188720 [Multi-domain] Cd Length: 54 Bit Score: 41.96 E-value: 4.15e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09334    3 CGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYC 50

F0F1 ATP synthase subunit B'; Validated

Pssm-ID: 235999 [Multi-domain] Cd Length: 140 Bit Score: 44.22 E-value: 4.36e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 116 EADTRRQLAEAEA-------KLVEERLRVQREKEESEEQQRKL-------VEAERQREREQAEKELQEQREAERRQLEAE 181
Cdd:PRK07353  45 RAEAKERLAEAEKleaqyeqQLASARKQAQAVIAEAEAEADKLaaealaeAQAEAQASKEKARREIEQQKQAALAQLEQQ 124

NIMA-related protein kinase; Provisional

Pssm-ID: 173502 [Multi-domain] Cd Length: 1021 Bit Score: 47.42 E-value: 4.57e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   92 GIRVDPAGDKRQALAAELARQQQIEadtrrqLAEAEAKLVEERLRVQREKEESEEQQRklveAERQR-EREQAEKELQEQ 170
Cdd:PTZ00266  427 GGRVDKDHAERARIEKENAHRKALE------MKILEKKRIERLEREERERLERERMER----IERERlERERLERERLER 496

                          90       100       110
                  ....*....|....*....|....*....|.
gi 320545982  171 REAERRQLEAEENQRKQREneEKERLENERR 201
Cdd:PTZ00266  497 DRLERDRLDRLERERVDRL--ERDRLEKARR 525

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.

Pssm-ID: 293879 [Multi-domain] Cd Length: 291 Bit Score: 46.42 E-value: 4.67e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 103 QALAAELARQQQIEAD-TRRQLAEAEAKLVEERLRVQREK----EESEEQQRKLVEAERQREREQAEKELQEQREAERRQ 177
Cdd:cd16269  188 QADQALTEKEKEIEAErAKAEAAEQERKLLEEQQRELEQKledqERSYEEHLRQLKEKMEEERENLLKEQERALESKLKE 267

                         90       100
                 ....*....|....*....|....
gi 320545982 178 LEAEENQRKQRENEEKERLENERR 201
Cdd:cd16269  268 QEALLEEGFKEQAELLQEEIRSLK 291

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase

Pssm-ID: 440475 [Multi-domain] Cd Length: 152 Bit Score: 44.39 E-value: 4.77e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 110 ARQQQIEADtrrqLAEAEaklvEERLRVQREKEESEEQQRKLvEAERQREREQAEKELQEQREAERRQLEAEENQRKQre 189
Cdd:COG0711   31 ERQEKIADG----LAEAE----RAKEEAEAALAEYEEKLAEA-RAEAAEIIAEARKEAEAIAEEAKAEAEAEAERIIA-- 99

                         90
                 ....*....|..
gi 320545982 190 nEEKERLENERR 201
Cdd:COG0711  100 -QAEAEIEQERA 110

The third LIM domain of Prickle; The third LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188804 Cd Length: 59 Bit Score: 42.04 E-value: 4.86e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 929 CTACVKPItGIGGTRfISFEDRHWH--HDCFVCASCKASLVGRGFITDGPDILC 980
Cdd:cd09420    3 CDTCGEHI-GVDQGQ-MTYDGQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYC 54

The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188735 [Multi-domain] Cd Length: 87 Bit Score: 42.92 E-value: 4.91e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCNKVI--TSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09349   34 CGICGQPLsrTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188865 Cd Length: 54 Bit Score: 41.66 E-value: 5.01e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 808 RCDGCGE-VFRAgtKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09481    1 KCGACEKtVYHA--EEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188851 [Multi-domain] Cd Length: 55 Bit Score: 41.84 E-value: 5.01e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 748 CEECNKIIgIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFgAKADKIYC 797
Cdd:cd09467    4 CAGCNQHI-VDRFILKVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYC 51

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188812 Cd Length: 54 Bit Score: 41.75 E-value: 5.22e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09428    1 CFHCKKTIMPGSrkLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPCF 54

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 47.07 E-value: 5.69e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  97 PAGDKRQALAAELARQQQieadTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREaERR 176
Cdd:COG4717   61 PQGRKPELNLKELKELEE----ELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLLPLYQ-ELE 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 177 QLEAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESerriVVAERQREQAEAEKERAEQQRILA 256
Cdd:COG4717  136 ALEAELAELPERLEELEERLEELRELEEELEELEAELAELQEELEELLEQLS----LATEEELQDLAEELEELQQRLAEL 211

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 320545982 257 EAEAAQAERRLfdAEIQRERDQADEEGQALRDAEIVERLLA 297
Cdd:COG4717  212 EEELEEAQEEL--EELEEELEQLENELEAAALEERLKEARL 250

AmiB activator; Provisional

Pssm-ID: 236942 [Multi-domain] Cd Length: 428 Bit Score: 46.61 E-value: 5.83e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 110 ARQQQIEA--DTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEA--ERQREREQAEKELQE--QREAERRQLEAE-E 182
Cdd:PRK11637 167 ARQETIAElkQTREELAAQKAELEEKQSQQKTLLYEQQAQQQKLEQArnERKKTLTGLESSLQKdqQQLSELRANESRlR 246

                         90
                 ....*....|....*....
gi 320545982 183 NQRKQRENEEKERLENERR 201
Cdd:PRK11637 247 DSIARAEREAKARAEREAR 265

The second Lim domain of pollen specific protein SF3; The second Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188825 [Multi-domain] Cd Length: 61 Bit Score: 41.69 E-value: 6.27e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 870 CIKCNKVITS-GGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECFGELFAKR 928
Cdd:cd09441    1 CVACGKTVYPiEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188817 Cd Length: 58 Bit Score: 41.51 E-value: 6.28e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 809 CDGCGEVFRA--GTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGC 861
Cdd:cd09433    1 CAGCTNPISGlgGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 47.06 E-value: 6.51e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   94 RVDPAGDKRQALAAELARQQQieaDTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQRE---REQAEKELQEQ 170
Cdd:PTZ00121 1153 RVEIARKAEDARKAEEARKAE---DAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEearKAEDAKKAEAV 1229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  171 REAERRQLEAEENQR--KQRENEEKERLENERRL--------IDAEREREENERRLQEAEEQREREESERRIVVAERQRE 240
Cdd:PTZ00121 1230 KKAEEAKKDAEEAKKaeEERNNEEIRKFEEARMAhfarrqaaIKAEEARKADELKKAEEKKKADEAKKAEEKKKADEAKK 1309

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  241 QAEaEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQA--DEEGQALRDAEIVERLLAAErELSPSATESELEEDAAIA 318
Cdd:PTZ00121 1310 KAE-EAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAakAEAEAAADEAEAAEEKAEAA-EKKKEEAKKKADAAKKKA 1387

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  319 EQSRRLISSRTDLEQKQRMIEENARRFLEAE--EEMVMLQQRQLQASHSKEEADEYAGMEPVVEELCVKKVAPPRFQEPP 396
Cdd:PTZ00121 1388 EEKKKADEAKKKAEEDKKKADELKKAAAAKKkaDEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAE 1467

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  397 EEPMVHKVKTQFGQGSGPEDaysAKSKTLTFPGVSDEG-SSLEPKTPFSIQQSSFSTQPSDEGNRIESERPEPEGEdQIQ 475
Cdd:PTZ00121 1468 EAKKADEAKKKAEEAKKADE---AKKKAEEAKKKADEAkKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAK-KAE 1543

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  476 EVQYTEDyLRSLDGIKNRPLMREDGSGRRRAFKKRRSSGSSNSSRESRASRDEELKMFTSLEE----EELRHGDREdynp 551
Cdd:PTZ00121 1544 EKKKADE-LKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKkmkaEEAKKAEEA---- 1618

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  552 iKYTSEptlRVKSHRRHKRSPAKDVRPTAESTTSLEMLGEESTNPWGEVVPEHYKDTEFWKREKALSIDEEEIELERPSR 631
Cdd:PTZ00121 1619 -KIKAE---ELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEAL 1694

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982  632 GEDVEEEATNEPKSSSFEEATEAQNEQAVAALKQQLSKEQLDKEAEKDNPQA----VDTSDSNKSNLIFSGEYTKA 703
Cdd:PTZ00121 1695 KKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAeeakKDEEEKKKIAHLKKEEEKKA 1770

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188723 [Multi-domain] Cd Length: 52 Bit Score: 41.22 E-value: 6.62e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09337    1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

ribonuclease E; Reviewed

Pssm-ID: 236766 [Multi-domain] Cd Length: 1068 Bit Score: 46.96 E-value: 6.71e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  120 RRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQReREQAEKELQEQ------REAERRQLEAEENQ-------RK 186
Cdd:PRK10811  643 RRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRRERQR-RRNDEKRQAQQeakalnVEEQSVQETEQEERvqqvqprRK 721

                          90
                  ....*....|...
gi 320545982  187 QRENEEKERLENE 199
Cdd:PRK10811  722 QRQLNQKVRIEQS 734

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 41.37 E-value: 6.92e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 867 ATRCIKCNKVITSGG--VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09427    1 SSKCVACGKTVMPGSrkLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCY 57

recombination and DNA strand exchange inhibitor protein; Reviewed

Pssm-ID: 234750 [Multi-domain] Cd Length: 782 Bit Score: 46.74 E-value: 7.32e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 112 QQQIEADTRRQLAEaeaklvEERLRVQREKEESEEQQRKLvEAERQREREQAEKELQEQREAERRqlEAEENQRKQRENE 191
Cdd:PRK00409 527 ELERELEQKAEEAE------ALLKEAEKLKEELEEKKEKL-QEEEDKLLEEAEKEAQQAIKEAKK--EADEIIKELRQLQ 597

                         90
                 ....*....|....*
gi 320545982 192 EKERLE-NERRLIDA 205
Cdd:PRK00409 598 KGGYASvKAHELIEA 612

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 41.19 E-value: 7.74e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 929 CTACVKPITGiggtRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09361    1 CAHCNQVIRG----PFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELC 51

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188817 Cd Length: 58 Bit Score: 41.51 E-value: 7.80e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 870 CIKCNKVITSGG----VTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09433    1 CAGCTNPISGLGgtkyISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 41.19 E-value: 8.13e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 320545982 690 NKSNLIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09361    2 AHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.

Pssm-ID: 293879 [Multi-domain] Cd Length: 291 Bit Score: 45.65 E-value: 8.40e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 124 AEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENE 199
Cdd:cd16269  181 AEAEAILQADQALTEKEKEIEAERAKAEAAEQERKLLEEQQRELEQKLEDQERSYEEHLRQLKEKMEEERENLLKE 256

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188871 [Multi-domain] Cd Length: 54 Bit Score: 41.25 E-value: 8.81e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECFG 922
Cdd:cd09840    1 CSRCGDsVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 54

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188838 [Multi-domain] Cd Length: 52 Bit Score: 41.12 E-value: 9.34e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09454    1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 46.19 E-value: 9.47e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 106 AAELARQQQIEADTRRQLAEAEAKlveerlrvQREKEESEEQQRKLVEAERQREREQAEkelQEQREAERRQLEAEENQR 185
Cdd:COG3064    1 AQEALEEKAAEAAAQERLEQAEAE--------KRAAAEAEQKAKEEAEEERLAELEAKR---QAEEEAREAKAEAEQRAA 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 186 KQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAAQAER 265
Cdd:COG3064   70 ELAAEAAKKLAEAEKAAAEAEKKAAAEKAKAAKEAEAAAAAEKAAAAAEKEKAEEAKRKAEEEAKRKAEEERKAAEAEAA 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 266 RLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENARRF 345
Cdd:COG3064  150 AKAEAEAARAAAAAAAAAAAAAARAAAGAAAALVAAAAAAVEAADTAAAAAAALAAAAAAAAADAALLALAVAARAAAAS 229

                        250       260
                 ....*....|....*....|....*....
gi 320545982 346 LEAEEEMVMLQQRQLQASHSKEEADEYAG 374
Cdd:COG3064  230 REAALAAVEATEEAALGGAEEAADLAAVG 258

The third LIM domain of the Enigma Homolog (ENH) family; The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188843 [Multi-domain] Cd Length: 55 Bit Score: 41.10 E-value: 9.97e-05

                         10        20
                 ....*....|....*....|....*....
gi 320545982 889 WHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09459   22 WHDTCFVCSVCCESLEGQTFFSKKDKPLC 50

The first LIM domain of the Enigma Homolog (ENH) family; The first LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188837 [Multi-domain] Cd Length: 52 Bit Score: 40.77 E-value: 1.10e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09453    1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52

The first LIM domain of Four and a half LIM domains protein 3 (FHL3); The first LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188807 Cd Length: 59 Bit Score: 41.06 E-value: 1.17e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 925 FAKRCTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09423    1 FANTCDECKELIGH--DSRELYYEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDC 57

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 45.59 E-value: 1.22e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  55 EELPRMRERLDKQIKEAAEREALAGTNVmqdGVLYVNGIRVDP------AGDkrqalAAELARQqqieADTRRQLAEAEA 128
Cdd:COG3883   65 AEIDKLQAEIAEAEAEIEERREELGERA---RALYRSGGSVSYldvllgSES-----FSDFLDR----LSALSKIADADA 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 129 KLVEErlrVQREKEESEEQQRKLVEAERQREREQAE-KELQEQREAERRQLEAEENQRKQRENEEKERLENERRLIDAER 207
Cdd:COG3883  133 DLLEE---LKADKAELEAKKAELEAKLAELEALKAElEAAKAELEAQQAEQEALLAQLSAEEAAAEAQLAELEAELAAAE 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 320545982 208 EREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQ 251
Cdd:COG3883  210 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAASAAGAGAAG 253

The first LIM domain of Testin; The first LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188797 Cd Length: 58 Bit Score: 40.91 E-value: 1.25e-04

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 320545982 766 DKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09413   23 DKLWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188750 [Multi-domain] Cd Length: 53 Bit Score: 40.55 E-value: 1.30e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982 858 CAGCyeekfatrcikCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFtSRDEKPYCAE 919
Cdd:cd09364    1 CAGC-----------RGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYF-EKDGKLYCRK 50

Borrelia P83/100 protein; This family consists of several Borrelia P83/P100 antigen proteins.

Pssm-ID: 114011 [Multi-domain] Cd Length: 489 Bit Score: 45.76 E-value: 1.37e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   99 GDKRQALAAELARQQQIEAD---------------TRRQLAEA--EAKLVEERLRVQREKEESEEQQRKLVEAER-QRER 160
Cdd:pfam05262 211 DAKRAQQLKEELDKKQIDADkaqqkadfaqdnadkQRDEVRQKqqEAKNLPKPADTSSPKEDKQVAENQKREIEKaQIEI 290

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 320545982  161 EQAEKELQEQREAERRQLEAEENQRKQRenEEKERLENERRLID 204
Cdd:pfam05262 291 KKNDEEALKAKDHKAFDLKQESKASEKE--AEDKELEAQKKREP 332

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188838 [Multi-domain] Cd Length: 52 Bit Score: 40.35 E-value: 1.40e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIgiDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09454    1 CGHCNNII--RGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188750 [Multi-domain] Cd Length: 53 Bit Score: 40.55 E-value: 1.50e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 320545982 692 SNLIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQrYVIRDDHPYCIKCY 740
Cdd:cd09364    5 RGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNW-YFEKDGKLYCRKDY 52

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 45.14 E-value: 1.52e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  50 AAADAEELPRMRERLDKQIKEAaeREALAGTNVMQDGVLyvngirvdpagDKRQALAAELARQQQIEADTRRQLAEAEAK 129
Cdd:COG4942   18 QADAAAEAEAELEQLQQEIAEL--EKELAALKKEEKALL-----------KQLAALERRIAALARRIRALEQELAALEAE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 130 LVEERLRVQREKEESEEQQRKLVEAERQ---------------------------------REREQAEKELQEQREAERR 176
Cdd:COG4942   85 LAELEKEIAELRAELEAQKEELAELLRAlyrlgrqpplalllspedfldavrrlqylkylaPARREQAEELRADLAELAA 164

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 177 QLEAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQR 253
Cdd:COG4942  165 LRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEELEALIARLEAEAAAAAE 241

The fourth LIM domain of Leupaxin; The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188796 [Multi-domain] Cd Length: 52 Bit Score: 40.10 E-value: 1.58e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09412    1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188715 [Multi-domain] Cd Length: 52 Bit Score: 40.38 E-value: 1.60e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 693 NLIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQrYVIRDDHPYCIKCY 740
Cdd:cd09329    6 QEIKNGQALLALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188871 [Multi-domain] Cd Length: 54 Bit Score: 40.48 E-value: 1.60e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 736 CIKCYENVFAntceeCNKIIGidskdlsyKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09840    1 CSRCGDSVYA-----AEKIMG--------AGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

The first LIM domain of Four and a half LIM domains protein 3 (FHL3); The first LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188807 Cd Length: 59 Bit Score: 40.29 E-value: 1.72e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 866 FATRCIKCNKVI--TSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09423    1 FANTCDECKELIghDSRELYYEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188785 [Multi-domain] Cd Length: 53 Bit Score: 40.02 E-value: 1.77e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320545982 695 IFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09401    8 VYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

DNA double-strand break repair Rad50 ATPase;

Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 45.42 E-value: 1.78e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  97 PAGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLrvqrekeeseEQQRKLVEAERQREREQAEKELQEQREAERR 176
Cdd:PRK02224 460 PVEGSPHVETIEEDRERVEELEAELEDLEEEVEEVEERL----------ERAEDLVEAEDRIERLEERREDLEELIAERR 529

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 177 QLEAEENQRKQRENEEKERLENErrlidaerereenerrlqeaeeqrereeserrivvAERQREQAEAEKERAEQQRILA 256
Cdd:PRK02224 530 ETIEEKRERAEELRERAAELEAE-----------------------------------AEEKREAAAEAEEEAEEAREEV 574

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 257 eaeaaqaerrlfdAEIQRERDQADEEGQALRD-AEIVERLLAAERELspsatESELEEDAAIAEQSRrlissrtdlEQKQ 335
Cdd:PRK02224 575 -------------AELNSKLAELKERIESLERiRTLLAAIADAEDEI-----ERLREKREALAELND---------ERRE 627

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 336 RMIEENAR-RFLEAEEEmvmlQQRQLQASHSKEEADEYagMEPVVEEL 382
Cdd:PRK02224 628 RLAEKRERkRELEAEFD----EARIEEAREDKERAEEY--LEQVEEKL 669

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.

Pssm-ID: 349951 [Multi-domain] Cd Length: 132 Bit Score: 42.42 E-value: 1.80e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 100 DKRQAL------AAELARQ--QQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQR 171
Cdd:cd06503   29 DEREEKiaesleEAEKAKEeaEELLAEYEEKLAEARAEAQEIIEEARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEK 108

                         90
                 ....*....|
gi 320545982 172 EAERRQLEAE 181
Cdd:cd06503  109 EKALAELRKE 118

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188866 [Multi-domain] Cd Length: 54 Bit Score: 40.38 E-value: 1.80e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAGTKKMEyKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09482    1 CPRCGKSVYAAEKVMG-GGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 45.70 E-value: 1.83e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 216 LQEAEEQREREESERRIVVAERQREQAEAEKERAEQQ--RILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEI-- 291
Cdd:COG1196  218 LKEELKELEAELLLLKLRELEAELEELEAELEELEAEleELEAELAELEAELEELRLELEELELELEEAQAEEYELLAel 297

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 292 --VERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQLQASHSKEEA 369
Cdd:COG1196  298 arLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEA 377


                 ..
gi 320545982 370 DE 371
Cdd:COG1196  378 EE 379

LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188783 [Multi-domain] Cd Length: 58 Bit Score: 40.32 E-value: 1.88e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 748 CEECNKII---GIDSKD--LSYKdkhWHEACFLCFKCHLSLVDK-QFGAKADKIYCGNCY 801
Cdd:cd09397    1 CRKCGLEIegkSISSKDgeLSGQ---WHRECFVCTTCGCPFQFSvPCYVLDDKPYCQQHY 57

The third LIM domain of Testin-like family; The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188728 Cd Length: 57 Bit Score: 40.07 E-value: 1.96e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 870 CIKCNKVITSGG--VTYKNEPWH--RECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09342    1 CDACGEPIGPDVqrVAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFC 52

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 39.97 E-value: 2.03e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 820 TKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYEEKFA 867
Cdd:cd09431   10 TGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188866 [Multi-domain] Cd Length: 54 Bit Score: 40.00 E-value: 2.07e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 870 CIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09482    1 CPRCGKsVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

The second LIM domain of lipoma preferred partner (LPP); The second LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188740 [Multi-domain] Cd Length: 60 Bit Score: 40.22 E-value: 2.30e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFT-SRDEKPYCAECFGELFAKR 928
Cdd:cd09354    1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTvDATNQIHCIEDFHKKFAPR 60

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.

Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 42.72 E-value: 2.36e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  101 KRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEqrEAERRQLEA 180
Cdd:pfam05672  44 RKEELRRRAEEERARREEEARRLEEERRREEEERQRKAEEEAEEREQREQEEQERLQKQKEEAEAKARE--EAERQRQER 121

                          90       100
                  ....*....|....*....|..
gi 320545982  181 EenqrKQRENEEKERLENERRL 202
Cdd:pfam05672 122 E----KIMQQEEQERLERKKRI 139

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 45.35 E-value: 2.41e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   119 TRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQA------EKELQEQRE------AERRQLEAEENQRK 186
Cdd:pfam02463  181 ETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEYllyldyLKLNEERIDllqellRDEQEEIESSKQEI 260

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   187 QRENEEKERLENERRLIDAEREREENERRLQEAEEQREreESERRIVV-----AERQREQAEAEKERAEQQRILAEAEAA 261
Cdd:pfam02463  261 EKEEEKLAQVLKENKEEEKEKKLQEEELKLLAKEEEEL--KSELLKLErrkvdDEEKLKESEKEKKKAEKELKKEKEEIE 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   262 QAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELS-----PSATESELEEDAAIAEQSRRLISSRTDLEQKQR 336
Cdd:pfam02463  339 ELEKELKELEIKREAEEEEEEELEKLQEKLEQLEEELLAKKKleserLSSAAKLKEEELELKSEEEKEAQLLLELARQLE 418

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 320545982   337 MIEENARRFLEAEEEMVMLQQRQLQASHSKEEADE 371
Cdd:pfam02463  419 DLLKEEKKEELEILEEEEESIELKQGKLTEEKEEL 453

DNA double-strand break repair Rad50 ATPase;

Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 45.03 E-value: 2.50e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 105 LAAELARQQQIEADTRRqlAEAEAKLVEERLRVQREKEESEEqqrklvEAERQREREQAEKELQEQREAERRQLEAEENQ 184
Cdd:PRK02224 307 ADAEAVEARREELEDRD--EELRDRLEECRVAAQAHNEEAES------LREDADDLEERAEELREEAAELESELEEAREA 378

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 185 RKQRENE----EKERLENERRLIDAEREREEnerrlqeaeeqrereeserrivvAERQREQAEAEKERAEQQRILAEAEA 260
Cdd:PRK02224 379 VEDRREEieelEEEIEELRERFGDAPVDLGN-----------------------AEDFLEELREERDELREREAELEATL 435

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 261 AQAERRLFDAEIQRERDQADEEGQALRDAEIVERL---------LAAERElSPSATESELEEDAAIAEQSRRLISSRTDL 331
Cdd:PRK02224 436 RTARERVEEAEALLEAGKCPECGQPVEGSPHVETIeedrerveeLEAELE-DLEEEVEEVEERLERAEDLVEAEDRIERL 514

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 320545982 332 EQKQRMIEEnarRFLEAEEEmvmLQQRQLQASHSKEEADEY 372
Cdd:PRK02224 515 EERREDLEE---LIAERRET---IEEKRERAEELRERAAEL 549

The first LIM domain of Cysteine Rich Protein 2 (CRP2); The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188864 Cd Length: 55 Bit Score: 39.97 E-value: 2.57e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 808 RCDGCG-EVFRAgtKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09480    1 KCGACGrTVYHA--EEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCY 54

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 39.73 E-value: 2.88e-04

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 320545982 705 DKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09343   23 DRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

The third LIM domain of the Enigma Homolog (ENH) family; The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188843 [Multi-domain] Cd Length: 55 Bit Score: 39.56 E-value: 2.88e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 929 CTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILC 980
Cdd:cd09459    1 CHGCEFPIEA--GDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLC 50

The third LIM domain of Enigma-like family; The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188749 [Multi-domain] Cd Length: 54 Bit Score: 39.73 E-value: 2.92e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 929 CTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILC 980
Cdd:cd09363    1 CHGCDFPIEA--GDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50

The LIM domain of Cysteine-Rich Intestinal Protein (CRIP); The LIM domain of Cysteine-Rich Intestinal Protein (CRIP): CRIP is a short protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188862 Cd Length: 54 Bit Score: 39.48 E-value: 2.93e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 320545982 870 CIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09478    1 CPKCDKeVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188838 [Multi-domain] Cd Length: 52 Bit Score: 39.58 E-value: 2.98e-04

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 320545982 828 RQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09454   18 RSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188726 Cd Length: 58 Bit Score: 39.51 E-value: 3.15e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCNKVITSGGVTYKNEP------WHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09340    1 CEKCKEPINPGEVAVFAERagedacWHPGCFVCETCNELLVDLIYFYHDGKIYC 54

The third LIM domain of the Enigma Homolog (ENH) family; The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188843 [Multi-domain] Cd Length: 55 Bit Score: 39.56 E-value: 3.25e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYC 858
Cdd:cd09459    1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLC 50

The third LIM domain of Testin; The third LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers at cell-cell-contact areas and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188803 Cd Length: 59 Bit Score: 39.48 E-value: 3.31e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWH--EACFLCFKCHLSLVDKQFGAKADKIYC 797
Cdd:cd09419    1 CQGCHNAIDPEVQRVSYNNFHWHaePECFLCSCCSKCLIGQKFMPVEGMVFC 52

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188779 Cd Length: 56 Bit Score: 39.22 E-value: 3.49e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 748 CEECNKIIGIDSkdLSYKDKHWHEACFLCFKCH----LSLVDKQFGAKADKIYCGNC 800
Cdd:cd09393    1 CASCGKSIEDEC--IKFEDKRWHLKCFTCSRCHreisSELSDAAFNNKDQRILCSNC 55

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188723 [Multi-domain] Cd Length: 52 Bit Score: 39.29 E-value: 3.96e-04

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 320545982 703 AMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09337   15 ALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

type I restriction enzyme EcoKI subunit R; Provisional

Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 44.56 E-value: 4.06e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   40 FQHPGDSSVDAAADAEELPRMRERLDKQIKEAAEREALAgtnvmqdgvlyvngirvdpagdkrQALAAELARQQQIEADT 119
Cdd:PRK11448  134 FVPPEDPENLLHALQQEVLTLKQQLELQAREKAQSQALA------------------------EAQQQELVALEGLAAEL 189

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982  120 RRQLAEAEAKLveERLRVQREKEESEEQQRklveaeRQREREQAEKELqEQREAERRQL 178
Cdd:PRK11448  190 EEKQQELEAQL--EQLQEKAAETSQERKQK------RKEITDQAAKRL-ELSEEETRIL 239

DNA translocase FtsK; Provisional

Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 44.31 E-value: 4.10e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   97 PAGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLrvqrEKEESEEQQRKLVEAERQREREQAEkELQEQREAerR 176
Cdd:PRK10263  594 PRPQVKEGIGPQLPRPKRIRVPTRRELASYGIKLPSQRA----AEEKAREAQRNQYDSGDQYNDDEID-AMQQDELA--R 666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  177 QLEAEENQRKQRENEEkerlenerrliDAEREreenerrlqeaeeqrereeserrivvAERQREQAEAEKER----AEQQ 252
Cdd:PRK10263  667 QFAQTQQQRYGEQYQH-----------DVPVN--------------------------AEDADAAAEAELARqfaqTQQQ 709

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  253 RILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVErllaaerelsPSATESELEEDAAIAEQSRRLISSRTDLE 332
Cdd:PRK10263  710 RYSGEQPAGANPFSLDDFEFSPMKALLDDGPHEPLFTPIVE----------PVQQPQQPVAPQQQYQQPQQPVAPQPQYQ 779

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  333 QKQRMIeenarrfleAEEEMVMLQQRQLQASHSKEEADEYAGMEPVVEELCVKKVAPPRFQEP-------PEEPMVHKVK 405
Cdd:PRK10263  780 QPQQPV---------APQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPqqpvapqPQDTLLHPLL 850

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 320545982  406 TQFGqgsgpeDAYSAKSKTLTFPG---VSDEGSSLEPKTPFSIQQ 447
Cdd:PRK10263  851 MRNG------DSRPLHKPTTPLPSldlLTPPPSEVEPVDTFALEQ 889

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 39.16 E-value: 4.13e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320545982 695 IFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09396    8 IGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication.

Pssm-ID: 432349 [Multi-domain] Cd Length: 1191 Bit Score: 44.44 E-value: 4.20e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    54 AEELPRMRERLDKQIKEAAE-REALAGTNVMQDGVLYVNGIRVDpagdkrqALAAELARQQQIEADTRRQLAE------A 126
Cdd:pfam12128  282 QETSAELNQLLRTLDDQWKEkRDELNGELSAADAAVAKDRSELE-------ALEDQHGAFLDADIETAAADQEqlpswqS 354

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   127 EAKLVEERLRVQREK----EESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENE-RR 201
Cdd:pfam12128  355 ELENLEERLKALTGKhqdvTAKYNRRRSKIKEQNNRDIAGIKDKLAKIREARDRQLAVAEDDLQALESELREQLEAGkLE 434

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   202 LIDAEREREENERRL---QEAEEQREREESERRIVVAERQREQAEAEKERAEQQRIlaeaeaaQAERRLFDAeiqrERDQ 278
Cdd:pfam12128  435 FNEEEYRLKSRLGELklrLNQATATPELLLQLENFDERIERAREEQEAANAEVERL-------QSELRQARK----RRDQ 503

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320545982   279 ADEegqALRDA-----EIVERLLAAERELSPSATE--SELEEDAAIAEQSR-RLISS----RTDL 331
Cdd:pfam12128  504 ASE---ALRQAsrrleERQSALDELELQLFPQAGTllHFLRKEAPDWEQSIgKVISPellhRTDL 565

ATP synthase B/B' CF(0); Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006

Pssm-ID: 425677 [Multi-domain] Cd Length: 132 Bit Score: 41.14 E-value: 4.36e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  118 DTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENE----EK 193
Cdd:pfam00430  29 DKRRELIADEIAEAEERRKDAAAALAEAEQQLKEARAEAQEIIENAKKRAEKLKEEIVAAAEAEAERIIEQAAAeieqEK 108


                  ....*...
gi 320545982  194 ERLENERR 201
Cdd:pfam00430 109 DRALAELR 116

The first LIM domain of Prickle 1; The first LIM domain of Prickle 1. Prickle contains three C-terminal LIM domains and a N-terminal PET domain Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in mainly expressed in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. In addition, Prickle 1 regulates cell movements during gastrulation and neuronal migration through interaction with the noncanonical Wnt11/Wnt5 pathway in zebrafish. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188867 Cd Length: 59 Bit Score: 39.13 E-value: 4.38e-04

                         10        20        30
                 ....*....|....*....|....*....|
gi 320545982 769 WHEACFLCFKCHLSLVDKQFGAKADKIYCG 798
Cdd:cd09483   26 WHPSCFVCFTCNELLVDLIYFYQDGKIHCG 55

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188718 [Multi-domain] Cd Length: 52 Bit Score: 38.86 E-value: 4.67e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAEC 920
Cdd:cd09332    1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 39.13 E-value: 4.88e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 915 PYCAECFGELFAKRCTACvkpitgiggtrfisfEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09341    1 PRCAACDELIFSGEYTQA---------------EGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDC 54

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.

Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 41.56 E-value: 5.10e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  124 AEAEAKLVEERLRVQREKEESEEQQRKLVE-AERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRL 202
Cdd:pfam05672   9 AEEAARILAEKRRQAREQREREEQERLEKEeEERLRKEELRRRAEEERARREEEARRLEEERRREEEERQRKAEEEAEER 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 320545982  203 IDAEREREENERRLQEAEEQREREEserrivvAERQREQAEAEKERAEQQR 253
Cdd:pfam05672  89 EQREQEEQERLQKQKEEAEAKAREE-------AERQRQEREKIMQQEEQER 132

Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown];

Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 43.32 E-value: 5.77e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 232 IVVAERQREQAEAEkERAEQQRILAEAEAAQAERRLFDAEIQRERDQAdeegQALRDAEIVERLLAAERELSPSATESEL 311
Cdd:COG2268  214 IAIAQANREAEEAE-LEQEREIETARIAEAEAELAKKKAEERREAETA----RAEAEAAYEIAEANAEREVQRQLEIAER 288

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 312 EEDAAIAEQSRrlissrtdlEQKQRMIEENARRFLEAEEEmVMLQQRQLQASHSKEEAD-EYAGMEPVVE 380
Cdd:COG2268  289 EREIELQEKEA---------EREEAELEADVRKPAEAEKQ-AAEAEAEAEAEAIRAKGLaEAEGKRALAE 348

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 43.98 E-value: 5.85e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   94 RVDPAGDKRQALA-AELAR--QQQIEADTRRQLAEAEAKLVEERLRVQREKEESE--EQQRKLVEAERQREREQAE--KE 166
Cdd:PTZ00121 1110 KAEEARKAEEAKKkAEDARkaEEARKAEDARKAEEARKAEDAKRVEIARKAEDARkaEEARKAEDAKKAEAARKAEevRK 1189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  167 LQEQREAER-RQLEAEENQRKQRENEEKERLENERRLIDAERERE-----------ENERRLQEAEEQREREESERRIVV 234
Cdd:PTZ00121 1190 AEELRKAEDaRKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEakkdaeeakkaEEERNNEEIRKFEEARMAHFARRQ 1269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  235 AERQREQAEAEKE--RAEQQRILAEAEAAQAERRLFDAEIQ-RERDQADEEGQALRDAEIVERLLAAERELSPSATESEL 311
Cdd:PTZ00121 1270 AAIKAEEARKADElkKAEEKKKADEAKKAEEKKKADEAKKKaEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAK 1349

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  312 EEDAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQLQASHSKEEADEY--AGMEPVVEELCVKKVAP 389
Cdd:PTZ00121 1350 AEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELkkAAAAKKKADEAKKKAEE 1429

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  390 PRFQEPPEEPMVHKVKTQFGQGSGPE--DAYSAKSKTLTFPGVSDEGSSLEP--KTPFSIQQSSFSTQPSDEGNRIESER 465
Cdd:PTZ00121 1430 KKKADEAKKKAEEAKKADEAKKKAEEakKAEEAKKKAEEAKKADEAKKKAEEakKADEAKKKAEEAKKKADEAKKAAEAK 1509

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  466 PEPEGEDQIQEVQYTEDYLRSLDGIKNRPLMREDGSGRRRAFKKRRS-SGSSNSSRESRASRDEELKMFTSLEEEELRHG 544
Cdd:PTZ00121 1510 KKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEElKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKA 1589

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  545 DREDYNPIKYTSEPTLRVKSHRRHKrspAKDVRPTAESTTSLEMLGEESTNPWGEVVPEHYKDTEFWKREKALSIDEEEI 624
Cdd:PTZ00121 1590 EEARIEEVMKLYEEEKKMKAEEAKK---AEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEE 1666

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  625 ELERPSRGEDVEEEATNEPKSSSFEEATEAQNEQAVAAlkqqlskEQLDKEAEKDNPQAVDTSDSNKSNLIFSGEYTKAM 704
Cdd:PTZ00121 1667 AKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKA-------EELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEA 1739


                  ...
gi 320545982  705 DKD 707
Cdd:PTZ00121 1740 EED 1742

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188809 Cd Length: 54 Bit Score: 38.57 E-value: 5.91e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 320545982 941 GTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09425   11 GMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPC 53

phosphodiesterase; Provisional

Pssm-ID: 237177 [Multi-domain] Cd Length: 520 Bit Score: 43.61 E-value: 5.98e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 120 RRQLAEAEAKLVEERLR--VQREKEESEEQQR-KLVEA--ERQREREQAEKELQEQR----EAERRQLEAEEN-QRKQRE 189
Cdd:PRK12704  25 RKKIAEAKIKEAEEEAKriLEEAKKEAEAIKKeALLEAkeEIHKLRNEFEKELRERRnelqKLEKRLLQKEENlDRKLEL 104

                         90
                 ....*....|....*..
gi 320545982 190 NEEKER-LENERRLIDA 205
Cdd:PRK12704 105 LEKREEeLEKKEKELEQ 121

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 43.75 E-value: 6.33e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  136 RVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLenerrlidaerereenerr 215
Cdd:COG4913   239 RAHEALEDAREQIELLEPIRELAERYAAARERLAELEYLRAALRLWFAQRRLELLEAELEE------------------- 299

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  216 lqeaeeqrereeserrivvAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDA------EIQRERDQADEE-GQALRD 288
Cdd:COG4913   300 -------------------LRAELARLEAELERLEARLDALREELDELEAQIRGNggdrleQLEREIERLERElEERERR 360

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982  289 AEIVERLLAAeRELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMIEENARRFLEAEEEMVMLQQRQLQASHS 365
Cdd:COG4913   361 RARLEALLAA-LGLPLPASAEEFAALRAEAAALLEALEEELEALEEALAEAEAALRDLRRELRELEAEIASLERRKS 436

The second LIM domain of protein LIMPETin and related proteins; The second LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188801 Cd Length: 56 Bit Score: 38.67 E-value: 6.69e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982 808 RCDGCGEVFRAG--TKKMEyktRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYE 863
Cdd:cd09417    2 RSVQCDELIFSGeyTKAMN---KDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 42.22 E-value: 6.73e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 103 QALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQ-REREQAEKELQEQ-------REAE 174
Cdd:COG1579   13 QELDSELDRLEHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEiEEVEARIKKYEEQlgnvrnnKEYE 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 175 RRQLEaEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAE 250
Cdd:COG1579   93 ALQKE-IESLKRRISDLEDEILELMERIEELEEELAELEAELAELEAELEEKKAELDEELAELEAELEELEAEREE 167

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 42.97 E-value: 7.20e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 101 KRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRklveaERQREREQAEKELQEQREaerrQLEA 180
Cdd:COG4372   21 KTGILIAALSEQLRKALFELDKLQEELEQLREELEQAREELEQLEEELE-----QARSELEQLEEELEELNE----QLQA 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 181 EENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILA--EA 258
Cdd:COG4372   92 AQAELAQAQEELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAalEQ 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 259 EAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMI 338
Cdd:COG4372  172 ELQALSEAEAEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKEEL 251

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 320545982 339 EENARRFLEAEEEMVMLQQRQLQASHSKEEADEYAGMEPVVEEL 382
Cdd:COG4372  252 LEEVILKEIEELELAILVEKDTEEEELEIAALELEALEEAALEL 295

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 43.51 E-value: 7.37e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982    53 DAEELPRMRERLD--KQIKEAAEREALAGTNVMQDGVLyvngiRVDPAGDKRQALAAELARQQQIEADTRRQLAEAEAKL 130
Cdd:TIGR02168  335 LAEELAELEEKLEelKEELESLEAELEELEAELEELES-----RLEELEEQLETLRSKVAQLELQIASLNNEIERLEARL 409

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320545982   131 VEERLRVQREKEESEEQQRKLVEAERQREREQAE--KELQEQREAERRQLEAE-ENQRKQRENEEKERLENERRL 202
Cdd:TIGR02168  410 ERLEDRRERLQQEIEELLKKLEEAELKELQAELEelEEELEELQEELERLEEAlEELREELEEAEQALDAAEREL 484

The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188745 Cd Length: 53 Bit Score: 38.40 E-value: 7.52e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 809 CDGCGEVFRAgTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09359    1 CARCGKIVYP-TEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188745 Cd Length: 53 Bit Score: 38.40 E-value: 7.52e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 748 CEECNKIIGIDSKdLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYC 797
Cdd:cd09359    1 CARCGKIVYPTEK-VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYC 49

The first LIM domain of Arrowhead (AWH); The first LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188759 [Multi-domain] Cd Length: 54 Bit Score: 38.51 E-value: 7.82e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 320545982 809 CDGCGEVFrAGTKKMEYKTRQWHENCFCCCVCKTAIGTK-SFIPREQEIYC 858
Cdd:cd09373    1 CTGCGEPI-TDRFLLKVSGRSWHVSCLRCCVCQTPLERQpSCFTRDRQIYC 50

The first LIM domain of Ajuba-like proteins; The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188738 Cd Length: 54 Bit Score: 38.57 E-value: 7.82e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCNKVITSGGVTYK--NEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09352    1 CVKCGKGVYGASQACQamGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 42.97 E-value: 7.99e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  98 AGDKRQALAAELARQQQIEADTRRQLAEAEAKLveERLRVQREKEESEEQQRKLVEAERQREREQAEKE---LQEQREAE 174
Cdd:COG4372   92 AQAELAQAQEELESLQEEAEELQEELEELQKER--QDLEQQRKQLEAQIAELQSEIAEREEELKELEEQlesLQEELAAL 169

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 175 RRQLEAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRI 254
Cdd:COG4372  170 EQELQALSEAEAEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSALLDALELEEDKE 249

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 255 LAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAErelspsATESELEEDAAIAEQSRRLISSRTDLEQK 334
Cdd:COG4372  250 ELLEEVILKEIEELELAILVEKDTEEEELEIAALELEALEEAALE------LKLLALLLNLAALSLIGALEDALLAALLE 323

                        250
                 ....*....|....*
gi 320545982 335 QRMIEENARRFLEAE 349
Cdd:COG4372  324 LAKKLELALAILLAE 338

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 38.11 E-value: 8.62e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 748 CEECNKIIgiDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09361    1 CAHCNQVI--RGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

The LIM domain of Mlp84B and Mlp60A; The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188788 Cd Length: 54 Bit Score: 38.24 E-value: 9.17e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 808 RCDGCGEVFRAGTKKME--YKtrqWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09404    1 KCPKCGKSVYAAEERLAggYK---WHKMCFKCGMCNKLLDSTNCAEHEGELYCKQCH 54

The first LIM domain of Cysteine Rich Protein 1 (CRP1); The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188863 Cd Length: 56 Bit Score: 38.07 E-value: 9.68e-04

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 320545982 828 RQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09479   21 RSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCY 55

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188739 [Multi-domain] Cd Length: 60 Bit Score: 38.37 E-value: 9.72e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320545982 929 CTACVKPITgiggTRFISFEDRHWHHDCFVCASCKASLVGRGFITD 974
Cdd:cd09353    1 CAVCDQKIT----DRMLKATGKSYHPQCFTCVVCKCPLEGESFIVD 42

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188712 Cd Length: 53 Bit Score: 37.96 E-value: 9.72e-04

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 320545982 767 KHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09326   19 KSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSCY 53

The first LIM domain of Cysteine Rich Protein (CRP); The first LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188786 Cd Length: 53 Bit Score: 38.02 E-value: 1.01e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 809 CDGCGE-VFRAgtKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09402    1 CGACEKtVYHA--EEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCKSCY 53

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]

Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 42.53 E-value: 1.11e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   97 PAGDKRQALAAELARQQQIEAdtRRQLAEAEAKLVEERLRvqreKEESEEQQRKLVEAERQREREQAEKELQE-QREAE- 174
Cdd:TIGR02794  97 RAAAEKAAKQAEQAAKQAEEK--QKQAEEAKAKQAAEAKA----KAEAEAERKAKEEAAKQAEEEAKAKAAAEaKKKAEe 170

                          90       100
                  ....*....|....*....|....*....
gi 320545982  175 -RRQLEAE-----ENQRKQRENEEKERLE 197
Cdd:TIGR02794 171 aKKKAEAEakakaEAEAKAKAEEAKAKAE 199

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 38.08 E-value: 1.11e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYDAQFA 806
Cdd:cd09331    1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

DDRGK domain; This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.

Pssm-ID: 370664 [Multi-domain] Cd Length: 188 Bit Score: 41.18 E-value: 1.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  111 RQQQIEADTRRQLAEAEAKLVEERLRVQ-------REKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEEN 183
Cdd:pfam09756   8 RAKLELKEAKRQQREAEEEEREEREKLEekreeeyKEREEREEEAEKEKEEEERKQEEEQERKEQEEYEKLKSQFVVEEE 87

                          90
                  ....*....|...
gi 320545982  184 QRKQRENEEKERL 196
Cdd:pfam09756  88 GTDKLSAEDESQL 100

Centromere protein H (CENP-H); This family consists of several eukaryotic centromere protein H (CENP-H) sequences. Macromolecular centromere-kinetochore complex plays a critical role in sister chromatid separation, but its complete protein composition as well as its precise dynamic function during mitosis has not yet been clearly determined. CENP-H contains a coiled-coil structure and a nuclear localization signal. CENP-H is specifically and constitutively localized in kinetochores throughout the cell cycle. CENP-H may play a role in kinetochore organization and function throughout the cell cycle. This the C-terminus of the region, which is conserved from fungi to humans.

Pssm-ID: 461756 [Multi-domain] Cd Length: 114 Bit Score: 39.49 E-value: 1.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   97 PAGDKRQALAAELARQQQIEADTRRQLAEAEAklveERLRVQREKEES-EEQQRKLVEAERQREREQAEKELQeqreaer 175
Cdd:pfam05837   3 PLINRRDELSSAILKLSSELRELQEELTEVEK----ENLRLKRKNRELaAELLELAKEKESRREDPKLRAQLE------- 71

                          90
                  ....*....|...
gi 320545982  176 rQLEAEENQRKQR 188
Cdd:pfam05837  72 -KLEAELKKSRRR 83

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 37.75 E-value: 1.15e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 320545982 929 CTACVKPITGiggtRFISFEDRHWHHDCFVCASCKASLVGRGF 971
Cdd:cd09336    1 CAACNKPIVG----QVVTALGKTWHPEHFVCVHCQTELGTSNF 39

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188844 Cd Length: 55 Bit Score: 38.10 E-value: 1.15e-03

                         10        20        30
                 ....*....|....*....|....*....|.
gi 320545982 889 WHRECFTCTHCNITLAGQRFTSRDEKPYCAE 919
Cdd:cd09460   22 WHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 52

The LIM domain of N-RAP; The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188830 Cd Length: 53 Bit Score: 37.98 E-value: 1.17e-03

                         10        20        30
                 ....*....|....*....|....*....|..
gi 320545982 886 NEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09446   18 DQTWHKACFHCEVCKMMLTVNNFVSHQKKPYC 49

The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188792 [Multi-domain] Cd Length: 52 Bit Score: 37.88 E-value: 1.20e-03

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 320545982 703 AMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIK 738
Cdd:cd09408   15 AMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRR 50

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188787 Cd Length: 54 Bit Score: 37.94 E-value: 1.22e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320545982 870 CIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECF 921
Cdd:cd09403    1 CPRCGKsVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 37.96 E-value: 1.29e-03

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 320545982 705 DKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYEN 742
Cdd:cd09422   23 DRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECYSN 60

The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188746 [Multi-domain] Cd Length: 52 Bit Score: 37.74 E-value: 1.29e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 929 CTACVKPITGIggtrFISFEDRHWHHDCFVCASCKASLVGRG--FITD 974
Cdd:cd09360    1 CDKCGNGIVGV----VVKARDKNRHPECFVCADCGLNLKNKGyfFIED 44

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188718 [Multi-domain] Cd Length: 52 Bit Score: 37.70 E-value: 1.31e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 929 CTACVKPITGiggtRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09332    1 CGKCGEFVIG----RVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

The third LIM domain of Enigma-like family; The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188749 [Multi-domain] Cd Length: 54 Bit Score: 37.80 E-value: 1.41e-03

                         10        20        30
                 ....*....|....*....|....*....|.
gi 320545982 769 WHEACFLCFKCHLSLVDKQFGAKADKIYCGN 799
Cdd:cd09363   22 WHDTCFVCAVCHVNLEGQTFYSKKDKPLCKN 52

The third LIM domain of Testin; The third LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers at cell-cell-contact areas and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188803 Cd Length: 59 Bit Score: 37.94 E-value: 1.42e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 870 CIKCNKVI--TSGGVTYKNEPWH--RECFTCTHCNITLAGQRFTSRDEKPYCA-EC 920
Cdd:cd09419    1 CQGCHNAIdpEVQRVSYNNFHWHaePECFLCSCCSKCLIGQKFMPVEGMVFCSvEC 56

phosphodiesterase; Provisional

Pssm-ID: 237177 [Multi-domain] Cd Length: 520 Bit Score: 42.46 E-value: 1.42e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  99 GDKRQALAAELARQQ----QIEADTRRQLAEAEAKlvEErlrVQREKEESE----EQQRKLVEAERQ-REREQAEKELQE 169
Cdd:PRK12704  29 AEAKIKEAEEEAKRIleeaKKEAEAIKKEALLEAK--EE---IHKLRNEFEkelrERRNELQKLEKRlLQKEENLDRKLE 103

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 320545982 170 QREAERRQLEAEENQRKQRENEEKERLENERRLID 204
Cdd:PRK12704 104 LLEKREEELEKKEKELEQKQQELEKKEEELEELIE 138

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 37.66 E-value: 1.45e-03

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 320545982 706 KDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09345   20 KFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 444066 [Multi-domain] Cd Length: 594 Bit Score: 42.25 E-value: 1.47e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 117 ADTRRQLAEAEAKLVEERLRVQREK-EESEEQQRKLVEAERQREREQAEKElqEQREAERRQLEAEENQRKQRENEEKER 195
Cdd:COG5185  252 SDKLEKLVEQNTDLRLEKLGENAESsKRLNENANNLIKQFENTKEKIAEYT--KSIDIKKATESLEEQLAAAEAEQELEE 329

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 196 LENERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQRE----------QAEAEKERAEQQRI----LAEAEAA 261
Cdd:COG5185  330 SKRETETGIQNLTAEIEQGQESLTENLEAIKEEIENIVGEVELSKsseeldsfkdTIESTKESLDEIPQnqrgYAQEILA 409

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 262 QAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDA----AIAEQSRRLISSRTDLEQKQRM 337
Cdd:COG5185  410 TLEDTLKAADRQIEELQRQIEQATSSNEEVSKLLNELISELNKVMREADEESQSrleeAYDEINRSVRSKKEDLNEELTQ 489

                        250       260       270
                 ....*....|....*....|....*....|....
gi 320545982 338 IEENARRFLEAEEEMVMLQQRQLQASHSKEEADE 371
Cdd:COG5185  490 IESRVSTLKATLEKLRAKLERQLEGVRSKLDQVA 523

Saccharomyces cerevisiae mitochondrial small ribosomal subunit protein mS26 and similar proteins; mS26, also known as mitochondrial 37S ribosomal protein PET12, is a component of the mitochondrial small ribosomal subunit (mt-SSU) of Saccharomyces cerevisiae mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane. The family also includes a group of uncharacterized proteins from pezizomycotina, which show high sequence similarity with mS26.

Pssm-ID: 467916 [Multi-domain] Cd Length: 179 Bit Score: 40.61 E-value: 1.48e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 107 AELARQQQIEADTRRQ------LAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQRER-------------------E 161
Cdd:cd23703   46 SEYQEWKRKMAELRRQnlreglRELEERKLKTEELRAKRSERKQAERERALNAPEREDERltlptiesallgplmrvrtD 125

                         90       100
                 ....*....|....*....|....*.
gi 320545982 162 QAEKELQEQREAERRQLEAEENQRKQ 187
Cdd:cd23703  126 PEREERAAKRRANREAKELAKKEARA 151

The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188748 [Multi-domain] Cd Length: 52 Bit Score: 37.46 E-value: 1.51e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09362    1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYC 48

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 42.75 E-value: 1.51e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   116 EADTRRQLAEAEAKLVEERLrvqrekeesEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENE--EK 193
Cdd:TIGR02169  167 EFDRKKEKALEELEEVEENI---------ERLDLIIDEKRQQLERLRREREKAERYQALLKEKREYEGYELLKEKEalER 237

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   194 ERLENERRLIDAEREREENERRLQeaeeqrereESERRIVVAERQREQAEAEKERAEQQRILAEAEAAQAerrlFDAEIQ 273
Cdd:TIGR02169  238 QKEAIERQLASLEEELEKLTEEIS---------ELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGE----LEAEIA 304

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   274 RERDQADEEGQALRDAEIVERLLAAERElspsATESELEE-DAAIAEQSRR-------LISSRTDLEQKQRMIEENARRF 345
Cdd:TIGR02169  305 SLERSIAEKERELEDAEERLAKLEAEID----KLLAEIEElEREIEEERKRrdklteeYAELKEELEDLRAELEEVDKEF 380

                          250       260
                   ....*....|....*....|...
gi 320545982   346 LEAEEEMVMLQQRQLQASHSKEE 368
Cdd:TIGR02169  381 AETRDELKDYREKLEKLKREINE 403

Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 42.63 E-value: 1.74e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  102 RQALAAELARqqqieADTRRQLAEAEAKLVEerlrVQREKEESEEQQRKLvEAERQrereQAEKELQEQREAERRQleaE 181
Cdd:COG3096   285 ERALELRREL-----FGARRQLAEEQYRLVE----MARELEELSARESDL-EQDYQ----AASDHLNLVQTALRQQ---E 347

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  182 ENQRKQRENEE-KERLEnerrlidaerereenerrlqeaeeqrereeserrivVAERQREQAEAEKERAEQQRILAEAEA 260
Cdd:COG3096   348 KIERYQEDLEElTERLE------------------------------------EQEEVVEEAAEQLAEAEARLEAAEEEV 391

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  261 AQAERRLfdAEIQRERD----QADEEGQALRDAEIVERLLAAErELSPSATESELEEDAAIAEQsrrLISSRTDLEQKQR 336
Cdd:COG3096   392 DSLKSQL--ADYQQALDvqqtRAIQYQQAVQALEKARALCGLP-DLTPENAEDYLAAFRAKEQQ---ATEEVLELEQKLS 465

                         250
                  ....*....|..
gi 320545982  337 MIEENARRFLEA 348
Cdd:COG3096   466 VADAARRQFEKA 477

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188787 Cd Length: 54 Bit Score: 37.56 E-value: 1.75e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 736 CIKCYENVFAntceeCNKIIGidskdlsyKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09403    1 CPRCGKSVYA-----AEKIIG--------AGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 37.54 E-value: 1.80e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 320545982 698 GEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09406   12 GQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

The first LIM domain of Lhx3 and Lhx4 family; The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188754 Cd Length: 52 Bit Score: 37.40 E-value: 1.86e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 748 CEECNKIIgIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFgAKADKIYC 797
Cdd:cd09368    1 CGGCQEHI-LDRFILKVLDRTWHAKCLKCNDCGAQLTDKCF-ARNGHVYC 48

recombination and DNA strand exchange inhibitor protein; Reviewed

Pssm-ID: 234750 [Multi-domain] Cd Length: 782 Bit Score: 42.12 E-value: 1.87e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  98 AGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQRE--------KEESEEQQRKLVEAERQREREQAEKELQE 169
Cdd:PRK00409 532 LEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEaqqaikeaKKEADEIIKELRQLQKGGYASVKAHELIE 611

                         90       100
                 ....*....|....*....|....*
gi 320545982 170 QREA-ERRQLEAEENQRKQRENEEK 193
Cdd:PRK00409 612 ARKRlNKANEKKEKKKKKQKEKQEE 636

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188712 Cd Length: 53 Bit Score: 37.19 E-value: 1.94e-03

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 320545982 827 TRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09326   18 GKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSCY 53

type I restriction enzyme EcoKI subunit R; Provisional

Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 42.25 E-value: 2.08e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   95 VDPAgDKRQALAAELARQQQieadtRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKeLQEQREAE 174
Cdd:PRK11448  138 EDPE-NLLHALQQEVLTLKQ-----QLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQELEAQLEQ-LQEKAAET 210

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 320545982  175 RRQLEAeenQRKQRENEEKERLE-NE---RRLIDA 205
Cdd:PRK11448  211 SQERKQ---KRKEITDQAAKRLElSEeetRILIDQ 242

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188838 [Multi-domain] Cd Length: 52 Bit Score: 37.27 E-value: 2.12e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 693 NLIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09454    5 NNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188791 [Multi-domain] Cd Length: 52 Bit Score: 37.24 E-value: 2.13e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09407    1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYC 48

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 37.16 E-value: 2.14e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 320545982 929 CTACVKPITGiggtRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPD 982
Cdd:cd09406    3 CASCQKPIAG----QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEE 52

transcription termination factor Rho; Provisional

Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 41.81 E-value: 2.35e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  44 GDSSVDAAADAEELPRMRERLDKQIKEAAEREALAGTnvmqdgvlyvngirvdPAGDKRQALAAELARQQQIEADTRRQL 123
Cdd:PRK12678  61 GGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEA----------------AAAKAEAAPAARAAAAAAAEAASAPEA 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 124 AEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEA-EENQRKQRENEEKERLENERRL 202
Cdd:PRK12678 125 AQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRqAEAERGERGRREERGRDGDDRD 204

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 203 IDAErereenerrlQEAEEQrereeserrivvAERQREQAEAEKERAEQQRilaeaEAAQAERRLFDAEIQRERDQADEE 282
Cdd:PRK12678 205 RRDR----------REQGDR------------REERGRRDGGDRRGRRRRR-----DRRDARGDDNREDRGDRDGDDGEG 257


                 ....*
gi 320545982 283 GQALR 287
Cdd:PRK12678 258 RGGRR 262

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188725 [Multi-domain] Cd Length: 52 Bit Score: 36.93 E-value: 2.49e-03

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 320545982 703 AMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09339   15 AMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

hypothetical protein; Provisional

Pssm-ID: 237178 [Multi-domain] Cd Length: 508 Bit Score: 41.62 E-value: 2.57e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 120 RRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRE--NEEKERLE 197
Cdd:PRK12705  29 QRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQKEEQLDARAEklDNLENQLE 108


                 ....*...
gi 320545982 198 NERRLIDA 205
Cdd:PRK12705 109 EREKALSA 116

The first LIM domain of actin binding LIM (abLIM) proteins; The first LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188713 [Multi-domain] Cd Length: 52 Bit Score: 36.85 E-value: 2.61e-03

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 320545982 948 EDRHWHHDCFVCASCKASLVGRGFITDGPDILCPD 982
Cdd:cd09327   16 QDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTD 50

Coiled-coil domain-containing protein 50 N-terminus;

Pssm-ID: 464621 [Multi-domain] Cd Length: 126 Bit Score: 38.94 E-value: 2.62e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982  129 KLVEERLRVQREKEESEEQQRKLVEAERQREREQAE----KELQE--QREAERRQLEAEENQRKQRENEEKERLENERR 201
Cdd:pfam15295  47 QLVQNDIRVAKQLQEEEELQAQTLFQRRLAQLEEQDeeiaKEIQEelQREAEERRRREEEDEEIARQLQERERERERRR 125

The first LIM domain of Prickle; The first LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188799 Cd Length: 59 Bit Score: 36.85 E-value: 2.63e-03

                         10        20        30
                 ....*....|....*....|....*....|
gi 320545982 769 WHEACFLCFKCHLSLVDKQFGAKADKIYCG 798
Cdd:cd09415   26 WHPACFVCSTCKELLVDLIYFYQDGKVYCG 55

The third LIM domain of protein PINCH; The third LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188719 Cd Length: 51 Bit Score: 36.97 E-value: 2.64e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGqrfTSRDEKpycaecfGELFAKRC 929
Cdd:cd09333    1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTA---DARELK-------GELYCLRC 50

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.

Pssm-ID: 293879 [Multi-domain] Cd Length: 291 Bit Score: 41.02 E-value: 2.78e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 101 KRQALAAELARQQQIEADTRRQLAEAEaKLVEERLRVQREKEEsEEQQRKLVEAERQREREQAEKE--LQEQREAERRQL 178
Cdd:cd16269  206 KAEAAEQERKLLEEQQRELEQKLEDQE-RSYEEHLRQLKEKME-EERENLLKEQERALESKLKEQEalLEEGFKEQAELL 283


                 ....*...
gi 320545982 179 EAEENQRK 186
Cdd:cd16269  284 QEEIRSLK 291

The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188793 [Multi-domain] Cd Length: 53 Bit Score: 36.74 E-value: 2.91e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09409    1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYC 48

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 40.97 E-value: 3.06e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  49 DAAADAEELPRMRERLDKQIKEAAER-------EALAGTNVMQDgvlYVNGI-RVDPAGDKRQALAAELARQQQIEADTR 120
Cdd:COG3883   73 EIAEAEAEIEERREELGERARALYRSggsvsylDVLLGSESFSD---FLDRLsALSKIADADADLLEELKADKAELEAKK 149

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 121 RQLAEAEAKLVEERLRVQREKEESE----EQQRKLVEAERQREREQAEK-ELQEQREAERRQLEAEENQRKQREN 190
Cdd:COG3883  150 AELEAKLAELEALKAELEAAKAELEaqqaEQEALLAQLSAEEAAAEAQLaELEAELAAAEAAAAAAAAAAAAAAA 224

Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; This model characterizes proteins similar to prohibitin (a lipid raft-associated integral membrane protein). Individual proteins of the SPFH (band 7) domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. These microdomains, in addition to being stable scaffolds, may also be dynamic units with their own regulatory functions. Prohibitin is a mitochondrial inner-membrane protein which may act as a chaperone for the stabilization of mitochondrial proteins. Human prohibitin forms a hetero-oligomeric complex with Bap-37 (prohibitin 2, an SPFH domain carrying homolog). This complex may protect non-assembled membrane proteins against proteolysis by the m-AAA protease. Prohibitin and Bap-37 yeast homologs have been implicated in yeast longevity and in the maintenance of mitochondrial morphology.

Pssm-ID: 259799 [Multi-domain] Cd Length: 195 Bit Score: 39.80 E-value: 3.08e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  53 DAEELPRMRERLDKQIKEAAeREALAGTNVMQDGVLYVNgIRVDPagdkrqalaaELarQQQIEAdtrRQLAEAEAKlvE 132
Cdd:cd03401  109 TAEELYTKREEVSAEIREAL-TERLAPFGIIVDDVLITN-IDFPD----------EY--EKAIEA---KQVAEQEAE--R 169

                         90       100
                 ....*....|....*....|....*..
gi 320545982 133 ERLRVQREKeesEEQQRKLVEAERQRE 159
Cdd:cd03401  170 AKFELEKAE---QEAERKVIEAEGEAE 193

The LIM domain of Mical (molecule interacting with CasL); The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188823 [Multi-domain] Cd Length: 55 Bit Score: 36.89 E-value: 3.08e-03

                         10        20        30
                 ....*....|....*....|....*....|....
gi 320545982 890 HRECFTCTHCNITL--AGQRFTSRDEKPYCAECF 921
Cdd:cd09439   22 HRSCFKCSYCGTTLrlGAYAFDRDDGKFYCKPHF 55

The first LIM domain of Prickle 2; The first LIM domain of Prickle 2: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188868 Cd Length: 59 Bit Score: 36.85 E-value: 3.14e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEECN-KIIGIDSKDLSYKDKH---WHEACFLCFKCHLSLVDKQFGAKADKIYCG 798
Cdd:cd09484    1 CEQCGgQINGGDIAVFASRAGHgvcWHPQCFVCSVCNELLVDLIYFYQDGKIYCG 55

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.

Pssm-ID: 349951 [Multi-domain] Cd Length: 132 Bit Score: 38.96 E-value: 3.17e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 110 ARQQQIEADtrrqLAEAEAKLVEerlrVQREKEESEEQQRKlVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRE 189
Cdd:cd06503   30 EREEKIAES----LEEAEKAKEE----AEELLAEYEEKLAE-ARAEAQEIIEEARKEAEKIKEEILAEAKEEAERILEQA 100

                         90
                 ....*....|..
gi 320545982 190 NEEkerLENERR 201
Cdd:cd06503  101 KAE---IEQEKE 109

DNA double-strand break repair Rad50 ATPase;

Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 41.56 E-value: 3.22e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 101 KRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRvQREKEESEEQQRKLVE--AERQREREQAEKELQEQREAERRQL 178
Cdd:PRK02224 214 ELAELDEEIERYEEQREQARETRDEADEVLEEHEER-REELETLEAEIEDLREtiAETEREREELAEEVRDLRERLEELE 292

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 179 EAEENQRKQRENEEKERLENERRLIDAEREREENERRLQEAEEQREREESErrivvAERQREQAEAEKERAEQQRilaea 258
Cdd:PRK02224 293 EERDDLLAEAGLDDADAEAVEARREELEDRDEELRDRLEECRVAAQAHNEE-----AESLREDADDLEERAEELR----- 362

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 259 eaaqAERRLFDAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAAIAEQSRRLISSRTDLEQKQRMI 338
Cdd:PRK02224 363 ----EEAAELESELEEAREAVEDRREEIEELEEEIEELRERFGDAPVDLGNAEDFLEELREERDELREREAELEATLRTA 438

                        250
                 ....*....|...
gi 320545982 339 EEN---ARRFLEA 348
Cdd:PRK02224 439 RERveeAEALLEA 451

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188818 Cd Length: 56 Bit Score: 36.66 E-value: 3.25e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 320545982 698 GEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKC 739
Cdd:cd09434   14 GKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188844 Cd Length: 55 Bit Score: 36.55 E-value: 3.28e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYC 858
Cdd:cd09460    1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 50

The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188735 [Multi-domain] Cd Length: 87 Bit Score: 37.53 E-value: 3.36e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 320545982 670 EQLDKEAEKDNPQAVDTSDSN---KSNLIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09349   14 QQLMQDMDHPPAAEAATNELCgicGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188846 [Multi-domain] Cd Length: 74 Bit Score: 37.17 E-value: 3.39e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320545982 695 IFSGEYTKAMDKDWHSGHFCCWQCDESLTgQRYVIRDDHPYCIKCY 740
Cdd:cd09462   29 IYDGQYLQALNSDWHADCFRCCECGASLS-HWYYEKDGRLFCKKDY 73

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188777 Cd Length: 57 Bit Score: 36.51 E-value: 3.67e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKP 915
Cdd:cd09391    1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDT 46

The first LIM domain of Cysteine Rich Protein 1 (CRP1); The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188863 Cd Length: 56 Bit Score: 36.53 E-value: 3.73e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 746 NTCEECNKIIGIdSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCY 801
Cdd:cd09479    1 KKCGVCQKTVYF-AEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCY 55

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 40.91 E-value: 3.83e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   7 ALTGVGELLFSLLIGYLGALeFAFVARHLYHWTFQHPGDSSVDAAADAEELPRMRERLDKQIKE--AAEREALAGTNVMQ 84
Cdd:COG4717  260 ALLGLGGSLLSLILTIAGVL-FLVLGLLALLFLLLAREKASLGKEAEELQALPALEELEEEELEelLAALGLPPDLSPEE 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  85 DGVLYVNGIRVDPAGDKRQALAAELaRQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQ-REREQA 163
Cdd:COG4717  339 LLELLDRIEELQELLREAEELEEEL-QLEELEQEIAALLAEAGVEDEEELRAALEQAEEYQELKEELEELEEQlEELLGE 417

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 164 EKELQEQREAERRQLEAEENQRKQRENEEK-ERLENERRLIDAEREREENERRLQEaeeqrereeserrivvAERQREQA 242
Cdd:COG4717  418 LEELLEALDEEELEEELEELEEELEELEEElEELREELAELEAELEQLEEDGELAE----------------LLQELEEL 481

                        250
                 ....*....|
gi 320545982 243 EAEKERAEQQ 252
Cdd:COG4717  482 KAELRELAEE 491

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 36.54 E-value: 3.93e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 320545982 870 CIKCN-------KVITSGGvtyknEPWHRECFTCTHCNITLAGQRFTSRDEKPYCAECFGELFA 926
Cdd:cd09331    1 CERCRegfepdeKIVNSNG-----ELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

lipase secretion chaperone;

Pssm-ID: 234937 [Multi-domain] Cd Length: 336 Bit Score: 40.43 E-value: 3.96e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 100 DKRQALAAELARQQQIEA-----DTRRQLAEaeaklveERLRVQREKEESEEQQRKLVEAERQrereQAEKELQEQREAE 174
Cdd:PRK01294 162 DARLALRARFFSDWEIQAffgeeNQYQRYAL-------ERLRIAQDPSLSDAQKAARLAALEA----QLPEDLRAALQES 230

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 175 RRQLEAEE--NQRKQRENEEKERLENERRLIDAErereenerrlqeaeeqrereeserrivVAER---QREQAEAEKER- 248
Cdd:PRK01294 231 QRQQALLQqlAQLQASGASPQELRLMRAQLVGPE---------------------------AAQRleqLDQQRAAWQQRy 283

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 320545982 249 ----AEQQRILAEAEAAQAERRlfdAEIQRERDQADEEGQALRdAEIVERLLAAERE 301
Cdd:PRK01294 284 ddylAQRAQILNAAGLSPQDRQ---AQIAQLRQQRFSPQEALR-LAALERIHDAGQT 336

The second LIM domain of Lhx2 and Lhx9 family; The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188763 Cd Length: 59 Bit Score: 36.48 E-value: 4.09e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 869 RCIKCNKVITSGGVTY--KNEPWHRECFTCTHCNITL-AGQRFTSRDEKPYC 917
Cdd:cd09377    4 RCARCHLGISASELVMraRDLVFHLNCFTCATCNKPLtKGDHFGMRDGLVYC 55

F0F1 ATP synthase subunit B; Provisional

Pssm-ID: 184696 [Multi-domain] Cd Length: 250 Bit Score: 40.18 E-value: 4.12e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 110 ARQQQIEadTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLV--------EAERQREREQAEKELQEQREAERRQLEAE 181
Cdd:PRK14474  36 KRQQRIA--NRWQDAEQRQQEAGQEAERYRQKQQSLEQQRASFmaqaqeaaDEQRQHLLNEAREDVATARDEWLEQLERE 113


                 ...
gi 320545982 182 ENQ 184
Cdd:PRK14474 114 KQE 116

The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188798 [Multi-domain] Cd Length: 58 Bit Score: 36.61 E-value: 4.16e-03

                         10        20
                 ....*....|....*....|....*....
gi 320545982 769 WHEACFLCFKCHLSLVDKQFGAKADKIYC 797
Cdd:cd09414   26 WHPACFRCSTCEELLVDLTYCVHDDQIYC 54

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.

Pssm-ID: 462322 Cd Length: 323 Bit Score: 40.24 E-value: 4.36e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  109 LARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKlvEAERQREREQAEKEL--QEQREAERRqlEAEENQRK 186
Cdd:pfam07946 248 LAKRAKLRPEALKKAKKTREEEIEKIKKAAEEERAEEAQEKK--EEAKKKEREEKLAKLspEEQRKYEEK--ERKKEQRK 323

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188802 Cd Length: 56 Bit Score: 36.25 E-value: 4.36e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 734 PYCIKCYENVFANTCEECnkiigidskdlsyKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYCGNCYD 802
Cdd:cd09418    1 PRCSACDEIIFADECTEA-------------EGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56

Two-component sensor histidine kinase, HisKA and HATPase domains [Signal transduction mechanisms];

Pssm-ID: 443125 [Multi-domain] Cd Length: 495 Bit Score: 40.66 E-value: 4.37e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  49 DAAADAEELPRMRERLDKQIKEAAEREALAGTNVMQDGVLYVNGIRVDPAGDKRQALAAELARQQQIEADTRRQLAEAEA 128
Cdd:COG3920   31 LALLALLLLALLLLALLLASALLALLALSAAALAAALAVALAAAVGAAAALLALLVLLLLLLLAAAALALALLLAALAGL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 129 KLVEERLRVQREKEESEEQQRkLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRLIDAERE 208
Cdd:COG3920  111 LLLAALLLLRLVALLAALALL-ALLLLLLLLLAILALAELAVALAELAAALLLLAEELAALRLAAAALLLLLAALLDLGL 189

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 209 REENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALRD 288
Cdd:COG3920  190 ALAALAAAALLALLLALELLLALLLLLLLLLALLLVLLAALLRLRAAVLEELERRRRARGLGRLLLLLLLLLLLLRALLL 269

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 289 AEIVERLLAAER-ELSPSATESELEEDAAIAEQSRR------LISSRTDLeQKQRMIEENARRFLEAeeemvmLQQR--- 358
Cdd:COG3920  270 LAAGIRLVITERkRAEEELEASLEEKELLLRELHHRvknnlqVVSSLLRL-QARRADDPEAREALEE------SQNRiqa 342

                        330       340
                 ....*....|....*....|....*..
gi 320545982 359 --QLQASHSKEEADEYAGMEPVVEELC 383
Cdd:COG3920  343 laLVHELLYQSEDWEGVDLRDYLRELL 369

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 40.58 E-value: 4.44e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  97 PAGDKRQALAAELARQQQIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAerQREREQAEKELQEQREAERR 176
Cdd:COG3883   13 FADPQIQAKQKELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKL--QAEIAEAEAEIEERREELGE 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 177 QLEAeeNQRKQRENEEKERL--------------------ENERRLIDAEREREENERRLQEAEEQREREESErriVVAE 236
Cdd:COG3883   91 RARA--LYRSGGSVSYLDVLlgsesfsdfldrlsalskiaDADADLLEELKADKAELEAKKAELEAKLAELEA---LKAE 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 237 RQREQAEAEKERAEQQRILAEAEAAQaerrlfdAEIQRERDQADEEGQALRDAEIVERLLAAERELSPSATESELEEDAA 316
Cdd:COG3883  166 LEAAKAELEAQQAEQEALLAQLSAEE-------AAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 238

                        250
                 ....*....|...
gi 320545982 317 IAEQSRRLISSRT 329
Cdd:COG3883  239 AAAAAASAAGAGA 251

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.

Pssm-ID: 460721 [Multi-domain] Cd Length: 297 Bit Score: 40.35 E-value: 4.63e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  119 TRRQLAEAEAKLVEERLR---VQREKEESEEQQRKLVEAERQRER--EQAEKELQEQREAERRQLEAE-ENQRKQRENEE 192
Cdd:pfam02841 195 TDQALTAKEKAIEAERAKaeaAEAEQELLREKQKEEEQMMEAQERsyQEHVKQLIEKMEAEREQLLAEqERMLEHKLQEQ 274


                  ....*..
gi 320545982  193 KERLENE 199
Cdd:pfam02841 275 EELLKEG 281

Caldesmon;

Pssm-ID: 460421 [Multi-domain] Cd Length: 495 Bit Score: 40.62 E-value: 4.73e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   49 DAAADAEELPRMRERLDKQIKEAAEREalagtnvmqdgvlyvnGIRVDPAGDKRQALAAELARQQQIEADTRRQLAEAEA 128
Cdd:pfam02029  60 EEEAFLDRTAKREERRQKRLQEALERQ----------------KEFDPTIADEKESVAERKENNEEEENSSWEKEEKRDS 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  129 KLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERRLIDAERE 208
Cdd:pfam02029 124 RLGRYKEEETEIREKEYQENKWSTEVRQAEEEGEEEEDKSEEAEEVPTENFAKEEVKDEKIKKEKKVKYESKVFLDQKRG 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  209 REENERRLQEAEEQREREESERRIVVAERQREQAEAEKERAEQQRILAeaeaaqaerrlfdaEIQRERDQADEEG----- 283
Cdd:pfam02029 204 HPEVKSQNGEEEVTKLKVTTKRRQGGLSQSQEREEEAEVFLEAEQKLE--------------ELRRRRQEKESEEfeklr 269

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  284 QALRDAEI-VERLLAAERELSPSATESELEEDAAIAEQSRRLissrtdLEQKQRMIEENARRFLEAEEEM 352
Cdd:pfam02029 270 QKQQEAELeLEELKKKREERRKLLEEEEQRRKQEEAERKLRE------EEEKRRMKEEIERRRAEAAEKR 333

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.

Pssm-ID: 188810 Cd Length: 57 Bit Score: 36.18 E-value: 4.79e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 929 CTACVKPItgIGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDCAKQK 987
Cdd:cd09426    1 CSECKKTI--MPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEKQ 57

Coiled-coil domain-containing protein 3; This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known.

Pssm-ID: 464032 [Multi-domain] Cd Length: 221 Bit Score: 39.69 E-value: 4.82e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  101 KRQALAAELARQQQiEADTRRQLAEA------EAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAE-KELQEQREA 173
Cdd:pfam13904  71 ELQAQKEEREKEEQ-EAELRKRLAKEkyqewlQRKARQQTKKREESHKQKAAESASKSLAKPERKVSQEEaKEVLQEWER 149

                          90       100
                  ....*....|....*....|....*...
gi 320545982  174 ERRQLEAEENQRKQRENEEKERLENERR 201
Cdd:pfam13904 150 KKLEQQQRKREEEQREQLKKEEEEQERK 177

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188739 [Multi-domain] Cd Length: 60 Bit Score: 36.45 E-value: 4.89e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEK-PYCAECFGELFAKR 928
Cdd:cd09353    1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANqPHCVNDYHRRYAPR 60

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.

Pssm-ID: 434558 [Multi-domain] Cd Length: 154 Bit Score: 38.62 E-value: 4.97e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982  142 EESEEQQRKLVEAERQREREQAEKELQEQREAERRQLE-AEENQRKQRENE-EKERLENERR 201
Cdd:pfam15236  45 EERERKRQKALEHQNAIKKQLEEKERQKKLEEERRRQEeQEEEERLRREREeEQKQFEEERR 106

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188844 Cd Length: 55 Bit Score: 36.17 E-value: 4.97e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 929 CTACVKPITGigGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILC 980
Cdd:cd09460    1 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 50

Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.

Pssm-ID: 460721 [Multi-domain] Cd Length: 297 Bit Score: 39.96 E-value: 4.97e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982  122 QLAEAEAKLVEERLRVQREKEESEEQQRK-LVEAERQREREQAeKELQEQREAERRQLEAEENQRKQRENEEKERLENE 199
Cdd:pfam02841 185 KEAVEEAILQTDQALTAKEKAIEAERAKAeAAEAEQELLREKQ-KEEEQMMEAQERSYQEHVKQLIEKMEAEREQLLAE 262

The third LIM domain of Prickle; The third LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188804 Cd Length: 59 Bit Score: 36.26 E-value: 5.05e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 320545982 857 YCAGCYEekfatrCIKcnkvITSGGVTYKNEPWH--RECFTCTHCNITLAGQRFTSRDEKPYCA 918
Cdd:cd09420    2 YCDTCGE------HIG----VDQGQMTYDGQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYCS 55

The first LIM domain of Prickle 3; The first LIM domain of Prickle 3/LIM domain only 6 (LM06): Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188872 Cd Length: 59 Bit Score: 36.39 E-value: 5.10e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 748 CEECNK-IIGIDSKDLSYKDKH---WHEACFLCFKCHLSLVDKQFGAKADKIYCG 798
Cdd:cd09841    1 CQQCGRqICGGDIAVFASRAGLgacWHPQCFQCASCQELLVDLIYFYQDGKIYCG 55

The third LIM domain of Enigma; The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188842 Cd Length: 55 Bit Score: 36.17 E-value: 5.32e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYC 858
Cdd:cd09458    1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLC 50

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188812 Cd Length: 54 Bit Score: 35.97 E-value: 5.39e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 929 CTACVKPItgIGGTRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPDILCPDC 983
Cdd:cd09428    1 CFHCKKTI--MPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPC 53

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188844 Cd Length: 55 Bit Score: 36.17 E-value: 5.48e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 320545982 748 CEECNKIIGIDSKDLSYKDKHWHEACFLCFKCHLSLVDKQFGAKADKIYC 797
Cdd:cd09460    1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 50

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188779 Cd Length: 56 Bit Score: 36.14 E-value: 5.56e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 320545982 825 YKTRQWHENCFCCCVCKTAIGTKS----FIPREQEIYCAGC 861
Cdd:cd09393   15 FEDKRWHLKCFTCSRCHREISSELsdaaFNNKDQRILCSNC 55

The third LIM domain of Enigma; The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188842 Cd Length: 55 Bit Score: 36.17 E-value: 5.70e-03

                         10        20
                 ....*....|....*....|....*....
gi 320545982 889 WHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09458   22 WHDTCFVCAICQINLEGKTFYSKKDKPLC 50

hypothetical protein; Provisional

Pssm-ID: 237178 [Multi-domain] Cd Length: 508 Bit Score: 40.46 E-value: 5.81e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  98 AGDKRQALAAELARQQ-QIEADTRRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERR 176
Cdd:PRK12705  26 KKRQRLAKEAERILQEaQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQKEEQLDARAEKLDNLEN 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 320545982 177 QLEAEENQRKQRENEEKERLEN-ERRLIDAEREREENERRLQEAEEQREREESERRIVVAERQREQAEAEKE 247
Cdd:PRK12705 106 QLEEREKALSARELELEELEKQlDNELYRVAGLTPEQARKLLLKLLDAELEEEKAQRVKKIEEEADLEAERK 177

The second LIM domain of the Enigma Homolog (ENH) family; The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188841 [Multi-domain] Cd Length: 52 Bit Score: 35.77 E-value: 5.93e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09457    1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYC 48

The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188840 [Multi-domain] Cd Length: 52 Bit Score: 35.74 E-value: 6.18e-03

                         10        20
                 ....*....|....*....|....*....
gi 320545982 830 WHENCFCCCVCKTAIGTKSFIPREQEIYC 858
Cdd:cd09456   20 WHVHCFTCAACKTPIRNRAFYMEEGAPYC 48

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 35.80 E-value: 6.25e-03

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 320545982 828 RQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCY 862
Cdd:cd09361   18 RSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

The second LIM domain of thymus LIM protein (TLP); The second LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188861 Cd Length: 54 Bit Score: 35.76 E-value: 6.30e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 858 CAGCYEEKFATRcikcnKVITSGgvtyKNepWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09477    1 CPGCGKPVYFAE-----KVMSLG----RN--WHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49

The first LIM domain of thymus LIM protein (TLP); The first LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188860 Cd Length: 54 Bit Score: 35.71 E-value: 6.58e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 320545982 870 CIKCNK-VITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09476    1 CPRCDKtVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49

recombination and DNA strand exchange inhibitor protein; Reviewed

Pssm-ID: 234750 [Multi-domain] Cd Length: 782 Bit Score: 40.20 E-value: 6.65e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545982 124 AEAEAKLVEERLRVQREKEESEEQQRKLveaerQREREQAEKELQEQrEAERRQLEAEENQRKQRENEEKERLENE 199
Cdd:PRK00409 505 EEAKKLIGEDKEKLNELIASLEELEREL-----EQKAEEAEALLKEA-EKLKEELEEKKEKLQEEEDKLLEEAEKE 574

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.

Pssm-ID: 188720 [Multi-domain] Cd Length: 54 Bit Score: 35.79 E-value: 6.67e-03

                         10        20        30
                 ....*....|....*....|....*....|....
gi 320545982 703 AMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYC 736
Cdd:cd09334   17 ALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYC 50

Troponin; Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin.

Pssm-ID: 460018 [Multi-domain] Cd Length: 132 Bit Score: 37.93 E-value: 6.87e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  106 AAELARQQQieadtrRQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQRereqaekelQEQREAERRQLEAEENQR 185
Cdd:pfam00992  12 AAEELEFEQ------EKKEEEKLRYLAERIPPLRLRGLSAEQLQELCEELHER---------IDKLEEERYDIEEKVAKK 76


                  ....*...
gi 320545982  186 KQRENEEK 193
Cdd:pfam00992  77 DKEINDLK 84

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188779 Cd Length: 56 Bit Score: 35.76 E-value: 6.98e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 929 CTACVKPITgiggTRFISFEDRHWHHDCFVCASCK----ASLVGRGFITDGPDILCPDCA 984
Cdd:cd09393    1 CASCGKSIE----DECIKFEDKRWHLKCFTCSRCHreisSELSDAAFNNKDQRILCSNCS 56

PAT complex subunit CCDC47; This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway.

Pssm-ID: 462322 Cd Length: 323 Bit Score: 39.86 E-value: 7.18e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545982  102 RQALAAELARQQQIEADTRRQLAEAEAKLVEERlrvQREKEESEEQQRKLVEAERQRE 159
Cdd:pfam07946 266 REEEIEKIKKAAEEERAEEAQEKKEEAKKKERE---EKLAKLSPEEQRKYEEKERKKE 320

ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440308 [Multi-domain] Cd Length: 836 Bit Score: 40.45 E-value: 7.33e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 125 EAEAKLveeRLRVQREKEESEEQQRKL--VEAERQ---REREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENE 199
Cdd:COG0542  397 EAAARV---RMEIDSKPEELDELERRLeqLEIEKEalkKEQDEASFERLAELRDELAELEEELEALKARWEAEKELIEEI 473

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 200 RRLIDAEREREENERRLqeaeeqrereeserrivvaerQREQAEAEKERAEQQRILaeaeaaqaerrlfdaeiqreRDQA 279
Cdd:COG0542  474 QELKEELEQRYGKIPEL---------------------EKELAELEEELAELAPLL--------------------REEV 512

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 280 DEEgqalrD-AEIV--------ERLLAAERE----LspsatESELEE-----DAAIAEQSRRLISSRTDLEQKQR 336
Cdd:COG0542  513 TEE-----DiAEVVsrwtgipvGKLLEGEREkllnL-----EEELHErvigqDEAVEAVADAIRRSRAGLKDPNR 577

Small VCP/p97-interacting protein; SVIP, small VCP/p97-interacting protein, is a family of proteins found in eukaryotes. SVIP was identified by yeast two-hybrid screening to be an interactive partner of VCP/p97. Mammalian VCP/p97 and its yeast counterpart Cdc48p participate in the formation of organelles, including the endoplasmic reticulum (ER), Golgi apparatus, and nuclear envelope. Over-expression of SVIP caused the formation of large vacuoles that seemed to be derived from the ER. The family has two putative coiled-coil regions and contains proteins of approximately 80 amino acids in length.

Pssm-ID: 464888 [Multi-domain] Cd Length: 77 Bit Score: 36.19 E-value: 7.74e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 320545982  105 LAAELARQQQIEADTRRQlAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQ 157
Cdd:pfam15811  19 PDAEERRQQQAEAAEKRQ-EEAESRGIKNPESVRRKQKRAEELEKREQEAARS 70

Crescentin protein; This entry represents a bacterial equivalent to Intermediate Filament proteins, named crescentin, whose cytoskeletal function is required for the vibrioid and helical shapes of Caulobacter crescentus. Without crescentin, the cells adopt a straight-rod morphology. Crescentin has characteriztic features of IF proteins including the ability to assemble into filaments in vitro without energy or cofactor requirements. In vivo, crescentin forms a helical structure that colocalizes with the inner cell curvatures beneath the cytoplasmic membrane.

Pssm-ID: 437057 [Multi-domain] Cd Length: 401 Bit Score: 39.67 E-value: 7.90e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  100 DKRQALAAELA--RQQQIEADTRRQLAEAEAKLVEERL-----RVQREKEESEEQQRKLVEAERQrereqaEKELQEQRE 172
Cdd:pfam19220 132 EQNRALEEENKalREEAQAAEKALQRAEGELATARERLalleqENRRLQALSEEQAAELAELTRR------LAELETQLD 205

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  173 AERRQLEAEEnQRKQRENEEKERLEneRRLIDAEREREENERRLQEAEEQREREESERRIVVAE-----RQREQA----- 242
Cdd:pfam19220 206 ATRARLRALE-GQLAAEQAERERAE--AQLEEAVEAHRAERASLRMKLEALTARAAATEQLLAEarnqlRDRDEAiraae 282

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  243 ----EAEKERAEQQRILAEAEAAQAERRLFDAEIQRERDQADEEGQALRDAeiverlLAAERELSPSATESELEEDAAIA 318
Cdd:pfam19220 283 rrlkEASIERDTLERRLAGLEADLERRTQQFQEMQRARAELEERAEMLTKA------LAAKDAALERAEERIASLSDRIA 356

                         250       260
                  ....*....|....*....|....*.
gi 320545982  319 EQSRRLISSRTDLEQKQRMIEENARR 344
Cdd:pfam19220 357 ELTKRFEVERAALEQANRRLKEELQR 382

The first LIM domain of actin binding LIM (abLIM) proteins; The first LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188713 [Multi-domain] Cd Length: 52 Bit Score: 35.31 E-value: 8.03e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320545982 809 CDGC-----GEVFRAGTKkmeyktrQWHENCFCCCVCKTAIGTKSFIPREQEIYC 858
Cdd:cd09327    1 CYKCgkkckGEVLRVQDK-------YFHIKCFTCKVCGCDLAQGGFFVKEGEYYC 48

Multidrug resistance efflux pump EmrA [Defense mechanisms];

Pssm-ID: 441174 [Multi-domain] Cd Length: 331 Bit Score: 39.65 E-value: 8.37e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 110 ARQQQIEAdtrrQLAEAEAKLveERLRVQREKEESEEQQRKLVEAeRQREREQAEKELQEQREAERRQLEAEEnqrkQRE 189
Cdd:COG1566   83 AALAQAEA----QLAAAEAQL--ARLEAELGAEAEIAAAEAQLAA-AQAQLDLAQRELERYQALYKKGAVSQQ----ELD 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982 190 NEEKERLENERRLIDAEREREENERRLQeaeeqrereeserrivvAERQREQAEAEKERAEQQRilaeaeaAQAERRLFD 269
Cdd:COG1566  152 EARAALDAAQAQLEAAQAQLAQAQAGLR-----------------EEEELAAAQAQVAQAEAAL-------AQAELNLAR 207


                 ...
gi 320545982 270 AEI 272
Cdd:COG1566  208 TTI 210

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188777 Cd Length: 57 Bit Score: 35.36 E-value: 8.73e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 320545982 929 CTACVKPITGiggtRFISFEDRHWHHDCFVCASCKASLVGRGFITDGPD 977
Cdd:cd09391    1 CAKCGKPITG----QFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPD 45

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

Pssm-ID: 464007 [Multi-domain] Cd Length: 341 Bit Score: 39.52 E-value: 8.81e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982   49 DAAADAEELPRMRERLDKQIKEAAEREALAgTNVMQDGVLYVNGIRVDPAGDKRQALAAEL--ARQQQIEADTR-----R 121
Cdd:pfam13868 178 IEEEKEREIARLRAQQEKAQDEKAERDELR-AKLYQEEQERKERQKEREEAEKKARQRQELqqAREEQIELKERrlaeeA 256

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  122 QLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENERR 201
Cdd:pfam13868 257 EREEEEFERMLRKQAEDEEIEQEEAEKRRMKRLEHRRELEKQIEEREEQRAAEREEELEEGERLREEEAERRERIEEERQ 336

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 35.60 E-value: 9.05e-03

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 320545982 705 DKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCYE 741
Cdd:cd09427   22 GQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCYE 58

Mitochondrial ribosome subunit S26; This family of proteins corresponds to mitochondrial ribosomal subunit S26 in eukaryotes

Pssm-ID: 464391 [Multi-domain] Cd Length: 168 Bit Score: 37.99 E-value: 9.13e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  102 RQALAAELARQQQIEADTRrqlAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAE 181
Cdd:pfam14943  44 RSFFREEVRKKYEEELGSE---SEEEAEEEEEHRELMAWNEEWNAEIAKLREERLAKEAEEREEEILERIEEKEEKEEEK 120

                          90
                  ....*....|....*..
gi 320545982  182 ENQRKQRENEEKERLEN 198
Cdd:pfam14943 121 KERAEEEVRQEKEESKT 137

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

Pssm-ID: 188736 Cd Length: 54 Bit Score: 35.46 E-value: 9.28e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 693 NLIFSGEYTKAMDKDWHSGHFCCWQCDESLTGQRYVIRDDHPYCIKCY 740
Cdd:cd09350    7 NVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 35.39 E-value: 9.35e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 320545982 809 CDGCGEVFRAGTKKMEYKTRQWHENCFCCCVCKTAIGTKSFIPREQEIYCAGCYEEKFA 867
Cdd:cd09331    1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188794 [Multi-domain] Cd Length: 53 Bit Score: 35.18 E-value: 9.52e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320545982 870 CIKCNKVITSGGVTYKNEPWHRECFTCTHCNITLAGQRFTSRDEKPYC 917
Cdd:cd09410    1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.

Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 37.21 E-value: 9.55e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  121 RQLAEAEAKLVEERLRVQREKEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQRENEEKERLENER 200
Cdd:pfam20492   6 REKQELEERLKQYEEETKKAQEELEESEETAEELEEERRQAEEEAERLEQKRQEAEEEKERLEESAEMEAEEKEQLEAEL 85


                  .
gi 320545982  201 R 201
Cdd:pfam20492  86 A 86

phosphodiesterase; Provisional

Pssm-ID: 237177 [Multi-domain] Cd Length: 520 Bit Score: 39.76 E-value: 9.78e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545982  62 ERLDKQIKEAAEREALAGtnvmqdgvlyvngirvdpagdKRQAL--AAELARQQQIEADTRRQLAEAEAKLVEERLRvQR 139
Cdd:PRK12704  37 EEEAKRILEEAKKEAEAI---------------------KKEALleAKEEIHKLRNEFEKELRERRNELQKLEKRLL-QK 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 320545982 140 E---KEESEEQQRKLVEAERQREREQAEKELQEQREAERRQLEAEENQRKQR 188
Cdd:PRK12704  95 EenlDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELER 146