NCBI Conserved Domain Search

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: 128.17 E-value: 1.42e-35

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09454     1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

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: 122.54 E-value: 1.19e-33

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 696
Cdd:cd09363     1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNHA 54

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: 121.68 E-value: 2.73e-33

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09460     1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55

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: 120.84 E-value: 5.81e-33

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09459     1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55

Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 121 and 170 amino acids in length. It is usually found in association with pfam00595 (PDZ) and pfam00412 (LIM), and often contains the conserved Zasp-like motif (IPR006643).

Pssm-ID: 464948 [Multi-domain] Cd Length: 98 Bit Score: 119.83 E-value: 4.03e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 156 TIIHAQYNTPISMYSQDAIMDAIAGQAQAQGSDFSGASPLASLPIKDLAVDSASPVYQAVIKNQNKPEDEAdewarrssn 235
Cdd:pfam15936   1 KVVHAQYNSPIGLYSSENIQDALSGQLSGLAGSSEGGKPPPSRPPKKPVVDADSEVYKMLQENQEPKEPPR--------- 71

                          90       100
                  ....*....|....*....|....*...
gi 1622965572 236 lQSRSFRILAQMTGTEFMQDPDEEALRR 263
Cdd:pfam15936  72 -QSGSFRVLQEILETEYLQPPEEELNRP 98

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: 116.04 E-value: 2.59e-31

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09362     1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 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: 110.91 E-value: 1.71e-29

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09361     1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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: 104.35 E-value: 3.58e-27

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 696
Cdd:cd09458     1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKSHA 54

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: 99.32 E-value: 1.96e-25

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09453     1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467235 [Multi-domain] Cd Length: 79 Bit Score: 98.37 E-value: 6.99e-25

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                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572  40 ITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 90
Cdd:cd06753    29 VTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKIKAATGSLSLTLER 79

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: 95.83 E-value: 2.67e-24

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09456     1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

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: 93.94 E-value: 1.37e-23

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09457     1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

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: 85.68 E-value: 1.06e-20

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 696
Cdd:cd09461     1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLHA 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: 80.44 E-value: 8.23e-19

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                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMG-EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd08368     1 CAGCGKPIEGrELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

The first LIM domain of an Enigma subfamily with unknown function; The first 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: 188839 Cd Length: 54 Bit Score: 79.42 E-value: 1.84e-18

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCA--YCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09455     1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCEYCF 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: 75.88 E-value: 2.77e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572  642 KCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:smart00132   1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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: 75.89 E-value: 3.09e-17

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09336     1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

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: 74.35 E-value: 1.18e-16

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09337     1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The first LIM domain of Enigma; The first 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: 188836 [Multi-domain] Cd Length: 52 Bit Score: 74.07 E-value: 1.52e-16

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09452     1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

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: 70.88 E-value: 2.08e-15

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572  584 CAKCNTKIMG--EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKD 634
Cdd:smart00132   2 CAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 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: 70.42 E-value: 2.37e-15

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHA 696
Cdd:cd08368     1 CAGCGKPIE-GRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 69.67 E-value: 5.95e-15

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 584 CAKCNTKIMG-EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLF 639
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: 67.34 E-value: 2.91e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd08368     1 CAGCGKPIEGRELLrALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 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: 66.82 E-value: 5.75e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09406     3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 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: 65.43 E-value: 1.27e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09338     1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 63.89 E-value: 6.14e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:pfam00412   1 CAGCNRPIYDRELVR-ALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHD 52

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: 62.72 E-value: 1.58e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 583 LCAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09405     1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 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: 62.02 E-value: 2.31e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09336     1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

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: 60.86 E-value: 5.35e-12

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572  525 CGHCNNVIRG--PFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:smart00132   2 CAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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: 60.82 E-value: 6.97e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09339     1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467281 [Multi-domain] Cd Length: 82 Bit Score: 61.39 E-value: 7.97e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572  39 QITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 90
Cdd:cd23068    31 KVNPGSPADKAGLRRGDVILRINGTDTSNLTHKQAQDLIKRAGNDLQLTVQR 82

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: 60.42 E-value: 8.77e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 572 CERCYEQFfAPlcakcNTKIM---GEVmhalrqtWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLFS 640
Cdd:cd09331     1 CERCREGF-EP-----DEKIVnsnGEL-------YHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

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: 60.04 E-value: 1.08e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09338     1 CGGCNKPIL--ENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 58.88 E-value: 2.88e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 525 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYEQFF 580
Cdd:pfam00412   1 CAGCNRPIYDRELVrALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

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: 56.75 E-value: 1.75e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09408     1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

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: 56.58 E-value: 1.79e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:cd09332     1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

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: 56.12 E-value: 2.75e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09407     1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

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: 55.82 E-value: 3.15e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 582 PLCAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09334     1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

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: 55.96 E-value: 3.51e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 635
Cdd:cd09364     1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYFE-KDGKLYCRKDY 52

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: 55.34 E-value: 5.29e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09327     1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.

Pssm-ID: 214570 [Multi-domain] Cd Length: 85 Bit Score: 55.85 E-value: 7.20e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572   39 QITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 89
Cdd:smart00228  32 SVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLTVL 82

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: 54.63 E-value: 7.94e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKpfgnsLFHME----DGEPYCEKDY 635
Cdd:cd09329     1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGK-----VLTGEymgkDGKPYCERDY 52

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: 54.28 E-value: 1.24e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 523 PLCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09334     1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

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: 54.32 E-value: 1.26e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09337     1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 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: 53.84 E-value: 1.64e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09345     1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVP 52

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: 53.86 E-value: 1.79e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 524 LCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09405     1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 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: 53.72 E-value: 2.48e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09406     3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

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: 53.20 E-value: 2.80e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 584 CAKCNTKIMGEVM--HALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09351     1 CVKCGEKVLGEGSgcTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

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: 53.03 E-value: 3.49e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPY 630
Cdd:cd09396     1 CAGCKSEIGhGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48

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: 52.39 E-value: 5.39e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09336     1 CAACNKPI-VG-QVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDYH 53

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: 52.13 E-value: 7.44e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09410     1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52

ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.

Pssm-ID: 128974 Cd Length: 26 Bit Score: 51.45 E-value: 7.81e-09

                           10        20
                   ....*....|....*....|....*.
gi 1622965572  156 TIIHAQYNTPISMYSQDAIMDAIAGQ 181
Cdd:smart00735   1 RVVHKQYNSPIGLYSSENIAETLQGQ 26

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: 51.77 E-value: 1.08e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09409     1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 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.

Pssm-ID: 188758 [Multi-domain] Cd Length: 53 Bit Score: 51.66 E-value: 1.24e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHM-EDGEPYCEKDY 635
Cdd:cd09372     1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVdEQNEVYCLDDY 53

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 58.41 E-value: 1.66e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  327 PRPQASSYSPATAASSAPATHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTP- 405
Cdd:PHA03247  2712 PHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASl 2791

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  406 SPAPAYTPSPaPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPPWVTddsFSQKFAPGKSTtsisK 485
Cdd:PHA03247  2792 SESRESLPSP-WDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLP---LGGSVAPGGDV----R 2863

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1622965572  486 QTLPRGGPAYTPAGPQVPP---LARGTVQRA-ERFP 517
Cdd:PHA03247  2864 RRPPSRSPAAKPAAPARPPvrrLARPAVSRStESFA 2899

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: 50.76 E-value: 2.35e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGE-----PYCEKDY 635
Cdd:cd09391     1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDtseqvPLCETDY 57

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: 50.72 E-value: 2.42e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09411     1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52

The second LIM domain on actin binding LIM (abLIM) proteins; The second 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: 188714 Cd Length: 56 Bit Score: 50.42 E-value: 2.70e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPF-GNSLFHMEDGEPYCEK 633
Cdd:cd09328     4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFpPGDRVTFNGKECLCQK 54

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: 51.04 E-value: 3.39e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 582 PLCAKCNTKIM-GEVMHALRQTWHTTCFVCAACkkpfGNSLFHM---EDGEPYCEKDY 635
Cdd:cd09462    20 PVCASCGQSIYdGQYLQALNSDWHADCFRCCEC----GASLSHWyyeKDGRLFCKKDY 73

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: 50.12 E-value: 3.43e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09412     1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

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: 50.14 E-value: 4.19e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09344     1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52

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: 49.91 E-value: 5.11e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 523 PLCGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYE 577
Cdd:cd09341     1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56

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: 49.26 E-value: 7.92e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09401     1 CPKCGKPVyFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 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.

Pssm-ID: 188758 [Multi-domain] Cd Length: 53 Bit Score: 49.34 E-value: 8.01e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCF-VEEQNNVYC 572
Cdd:cd09372     1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFaVDEQNEVYC 49

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467153 [Multi-domain] Cd Length: 81 Bit Score: 49.85 E-value: 9.25e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572  39 QITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 89
Cdd:cd00136    30 RVEPGGPAARDgRLRVGDRILEVNGVSLEGLTHEEAVELLKSAGGEVTLTVR 81

The second LIM domain of Ajuba-like proteins; The second 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: 188741 [Multi-domain] Cd Length: 53 Bit Score: 48.88 E-value: 9.72e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCF-VEEQNNVYCERCY 576
Cdd:cd09355     1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFtVDVENNIYCVKDY 53

PDZ domain; PDZ domains are found in diverse signaling proteins.

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 49.59 E-value: 1.17e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572  40 ITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 89
Cdd:pfam00595  32 VLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81

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: 48.02 E-value: 2.05e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09396     1 CAGCKSEIgHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 54.56 E-value: 2.14e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  325 DSPRPQASSYSPATAASSAPATHTSYSEGPAAPAPKPRVVT-TASIRPsvyqPVPASTYSPSPGANYSPTPYTPSPTPAY 403
Cdd:PHA03247  2654 DDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSlTSLADP----PPPPPTPEPAPHALVSATPLPPGPAAAR 2729

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  404 TPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPnyNPAPSAAYSGGPAEPASRPPwVTDDSFSQKFAPGKSTTSI 483
Cdd:PHA03247  2730 QASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPP--APAPPAAPAAGPPRRLTRPA-VASLSESRESLPSPWDPAD 2806

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1622965572  484 SKQTLPRGGPAY----TPAGPQVPPL-ARGTVQRAERFPASSRTPLCG 526
Cdd:PHA03247  2807 PPAAVLAPAAALppaaSPAGPLPPPTsAQPTAPPPPPGPPPPSLPLGG 2854

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second 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: 188778 [Multi-domain] Cd Length: 53 Bit Score: 47.74 E-value: 2.64e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSL-ADVCFVEEQNNVYCERCY 576
Cdd:cd09392     1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFgPNDSYYEHEGKIYCHYHY 53

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: 47.72 E-value: 2.90e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09347     1 CAACTKPITGlgGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPE 54

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: 47.34 E-value: 3.95e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFG-NSLFHMEDGEPYCEKDY 635
Cdd:cd09335     1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCY 53

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: 47.04 E-value: 4.07e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 584 CAKCNTKIMG--EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09352     1 CVKCGKGVYGasQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54

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: 47.30 E-value: 4.35e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09456     1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

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: 46.96 E-value: 4.56e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:cd09334     3 CGACRRPIE--GRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETH 53

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: 46.94 E-value: 5.71e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09338     1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

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: 46.74 E-value: 5.87e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCER 574
Cdd:cd09408     1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRR 50

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: 46.68 E-value: 6.57e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09424     1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50

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: 6.92e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLFS 640
Cdd:cd09431     1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of 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, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. 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. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. 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: 188847 [Multi-domain] Cd Length: 53 Bit Score: 46.40 E-value: 8.35e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 635
Cdd:cd09463     1 CTGCGGRIQdSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYE-KDGKLYCHKHY 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: 46.44 E-value: 8.38e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKI-MGEV-----MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09340     1 CEKCKEPInPGEVavfaeRAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b 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. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. 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: 188757 [Multi-domain] Cd Length: 53 Bit Score: 46.22 E-value: 8.53e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFYskKDRPL-CKK 694
Cdd:cd09371     1 CAGCQRPIS--DRYLlRVNERSWHEECLQCSVCQQPLTTSCYF--RDRKLyCKQ 50

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 52.63 E-value: 1.06e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  354 PAA----PAPKPRVVTTASIRP----SVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPsPAPAYTPSPAPAYTPSPAP 425
Cdd:PHA03247  2701 PPPppptPEPAPHALVSATPLPpgpaAARQASPALPAAPAPPAVPAGPATPGGPARPARP-PTTAGPPAPAPPAAPAAGP 2779

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  426 TYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPP- 504
Cdd:PHA03247  2780 PRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPg 2859

                          170       180
                   ....*....|....*....|..
gi 1622965572  505 ---LARGTVQRAERFPASSRTP 523
Cdd:PHA03247  2860 gdvRRRPPSRSPAAKPAAPARP 2881

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: 46.02 E-value: 1.15e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 639 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09421     1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYC 54

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: 45.72 E-value: 1.37e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 584 CAKCNTKIMGEVMH----ALRQTWHTTCFVCAACKKPF-GNSLFHMEDGEPYCEKDY 635
Cdd:cd09397     1 CRKCGLEIEGKSISskdgELSGQWHRECFVCTTCGCPFqFSVPCYVLDDKPYCQQHY 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: 45.40 E-value: 1.55e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKI-MGEVMHAlRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09346     1 CAKCKKAItSGGVTYR-DQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

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: 45.58 E-value: 1.75e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09410     1 CSGCGRPVK--ENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53

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: 45.06 E-value: 2.13e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCfVEEQNNVYCERCY 576
Cdd:cd09333     1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTADA-RELKGELYCLRCH 51

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: 45.03 E-value: 2.41e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 525 CGHCNNVIRGP----FLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:cd09347     1 CAACTKPITGLggakFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55

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: 46.00 E-value: 2.80e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09349    34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCE 84

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: 44.73 E-value: 2.91e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 582 PLCAKCNTKIMG-EVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09418     1 PRCSACDEIIFAdECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

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: 44.56 E-value: 2.97e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09407     1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

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: 44.74 E-value: 3.51e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 639 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09343     1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLC 54

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: 44.43 E-value: 3.58e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09410     1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52

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: 44.29 E-value: 3.86e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVC--FVEEQnnVYCE 573
Cdd:cd09360     1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGyfFIEDE--LYCE 49

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: 44.21 E-value: 4.00e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 584 CAKCNTKIMGEV--MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09345     1 CKACGKAIMPGSkkMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

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: 44.45 E-value: 4.26e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09409     1 CGGCARAIL--ENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53

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: 44.31 E-value: 4.36e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 525 CGHCNNVI-RGPFLVAMGRS-----WHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09414     1 CGGCSEPLkYGELAVTAPKFgesllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

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: 44.54 E-value: 4.41e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 582 PLCAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGePYCEKDY 635
Cdd:cd09467     2 PLCAGCNQHIVDRfILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDS-VYCKDDF 55

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: 44.34 E-value: 4.58e-06

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                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09351     1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCE 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: 44.21 E-value: 4.81e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09433     1 CAGCTNPISGlgGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILC 52

The second LIM domain of Lhx1 (also known as Lim1) and Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members 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. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. 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: 188761 Cd Length: 56 Bit Score: 44.27 E-value: 5.39e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 584 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF--GNSLFHMEDGEPYCEKDY 635
Cdd:cd09375     1 CAGCDQGISPNdlVRRARDKVFHLNCFTCMVCRKQLstGEELYILDENKFICKEDY 56

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: 44.07 E-value: 5.73e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 640 STKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09427     1 SSKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53

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: 43.89 E-value: 5.88e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:cd09361     1 CAHCNQVIR--GPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELC 51

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: 44.09 E-value: 6.02e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09406     3 CASCQKPI-AG-QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDYH 55

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: 43.94 E-value: 6.30e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNN-VIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09840     1 CSRCGDsVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

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: 43.86 E-value: 6.34e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 633
Cdd:cd09332     1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50

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: 6.63e-06

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                  ....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09429     1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

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: 43.75 E-value: 6.87e-06

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                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:cd09446     1 CARCGYGVYPAEK-INCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

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: 43.87 E-value: 6.87e-06

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                  ....*....|....*....|....*....|....*....
gi 1622965572 538 VAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09401    15 TSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 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: 43.74 E-value: 7.50e-06

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 639 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09422     1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLC 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: 43.47 E-value: 7.69e-06

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gi 1622965572 664 WHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09346    20 WHKECFVCTGCKKQLAGQRFTSRDEYPYC 48

The first LIM domain of Lhx2 and Lhx9 family; The first 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: 188755 [Multi-domain] Cd Length: 54 Bit Score: 43.48 E-value: 9.85e-06

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                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 584 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFG--NSLFhMEDGEPYCEKDY 635
Cdd:cd09369     1 CAGCGEKIQDRfYLLAVDRQWHASCLKCCECRLPLDseLSCF-SRDGNIYCKEDY 54

The second LIM domain on actin binding LIM (abLIM) proteins; The second 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: 188714 Cd Length: 56 Bit Score: 43.49 E-value: 1.02e-05

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                  ....*....|....*....|....*....|....*....|...
gi 1622965572 641 TKCHGCDFPVEagDKFIEALGHTWHDTCFICAVChvnleGQPF 683
Cdd:cd09328     2 TKCDSCQDFVE--GEVVSALGKTYHPKCFVCSVC-----RQPF 37

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: 43.23 E-value: 1.06e-05

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09432     1 CAACGKPITGigGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILC 52

This family represents the LIM domain of ALP, actinin-associated LIM protein; This family represents the LIM domain of ALP, actinin-associated LIM protein. ALP contains an N-terminal PDZ domain, a C-terminal LIM domain and an ALP-subfamily-specific 34-amino-acid motif termed ALP-like motif (AM), which contains a putative consensus protein kinase C (PKC) phosphorylation site and two alpha-helices. ALP proteins are found in heart and in skeletal muscle. ALP may act as a signaling molecule which is regulated by PKC-dependent signaling. ALP plays an essential role in the development of RV (right ventricle) chamber. 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: 188834 [Multi-domain] Cd Length: 53 Bit Score: 42.97 E-value: 1.29e-05

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                  ....*....|....*....|....*....|....*....|....*....
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 632
Cdd:cd09450     1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49

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: 42.74 E-value: 1.32e-05

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                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 633
Cdd:cd09360     1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCET 50

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: 42.85 E-value: 1.40e-05

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                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 525 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:cd09432     1 CAACGKPITGiggtKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55

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: 43.09 E-value: 1.51e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAHT 698
Cdd:cd09331     1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQV 56

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: 43.00 E-value: 1.52e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 523 PLCGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKSSLADVCFvEEQNNVYCE 573
Cdd:cd09467     2 PLCAGCNQHIVDRFILkVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 48.40 E-value: 1.61e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  348 TSYSEGPAAPAPKPRVVTTASIRPSVYQP-------VPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYT 420
Cdd:PHA03247  2636 NEPDPHPPPTVPPPERPRDDPAPGRVSRPrrarrlgRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHAL 2715

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  421 PSPAPTyTPSPALAYTPSPAPNYNPAPSAAySGGPAEPASRPPwvtddsfsqkfAPGKSTTSISKQTLPRGGPAYTPAGP 500
Cdd:PHA03247  2716 VSATPL-PPGPAAARQASPALPAAPAPPAV-PAGPATPGGPAR-----------PARPPTTAGPPAPAPPAAPAAGPPRR 2782

                          170       180
                   ....*....|....*....|
gi 1622965572  501 QVPPLARGTVQRAERFPASS 520
Cdd:PHA03247  2783 LTRPAVASLSESRESLPSPW 2802

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: 42.83 E-value: 1.66e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09434     1 CAACNKPITGfgGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCR 53

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: 42.65 E-value: 1.68e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 635
Cdd:cd09468     1 CAGCNQHILDKfILKVLDRHWHSSCLKCADCQMQLAERCFS-RAGNVYCKEDF 52

PDZ domain 4 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467216 [Multi-domain] Cd Length: 84 Bit Score: 43.37 E-value: 1.89e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572  39 QITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 90
Cdd:cd06734    32 RIIPGSPADRCgQLKVGDRILAVNGISILNLSHGDIVNLIKDSGLSVTLTIVP 84

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: 42.42 E-value: 1.97e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09352     1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEE 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: 42.83 E-value: 2.01e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 525 CGHCNNVI----RGPFLVAM-GRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:cd09348     5 CSGCQNPItgfgKGTNVVNYeGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60

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: 2.07e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622965572 584 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09326     1 CPRCGKSVyAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYC 49

PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467254 [Multi-domain] Cd Length: 87 Bit Score: 43.35 E-value: 2.08e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572  39 QITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 90
Cdd:cd06792    35 SLVPGGAAEQDgRIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVTLVLER 87

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: 42.46 E-value: 2.11e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09430     1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

The first LIM domain of Enigma; The first 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: 188836 [Multi-domain] Cd Length: 52 Bit Score: 42.48 E-value: 2.12e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09452     1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 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: 42.43 E-value: 2.27e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09425     1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50

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: 42.09 E-value: 2.29e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKSSLADVCFvEEQNNVYCERCY 576
Cdd:cd09364     1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYF-EKDGKLYCRKDY 52

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second 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: 188778 [Multi-domain] Cd Length: 53 Bit Score: 42.35 E-value: 2.29e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFG-NSLFHMEDGEPYCEKDY 635
Cdd:cd09392     1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGpNDSYYEHEGKIYCHYHY 53

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 47.79 E-value: 2.32e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 402 AYTPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPPWVTDDSfsqkfAPGKSTT 481
Cdd:PRK14951  386 AAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPA-----QAAPETV 460

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1622965572 482 SISKQTLPRGG---PAYTPAGPQVPPLARGT 509
Cdd:PRK14951  461 AIPVRVAPEPAvasAAPAPAAAPAAARLTPT 491

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: 42.22 E-value: 2.51e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 683
Cdd:cd09353     1 CAVCDQKIT--DRMLKATGKSYHPQCFTCVVCKCPLEGESF 39

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: 42.26 E-value: 2.69e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 584 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF-GNSLFHMEDGEPYCEKDY 635
Cdd:cd09377     5 CARCHLGISASelVMRARDLVFHLNCFTCATCNKPLtKGDHFGMRDGLVYCRLHY 59

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: 41.98 E-value: 2.86e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPF-YSKKDRPLCK 693
Cdd:cd09373     1 CTGCGEPIT--DRFLlKVSGRSWHVSCLRCCVCQTPLERQPScFTRDRQIYCK 51

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: 41.92 E-value: 2.91e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 572 CERCYEQFFAPlcakcnTKIMGEvmhalRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09482     1 CPRCGKSVYAA------EKVMGG-----GKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

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: 42.03 E-value: 2.93e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09412     1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48

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: 42.09 E-value: 3.05e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQpfYSKKDRPL-CKKH 695
Cdd:cd09364     1 CAGCRGKILDSQ-YVQALNQDWHCDCFRCSVCSDSLSNW--YFEKDGKLyCRKD 51

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: 41.69 E-value: 3.06e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09430     1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48

The first LIM domain of an Enigma subfamily with unknown function; The first 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: 188839 Cd Length: 54 Bit Score: 41.67 E-value: 3.36e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCA--ACKKPFGNSLFHMEDGEPYCE 632
Cdd:cd09455     1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCE 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: 41.82 E-value: 3.55e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 582 PLCAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09341     1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51

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: 41.62 E-value: 3.73e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 584 CAKCNTKIMGEV--MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09350     1 CGRCGENVVGEGtgCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467249 [Multi-domain] Cd Length: 80 Bit Score: 42.43 E-value: 3.83e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572  39 QITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 88
Cdd:cd06768    29 EVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQVVEKIKASGNQVTLLV 78

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: 41.52 E-value: 4.10e-05

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1622965572 657 IEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09456    13 MHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCER 50

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: 41.63 E-value: 4.11e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09840     1 CSRCGDSVyAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184923 [Multi-domain] Cd Length: 624 Bit Score: 46.98 E-value: 4.20e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 361 PRVVTTASIRPSVYQPVPAS-TYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAPtyTPSPALAYTPSP 439
Cdd:PRK14959  363 PRLMPVESLRPSGGGASAPSgSAAEGPASGGAATIPTPGTQGPQGTAPAAGMTPSSAAPATPAPSA--APSPRVPWDDAP 440

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 440 apnynPAPSAaySGGPAEPASRPPWVTDdsfsqkfAPGK-STTSISKQTLPRGGPAYTPA 498
Cdd:PRK14959  441 -----PAPPR--SGIPPRPAPRMPEASP-------VPGApDSVASASDAPPTLGDPSDTA 486

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: 41.47 E-value: 4.28e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 632
Cdd:cd09411     1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCH 49

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: 41.47 E-value: 4.37e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1622965572 643 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRP 690
Cdd:cd09396     1 CAGCKSEIGHGR-FLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDP 47

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: 41.44 E-value: 4.41e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCD---FpveaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09341     3 CAACDeliF----SGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51

PDZ domain 12 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 10 of protein-associated tight junction (PATJ, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 12 of MUPP1, PDZ domain 10 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like PDZ12 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F

Pssm-ID: 467163 [Multi-domain] Cd Length: 86 Bit Score: 42.35 E-value: 4.44e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622965572  40 ITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 87
Cdd:cd06675    35 IQPNGVAAQTGkLKVGDRIVSINGQSTDGLTHSEAVNLLKNASGTIILQ 83

The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a 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. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. 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: 188756 [Multi-domain] Cd Length: 52 Bit Score: 41.29 E-value: 4.57e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNNVIRGPFLVAMGRS-WHPEEFNCAYCKSSLADVCFVEEQnNVYCERCY 576
Cdd:cd09370     1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCFYRDK-KLYCKEDY 52

The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of 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, altering the rate of actin depolymerisation. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. 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. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. 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: 188849 [Multi-domain] Cd Length: 59 Bit Score: 41.46 E-value: 4.76e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 580 FAPLCAKCNTKIMGEVMHALRQTWHTTCFVCAACKkpfgnslFHMEDGEPYCEKDYINLFSTKCH 644
Cdd:cd09465     2 FGELCHGCSLLMTGPAMVAGEYKYHPECFACMSCK-------VIIEDGDTYALVQHTTLYCGKCH 59

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: 41.45 E-value: 5.00e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNV-YCERCYEQFFAP 582
Cdd:cd09353     1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQpHCVNDYHRRYAP 59

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: 41.22 E-value: 5.88e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWH--DTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09342     1 CDACGEPIGPDVQRVAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFC 52

The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of 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, altering the rate of actin depolymerisation. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. 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. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. 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: 188849 [Multi-domain] Cd Length: 59 Bit Score: 41.08 E-value: 6.52e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 524 LCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSL--ADVCFVEEQNNVYCERCY 576
Cdd:cd09465     5 LCHGCSLLMTGPAMVAGEYKYHPECFACMSCKVIIedGDTYALVQHTTLYCGKCH 59

The second LIM domain of LIMK (LIM domain Kinase ); The second 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 depolymerization. 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: 188751 [Multi-domain] Cd Length: 54 Bit Score: 40.81 E-value: 6.57e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLAD---VCFVeEQNNVYCERCY 576
Cdd:cd09365     1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCKAFIGDgdsYALV-ERSKLYCGVCY 54

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 46.38 E-value: 6.63e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 355 AAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAPTYTPSPALA 434
Cdd:PRK07003  396 VPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSG 475

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 435 YTPSPAPNYNPAPSAAysggPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGP 500
Cdd:PRK07003  476 SASAPASDAPPDAAFE----PAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTP 537

LIM domain in proteins of unknown function; LIM domain in proteins of unknown function: 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. The 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: 188784 Cd Length: 61 Bit Score: 41.26 E-value: 6.67e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 642 KCHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09400     4 PCASCGLPVFLAER-LLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b 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. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. 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: 188757 [Multi-domain] Cd Length: 53 Bit Score: 40.82 E-value: 6.94e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 525 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKSSLADVCFVEEQnNVYCERCYE 577
Cdd:cd09371     1 CAGCQRPISDRYLLrVNERSWHEECLQCSVCQQPLTTSCYFRDR-KLYCKQDYQ 53

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: 40.80 E-value: 7.40e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 584 CAKCNTKIM--GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09426     1 CSECKKTIMpgTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 46.47 E-value: 7.84e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  354 PAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPG--------ANYSPTPYTPSPTPAYTPSPAPAyTPSPAPAYTPSPAP 425
Cdd:PHA03247  2626 PPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGrvsrprraRRLGRAAQASSPPQRPRRRAARP-TVGSLTSLADPPPP 2704

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  426 TYTPSPAlaytPSPAPNYNPAPSAAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTlPRGGPAYT-PAGPQVPP 504
Cdd:PHA03247  2705 PPTPEPA----PHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPT-TAGPPAPApPAAPAAGP 2779


                   ....*.
gi 1622965572  505 LARGTV 510
Cdd:PHA03247  2780 PRRLTR 2785

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 46.02 E-value: 7.93e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 173 AIMDAIAGQAQAQGSDFSGA-SPLASLPIKdlaVDSASPVYQAViknqnkPED--EADEWARRSSNLQSRSFRILAQMTG 249
Cdd:PRK12323  267 AALLAIADEMAGRSLSFAGAlQDLASLLQK---IALAQVVPAAV------QDDwpEADDIRRLAGRFDAQEVQLFYQIAN 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 250 T---EFMQDPDEE-----------ALRRSSTPIEHAPVCTSQATTPLLPASAQPPAAASPSAASPPLATAAAHTAITSAA 315
Cdd:PRK12323  338 LgrsELALAPDEYagftmtllrmlAFRPGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAAR 417

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 316 TTAPASSPAdSPRPQASSYSPATAASSAPATHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPY 395
Cdd:PRK12323  418 AVAAAPARR-SPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDP 496

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 396 TPSPTPAYTPSPAPAYTPSPAPA---YTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPAsRPPWVTDDSFSQ 472
Cdd:PRK12323  497 PPWEELPPEFASPAPAQPDAAPAgwvAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAP-RPPRASASGLPD 575


                  ...
gi 1622965572 473 KFA 475
Cdd:PRK12323  576 MFD 578

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: 40.45 E-value: 8.35e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09337     1 CAYCNGPIL--DKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCRE 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: 41.76 E-value: 8.42e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 583 LCAKCNTKIM--GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09349    33 LCGICGQPLSrtQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

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: 40.87 E-value: 8.80e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 523 PLCGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYE 577
Cdd:cd09418     1 PRCSACDEIIFADECTeAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56

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: 40.34 E-value: 9.64e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 525 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKSSLADVCFvEEQNNVYCE 573
Cdd:cd09468     1 CAGCNQHILDKFILkVLDRHWHSSCLKCADCQMQLAERCF-SRAGNVYCK 49

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: 41.02 E-value: 9.67e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 645 GCDFPVEAG-------DKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDRPLCKKH 695
Cdd:cd09462    16 GNVLPVCAScgqsiydGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKD 72

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: 40.42 E-value: 1.08e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09426     1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50

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: 40.15 E-value: 1.16e-04

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1622965572 661 GHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09430    17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48

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: 40.01 E-value: 1.19e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGC-DFPVeagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09332     1 CGKCgEFVI---GRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50

PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNPO2, SYNPO2L, and related domains. SYNPO2 (also known as genethonin-2, myopodin) is a cytoskeleton adaptor protein. It participates in chaperone-assisted selective autophagy (CASA), a mechanism for the disposal of misfolded and damaged proteins and provides a link between the CASA chaperone complex and a membrane-tethering and fusion machinery that generates autophagosome membranes. The SYNPO2 PPxY motif binds CASA cochaperone BCL2-associated athanogene 3 (BAG3) and the SYNPO2 PDZ domain binds vacuolar protein sorting 18 homolog (VPS18). There are three isoforms of SYNPO2, which possess an amino-terminal PDZ domain (SYNPO2a, b, c); the short isoform SYNPO2d, lacks the PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNPO2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467264 [Multi-domain] Cd Length: 78 Bit Score: 40.76 E-value: 1.23e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572  38 LQITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 89
Cdd:cd10820    27 AKIRKKSKAALAGLCEGDELLSINGKPCADLSHSEAMDLIDSSGDTLQLLIK 78

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: 40.00 E-value: 1.23e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09346     1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The second LIM domain of Arrowhead (AWH); The second 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: 188765 Cd Length: 55 Bit Score: 40.10 E-value: 1.25e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDRPLCKKH 695
Cdd:cd09379     1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLStGEEFALIEDRVLCKAH 54

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: 40.11 E-value: 1.33e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1622965572 601 QTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09425    20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.

Pssm-ID: 434634 [Multi-domain] Cd Length: 1288 Bit Score: 45.26 E-value: 1.34e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  356 APAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPspaptyTPSPALAY 435
Cdd:pfam15324  986 TPVPTPQPTPPCSPPSPLKEPSPVKTPDSSPCVSEHDFFPVKEIPPEKGADTGPAVSLVITPTVTP------IATPPPAA 1059

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  436 TPSPAPNYNPAPSAAYSggpaEPASRPPWVTDD---------SFSQKFAPGKSTTSISKQTLPRG--GPAYTPAGPQVPP 504
Cdd:pfam15324 1060 TPTPPLSENSIDKLKSP----SPELPKPWEDSDlpleeenpnSEQEELHPRAVVMSVARDEEPESvvLPASPPEPKPLAP 1135

                          170
                   ....*....|....*....
gi 1622965572  505 LARGTvqraeRFPASSRTP 523
Cdd:pfam15324 1136 PPLGA-----APPSPPQSP 1149

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: 40.08 E-value: 1.41e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09350     1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCE 51

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: 40.52 E-value: 1.42e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 642 KCHGCDFPVEA---GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09348     4 KCSGCQNPITGfgkGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYC 57

The first LIM domain of LMO2 (LIM domain only protein 2); The first LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. 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: 188770 Cd Length: 56 Bit Score: 40.22 E-value: 1.51e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVeaGDK-FIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDRPLCKK 694
Cdd:cd09384     1 CGGCQQNI--GDRyFLKAIDQYWHEDCLSCDLCGCRLGevGRRLYYKLGRKLCRR 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: 40.02 E-value: 1.58e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLA-DVCFVEEQNNVYCERCYE 577
Cdd:cd09335     1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCYD 54

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: 39.83 E-value: 1.79e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCF-VEEQNNVYCERCYEQFFAP 582
Cdd:cd09354     1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFtVDATNQIHCIEDFHKKFAP 59

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: 39.74 E-value: 1.79e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1622965572 541 GRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYEQFF 580
Cdd:cd09424    19 GNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 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: 39.74 E-value: 1.85e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEV--MHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 633
Cdd:cd09344     1 CAECRKPIGADSkeLHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52

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: 39.56 E-value: 1.85e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:cd09359     1 CARCGKIVYPTEK-VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAH 52

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 44.98 E-value: 1.86e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 353 GPAAPAPKPRVVTTASIRPSvyqPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPA-YTPSPAPTYTPSP 431
Cdd:PRK07764  617 APAAPAAPAAPAPAGAAAAP---AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAaPPPAPAPAAPAAP 693

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 432 ALAYTPSPAPNYNPAPSAAYSGGPAEPASRPPWvtddsfsqkfAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQ 511
Cdd:PRK07764  694 AGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQ----------GASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPA 763

                         170
                  ....*....|..
gi 1622965572 512 RAERFPASSRTP 523
Cdd:PRK07764  764 PAPAAAPAAAPP 775

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: 39.83 E-value: 1.88e-04

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1622965572 601 QTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09427    23 QTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53

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: 39.61 E-value: 2.02e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKHAH 697
Cdd:cd09405     2 CGACKKPI-AG-QVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54

The second LIM domain of Lhx3-Lhx4 family; The second 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: 188762 Cd Length: 56 Bit Score: 39.64 E-value: 2.06e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDRPL-CKK 694
Cdd:cd09376     1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLEtGDEFYLMEDDRLvCKK 54

The second LIM domain of Ajuba-like proteins; The second 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: 188741 [Multi-domain] Cd Length: 53 Bit Score: 39.63 E-value: 2.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHME-DGEPYCEKDY 635
Cdd:cd09355     1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDvENNIYCVKDY 53

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: 39.61 E-value: 2.12e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQpfYSKKDR-PLCKK 694
Cdd:cd09329     1 CAGCGQEIKNGQALL-ALDKQWHVWCFKCKECGKVLTGE--YMGKDGkPYCER 50

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 44.48 E-value: 2.14e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 349 SYSEGPAAPAPkPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPaytPSPAPAYTPSPAPTYT 428
Cdd:PRK12323  366 GQSGGGAGPAT-AAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPAR---RSPAPEALAAARQASA 441

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1622965572 429 PSPALAYTPSPAPNYNPAPSAAysggPAEPASRPPWVTDDSFSQKFAP 476
Cdd:PRK12323  442 RGPGGAPAPAPAPAAAPAAAAR----PAAAGPRPVAAAAAAAPARAAP 485

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: 39.33 E-value: 2.18e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 525 CGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKSSLADVCFvEEQNNVYCE 573
Cdd:cd09368     1 CGGCQEHILDRFiLKVLDRTWHAKCLKCNDCGAQLTDKCF-ARNGHVYCK 49

PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form domain-swapping dimers; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467210 [Multi-domain] Cd Length: 79 Bit Score: 40.28 E-value: 2.26e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572  40 ITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 90
Cdd:cd06728    27 ITPDSLAAKDgNLQEGDIILKINGTPVENLSLSEAKKLIEKSKDKLQLVVLR 78

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: 39.28 E-value: 2.29e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCN-TKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09447     1 CARCGkTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467196 [Multi-domain] Cd Length: 78 Bit Score: 40.26 E-value: 2.36e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572  39 QITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNlSLTLQ 89
Cdd:cd06712    27 SVDPGSCAAEAGLKEGDYIVSVGGVDCKWSKHSEVVKLLKSAGEE-GLELQ 76

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: 39.34 E-value: 2.38e-04

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1622965572 541 GRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09425    19 GQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 44.54 E-value: 2.42e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  256 PDEEALRRSSTPIEHAPVCTSQATTPLLPASAQPPAAASPSAASPPLATAAAHTAITSAATTAPASSPADSPRPQASSYS 335
Cdd:PHA03247  2723 PGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPW 2802

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  336 PATAASSAPATHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSP-----SPGANYSPTPYTPSPTPAYTPSPAPA 410
Cdd:PHA03247  2803 DPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRRPPSRSPAAKPAAPARPP 2882

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  411 YTPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAE-PASRPPWVTDdsfsqkfAPGKSTTSISKQTLP 489
Cdd:PHA03247  2883 VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPqPPPPPPPRPQ-------PPLAPTTDPAGAGEP 2955

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....
gi 1622965572  490 RGGPAYTPAGPQVP-----PLARGTVQRAER-FPASSRTPLCGH 527
Cdd:PHA03247  2956 SGAVPQPWLGALVPgrvavPRFRVPQPAPSReAPASSTPPLTGH 2999

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 44.46 E-value: 2.49e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 353 GPAAPAPKPRVVttasirpsvyqPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPA----YTPSPAPAYTPSPAPTYT 428
Cdd:PRK07003  369 GGGVPARVAGAV-----------PAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAaaaaATRAEAPPAAPAPPATAD 437

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 429 PSPALAYTPSPAPNYNPAPSAAYSgGPAEPASRPPwvtDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARG 508
Cdd:PRK07003  438 RGDDAADGDAPVPAKANARASADS-RCDERDAQPP---ADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAP 513

                         170
                  ....*....|....*
gi 1622965572 509 TVQRAERFPASSRTP 523
Cdd:PRK07003  514 AAASREDAPAAAAPP 528

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 44.67 E-value: 2.51e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 354 PAAPAP-KPRVVTTASIRPSVYQPVPASTYSPSPG-ANYSPTPYTPSPTPAYTPS----PAPAYTPSPAPAYTPSpAPTY 427
Cdd:PHA03378  698 PRAPTPmRPPAAPPGRAQRPAAATGRARPPAAAPGrARPPAAAPGRARPPAAAPGrarpPAAAPGRARPPAAAPG-APTP 776

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 428 TPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQ-----TLPRGGPAYTPAGPQV 502
Cdd:PHA03378  777 QPPPQAPPAPQQRPRGAPTPQPPPQAGPTSMQLMPRAAPGQQGPTKQILRQLLTGGVKRgrpslKKPAALERQAAAGPTP 856


                  ..
gi 1622965572 503 PP 504
Cdd:PHA03378  857 SP 858

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: 2.55e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAGDK--FIEALGH--TWHDTCFICAVCH---VNLegQPFYsKKDRPLCKKH 695
Cdd:cd09340     1 CEKCKEPINPGEVavFAERAGEdaCWHPGCFVCETCNellVDL--IYFY-HDGKIYCGRH 57

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: 39.30 E-value: 2.79e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKI----MGEVMHALRQT--WHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09414     1 CGGCSEPLkygeLAVTAPKFGESllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

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: 39.34 E-value: 2.86e-04

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1622965572 661 GHTWH--DTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09420    21 GQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYCSR 56

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: 39.53 E-value: 2.91e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDG-EPYCEKDY 635
Cdd:cd09353     1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQAnQPHCVNDY 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: 39.17 E-value: 2.94e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09359     1 CARCGKIVYpTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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: 39.34 E-value: 3.10e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1622965572 542 RSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09343    24 RHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

The second LIM domain of Lhx3-Lhx4 family; The second 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: 188762 Cd Length: 56 Bit Score: 39.26 E-value: 3.15e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 584 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF--GNSLFHMEDGEPYCEKDY 635
Cdd:cd09376     1 CAGCDEGIPPTqvVRRAQDNVYHLECFACFMCKRQLetGDEFYLMEDDRLVCKKDY 56

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: 38.84 E-value: 3.18e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 525 CGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKSSLAdvcfvEE---QNNV-YCERCY 576
Cdd:cd09329     1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGKVLT-----GEymgKDGKpYCERDY 52

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237874 [Multi-domain] Cd Length: 614 Bit Score: 44.00 E-value: 3.31e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 360 KPRVVTTASIRPSVYQPVPAstYSPSPGANYSPTPYTpsptpAYTPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSP 439
Cdd:PRK14971  370 SGGRGPKQHIKPVFTQPAAA--PQPSAAAAASPSPSQ-----SSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPST 442

                          90
                  ....*....|.
gi 1622965572 440 APNYNPAPSAA 450
Cdd:PRK14971  443 APQAVRPAQFK 453

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: 39.20 E-value: 3.39e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 525 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:cd09433     1 CAGCTNPISGlggtKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55

PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PSZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467246 [Multi-domain] Cd Length: 77 Bit Score: 39.64 E-value: 3.71e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572  40 ITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKSK 92
Cdd:cd06765    23 IVPGSPAAkEGSLTVGDRIIAINGIALDNKSLSECEALLRSCRDSLSLSLMKVF 76

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: 38.86 E-value: 3.71e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1622965572 657 IEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09457    13 INALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCE 49

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: 38.97 E-value: 3.76e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1622965572 541 GRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:cd09344    19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.

Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 43.75 E-value: 3.79e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 350 YSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSpgANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAP--TY 427
Cdd:pfam05109 421 FSKAPESTTTSPTLNTTGFAAPNTTTGLPSSTHVPT--NLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPrdNG 498

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 428 TPSPALAYTPSPAPNYNPAPSAAysgGPAEPASRP-PWVTDDSFSQKFAPGKSTTSISKQTLPRggPAYTPAGPQ--VPP 504
Cdd:pfam05109 499 TESKAPDMTSPTSAVTTPTPNAT---SPTPAVTTPtPNATSPTLGKTSPTSAVTTPTPNATSPT--PAVTTPTPNatIPT 573

                         170
                  ....*....|....*...
gi 1622965572 505 LARGTVQRAERFPASSRT 522
Cdd:pfam05109 574 LGKTSPTSAVTTPTPNAT 591

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: 38.79 E-value: 3.91e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 643 CHGCD---FPVEagdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:cd09358     1 CAVCGktvYPME----RLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPH 52

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: 38.46 E-value: 4.61e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 523 PLCGhcNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09482     2 PRCG--KSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second 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: 188742 Cd Length: 53 Bit Score: 38.70 E-value: 4.74e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 683
Cdd:cd09356     1 CSVCSKPIM--ERILRATGKAYHPHCFTCVVCHRSLDGIPF 39

The second LIM domain of LMO4 (LIM domain only protein 4); The second LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. 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: 188773 Cd Length: 55 Bit Score: 38.62 E-value: 4.95e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACkkpfGNSL-----FHMEDGEPYCEKD 634
Cdd:cd09387     1 CSACGQSIPASelVMRAQGNVYHLKCFTCSTC----HNQLvpgdrFHYVNGSLFCEHD 54

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: 5.16e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 523 PLCGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYE 577
Cdd:cd09417     1 DRSVQCDELIFsGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b 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. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. 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: 188757 [Multi-domain] Cd Length: 53 Bit Score: 38.51 E-value: 5.48e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 584 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFhMEDGEPYCEKDYI 636
Cdd:cd09371     1 CAGCQRPISDRyLLRVNERSWHEECLQCSVCQQPLTTSCY-FRDRKLYCKQDYQ 53

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.44 E-value: 5.51e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 352 EGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAPTYTPSP 431
Cdd:PRK07764  393 APAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAA 472

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1622965572 432 ALAYTPSPAPNYNPAPSAAYSGGPAEPASRPPWVTDD 468
Cdd:PRK07764  473 APEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDA 509

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 43.16 E-value: 5.56e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 328 RPQASSYSPATAASSapathTSYSEGPAAPAPKPRVVTTASIRPSVyqPVPASTYSPS-PGANYSPTPYTPSPTPAYTPS 406
Cdd:PRK14951  365 KPAAAAEAAAPAEKK-----TPARPEAAAPAAAPVAQAAAAPAPAA--APAAAASAPAaPPAAAPPAPVAAPAAAAPAAA 437

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 407 PAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPnynPAPSAAYSGGPAEPASRP 462
Cdd:PRK14951  438 PAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAV---ASAAPAPAAAPAAARLTP 490

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: 38.18 E-value: 6.18e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 642 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09418     2 RCSACDEIIFA-DECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.05 E-value: 6.26e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 404 TPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPnynPAPSAAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSI 483
Cdd:PRK07764  387 VAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPA---PAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPS 463

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 484 SKQTLPRGGPAYTPAGPQVPPLARGTVQRAERFPASSRTPLCGHCNNVIRG 534
Cdd:PRK07764  464 AQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRE 514

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.05 E-value: 6.43e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 327 PRPQASSYSPATAASSAPATHTSYSEGPAAPAPKPRVVTTASirPSVYQPVPASTYSPSPGAnysPTPYTPSPTPAYTPS 406
Cdd:PRK07764  636 PAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAA--PAAPPPAPAPAAPAAPAG---AAPAQPAPAPAATPP 710

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 407 PAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPP 463
Cdd:PRK07764  711 AGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPA 767

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: 38.09 E-value: 6.72e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09401     1 CPKCGKPVYFAEK-KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

The second LIM domain of Ajuba-like proteins; The second 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: 188741 [Multi-domain] Cd Length: 53 Bit Score: 38.09 E-value: 7.04e-04

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1622965572 653 GDKFIEALGHTWHDTCFICAVCHVNLEGQPF 683
Cdd:cd09355     9 MEMILQALGKSYHPGCFRCCVCNECLDGVPF 39

PDZ domain 7 of PDZ domain containing 2 (PDZD2), PDZ domain 4 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of PDZD2, also known as KIAA0300, PIN-1, PAPIN, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family include the PDZ domain of the secreted mature form of human interleukin-16 (IL-16); this is the fourth PDZ domain (PDZ4) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467244 [Multi-domain] Cd Length: 86 Bit Score: 39.13 E-value: 7.47e-04

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1622965572  43 GSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKS 79
Cdd:cd06763    38 GGAAEQSgVLQVGDEILQINGTSLQGLTRFEAWNIIKS 75

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This CPP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.

Pssm-ID: 467623 [Multi-domain] Cd Length: 88 Bit Score: 39.00 E-value: 7.47e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1622965572  38 LQITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIK 78
Cdd:cd06782    19 VSPIPGGPAEKAGIKPGDVIVAVDGESVRGMSLDEVVKLLR 59

flagellar biosynthesis protein FlhF;

Pssm-ID: 237182 [Multi-domain] Cd Length: 559 Bit Score: 42.67 E-value: 7.59e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 355 AAPAPKPrVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAY---TPSPAPAYTPSPAPAYTPSPAPTyTPSP 431
Cdd:PRK12727  123 QAPAAAP-VRAASIPSPAAQALAHAAAVRTAPRQEHALSAVPEQLFADFlttAPVPRAPVQAPVVAAPAPVPAIA-AALA 200

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 432 ALAYTPSPAPNYNPAPSAAYSGGPA---EPASRPPWVTDDSFSQKFAPGKSTT 481
Cdd:PRK12727  201 AHAAYAQDDDEQLDDDGFDLDDALPqilPPAALPPIVVAPAAPAALAAVAAAA 253

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: 38.09 E-value: 7.60e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09339     1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

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: 8.00e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1622965572 541 GRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYEQFFA 581
Cdd:cd09331    19 GELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

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: 38.17 E-value: 8.03e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09840     1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50

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: 37.87 E-value: 8.21e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYE 577
Cdd:cd09429     1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

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: 38.05 E-value: 8.34e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09431     1 CVQCKKPITTGG--VTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYC 48

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: 38.01 E-value: 8.40e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09407     1 CYYCNGPIL--DKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRK 50

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 42.41 E-value: 8.46e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 357 PAPKPRVVTTASIR---PSVyQPVPASTYSPSPgANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYT--------PSPAP 425
Cdd:PHA03269   25 NIPIPELHTSAATQkpdPAP-APHQAASRAPDP-AVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHqaasrapdPAVAP 102

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1622965572 426 TY--TPSPALAYTPSPAPNYNPAPSAAysggPAEPASRPP 463
Cdd:PHA03269  103 QLaaAPKPDAAEAFTSAAQAHEAPADA----GTSAASKKP 138

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 42.96 E-value: 8.64e-04

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  404 TPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPP 463
Cdd:PRK12270    49 AAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAP 108

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: 37.82 E-value: 8.65e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1622965572 603 WHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDYINLF 639
Cdd:cd09424    22 WHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

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: 37.98 E-value: 8.85e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 584 CAKCNTKI-MGEV-MHALRQ----TWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09483     1 CEQCGIKInGGEVaVFASRAgpgvCWHPSCFVCFTCNELLVDLIYFYQDGKIHC 54

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: 9.11e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 572 CERCYEQFFAPlcakcnTKIMGEvmhalRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09403     1 CPRCGKSVYAA------EKIIGA-----GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

PDZ domain of tyrosine-protein phosphatase non-receptor type 3 (PTPN3), tyrosine-protein phosphatase non-receptor type 4 (PTNP4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PTPN3, PTPN4 and related domains. PTPN3 (also known as protein-tyrosine phosphatase H1, PTP-H1) has a tumor-suppressive or a tumor-promoting role in many cancers. It serves as a specific phosphatase for the MAP kinase p38gamma; the two interact via their PDZ domains and cooperate to promote Ras-induced oncogenesis. Interaction partners of the PTPN3 PDZ domain include p38gamma and human papillomavirus E6 oncoprotein. PTPN4 (also known as protein-tyrosine phosphatase MEG1) plays a role in immunity, learning, synaptic plasticity or cell homeostasis. p38gamma is also an interaction partner of the PTPN4 PDZ domain: PTPN4 regulates neuronal cell homeostasis by protecting neurons against apoptosis; binding of the C terminus of p38gamma to the PDZ domain of PTPN4, antagonizes the catalytic autoinhibition of PTPN4, leading to cell apoptosis. Other interaction partners of the PTPN4 PDZ domain include glutamate receptor subunit GluN2A, and RABV strain G protein, among others. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467190 [Multi-domain] Cd Length: 90 Bit Score: 38.83 E-value: 9.80e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1622965572  40 ITPGSKAAQSQ--LSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 80
Cdd:cd06706    35 VAPGTPADLCIprLNEGDQVLLINGRDISEHTHDQVVMFIKAS 77

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 42.36 E-value: 1.01e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 371 PSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTP--SPAPAYTPSPAPTYTPSPALAYTPSPAPNYNP--A 446
Cdd:PHA03378  655 PQVEITPYKPTWTQIGHIPYQPSPTGANTMLPIQWAPGTMQPPprAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPgrA 734

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 447 PSAAYSGGPAEP-------ASRPPWVTDDSFSQKFAPGKSTTSISKQT------LPRGGPAYTPAgPQVPPLArgtVQRA 513
Cdd:PHA03378  735 RPPAAAPGRARPpaaapgrARPPAAAPGRARPPAAAPGAPTPQPPPQAppapqqRPRGAPTPQPP-PQAGPTS---MQLM 810

                         170
                  ....*....|
gi 1622965572 514 ERFPASSRTP 523
Cdd:PHA03378  811 PRAAPGQQGP 820

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: 1.06e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 525 CGHCNN-VIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09403     1 CPRCGKsVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

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: 37.51 E-value: 1.08e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 584 CAKCNTKIM--GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09428     1 CFHCKKTIMpgSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50

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: 37.67 E-value: 1.12e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVY-----CERCY 576
Cdd:cd09391     1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDTSeqvplCETDY 57

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: 37.63 E-value: 1.13e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1622965572 664 WHDTCFICAVCHVNLEGQ-PFYSKKDRPLCKKHAH 697
Cdd:cd09397    24 WHRECFVCTTCGCPFQFSvPCYVLDDKPYCQQHYH 58

The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of 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, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. 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. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. 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: 188847 [Multi-domain] Cd Length: 53 Bit Score: 37.54 E-value: 1.16e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEAGdKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDRPLCKKH 695
Cdd:cd09463     1 CTGCGGRIQDS-FHYRVVQEAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHKH 51

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: 37.33 E-value: 1.17e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEaGDkFIEALGHTWHDTCFICAVCHVNLEGQ-PFYSKKDRPLCKK 694
Cdd:cd09335     1 CYHCNQVIE-GD-VVSALNKTWCVDHFSCSFCDTKLTLKsKFYEFDMKPVCKK 51

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467193 [Multi-domain] Cd Length: 86 Bit Score: 38.43 E-value: 1.17e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1622965572  43 GSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 89
Cdd:cd06709    40 GAAAIDGRLQEGDKILEINGQSLENLTHQDAVELFRNAGEDVKLKVQ 86

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: 37.58 E-value: 1.21e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1622965572 542 RSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09422    24 RHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECY 58

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: 37.30 E-value: 1.28e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09482     1 CPRCGKSVYAAEKVMGG-GKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50

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: 37.55 E-value: 1.31e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 525 CGHCNNVI--RGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYE 577
Cdd:cd09421     5 CEECSKIIgiDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCYD 59

The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a 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. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. 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: 188756 [Multi-domain] Cd Length: 52 Bit Score: 37.06 E-value: 1.35e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGEVMHALRQT-WHTTCFVCAACKKPFGNSLFhMEDGEPYCEKDY 635
Cdd:cd09370     1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCF-YRDKKLYCKEDY 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: 37.10 E-value: 1.41e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09429     1 CVKCNKPITSGG--VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

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: 37.14 E-value: 1.42e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 642 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09416     2 RCAGCDELIFS-NEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCK 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: 37.27 E-value: 1.43e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1622965572 541 GRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09345    19 GKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

The second LIM domain on actin binding LIM (abLIM) proteins; The second 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: 188714 Cd Length: 56 Bit Score: 37.33 E-value: 1.47e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLAD---VCFVEeqNNVYCERC 575
Cdd:cd09328     4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFPPgdrVTFNG--KECLCQKC 55

Chitinase [Carbohydrate transport and metabolism];

Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 41.66 E-value: 1.47e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 347 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPA-YTPSPAPAYTPSPAPAYTPSPAP 425
Cdd:COG3469   104 GANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETAtGGTTTTSTTTTTTSASTTPSATT 183

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1622965572 426 TYTPSPALAYTPSPAPNYNPAPSAAYSGGPA 456
Cdd:COG3469   184 TATATTASGATTPSATTTATTTGPPTPGLPK 214

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: 37.38 E-value: 1.61e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1622965572 643 CHGCDFPVEAGD------KFIEALGhtWHDTCFICAVC 674
Cdd:cd09414     1 CGGCSEPLKYGElavtapKFGESLL--WHPACFRCSTC 36

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: 37.13 E-value: 1.61e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09428     1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50

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: 37.05 E-value: 1.63e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 643 CHGCDFPVEAGDK--FIEALGHT--WHDTCFICAVCHVNLEGQPFYSKKDRPLCKKH 695
Cdd:cd09413     1 CYCCKQPMKEGDPavYAERAGYDklWHPACFVCSTCGELLVDMIYFWKNGKLYCGRH 57

The first LIM domain of Lhx2 and Lhx9 family; The first 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: 188755 [Multi-domain] Cd Length: 54 Bit Score: 36.93 E-value: 1.71e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 643 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLEGQ-PFYSKKDRPLCKK 694
Cdd:cd09369     1 CAGCGEKIQ--DRFyLLAVDRQWHASCLKCCECRLPLDSElSCFSRDGNIYCKE 52

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236138 [Multi-domain] Cd Length: 647 Bit Score: 41.39 E-value: 1.79e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 370 RPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTP---SPAPNYNPA 446
Cdd:PRK07994  360 HPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQqlqRAQGATKAK 439

                          90
                  ....*....|....
gi 1622965572 447 PSAAYSGGPAEPAS 460
Cdd:PRK07994  440 KSEPAAASRARPVN 453

The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group 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. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. 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: 188752 [Multi-domain] Cd Length: 55 Bit Score: 36.94 E-value: 1.79e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 584 CAKCNTKIMGEVMhaLR----QTWHTTCFVCAACKKPFGNS--LFhMEDGEPYCEKDY 635
Cdd:cd09366     1 CVGCGGKIHDQYI--LRvapdLEWHAACLKCAECGQYLDETctCF-VRDGKTYCKRDY 55

PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467219 [Multi-domain] Cd Length: 85 Bit Score: 37.62 E-value: 1.94e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1622965572  39 QITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 82
Cdd:cd06737    33 HVSPGSQADNKGLRVGDEIVRINGYSISQCTHEEVINLIKTKKT 76

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members 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. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. 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: 188753 [Multi-domain] Cd Length: 52 Bit Score: 36.64 E-value: 2.09e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPFGNSLFHmEDGEPYCEKDY 635
Cdd:cd09367     1 CAGCDRPILDKfLLNVLDRAWHAKCVQCCDCKCPLTEKCFS-REGKLYCRNDF 52

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.31 E-value: 2.41e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  353 GPAAPAPKPRVVTTASIRPSVYQPV-PASTYSPSPGAnysptPYTPSPTPAYTPSPAPAytPSPAPAYTPSPAPTYTPSP 431
Cdd:PHA03307    74 GPGTEAPANESRSTPTWSLSTLAPAsPAREGSPTPPG-----PSSPDPPPPTPPPASPP--PSPAPDLSEMLRPVGSPGP 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  432 ALAYTPSPAPNYNPAP--SAAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLP--RGGPAYTPAGPQVPPLAR 507
Cdd:PHA03307   147 PPAASPPAAGASPAAVasDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPprRSSPISASASSPAPAPGR 226

                          170       180
                   ....*....|....*....|....*..
gi 1622965572  508 GTVQRAERFPASSRTPLCGHCNNVIRG 534
Cdd:PHA03307   227 SAADDAGASSSDSSSSESSGCGWGPEN 253

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 41.24 E-value: 2.47e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 354 PAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGAnysptpytpsptpAYTPSPAPAYTPSPAPAYTPSPAPtytPSPAL 433
Cdd:PRK14951  367 AAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAP-------------APAAAPAAAASAPAAPPAAAPPAP---VAAPA 430

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 434 AYTPSPAPNYNPAPSAAYSGGPAEPASRPpwvtdDSFSQKFAPGKSTTSiskqtlPRGGPAYTPAGPQVPPLARGTV 510
Cdd:PRK14951  431 AAAPAAAPAAAPAAVALAPAPPAQAAPET-----VAIPVRVAPEPAVAS------AAPAPAAAPAAARLTPTEEGDV 496

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: 36.42 E-value: 2.54e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09326     1 CPRCGKSVYAAEEVI-AAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50

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: 36.61 E-value: 2.70e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572 525 CGHCNN--VIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09350     1 CGRCGEnvVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 41.03 E-value: 2.80e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  374 YQPvPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSG 453
Cdd:PRK12270    36 YGP-GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVE 114


                   ....*
gi 1622965572  454 GPAEP 458
Cdd:PRK12270   115 DEVTP 119

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: 36.40 E-value: 2.86e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 643 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCK 693
Cdd:cd09403     1 CPRCGKSVYAAEKIIGA-GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 40.95 E-value: 2.89e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 405 PSPAPAYTPSPAPAyTPSPAPTYTPSPALAYTPSPAPnynPAPSAAYSGGPAEPASRPPWVTddsfSQKFAPGKSTTSIS 484
Cdd:PRK14950  366 PQPAKPTAAAPSPV-RPTPAPSTRPKAAAAANIPPKE---PVRETATPPPVPPRPVAPPVPH----TPESAPKLTRAAIP 437

                          90
                  ....*....|....*..
gi 1622965572 485 KQTlprgGPAYTPAGPQ 501
Cdd:PRK14950  438 VDE----KPKYTPPAPP 450

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: 36.28 E-value: 2.90e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 525 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERC 575
Cdd:cd09434     1 CAACNKPITGfgggKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440035 [Multi-domain] Cd Length: 274 Bit Score: 40.13 E-value: 2.97e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622965572  19 LTPLTGTTREALGRPVPSQLQIT---PGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQ 74
Cdd:COG0265   184 IQPVTPELAEALGLPEPEGVLVArvePGSPAAKAGLRPGDVILAVDGKPVTSARDLQRL 242

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 40.63 E-value: 3.20e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 405 PSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSiS 484
Cdd:PRK12323  375 ATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAP-A 453

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1622965572 485 KQTLPRGGPAYTPAGPQVPPLARGTVQRAERFPASSR 521
Cdd:PRK12323  454 PAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPA 490

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: 36.31 E-value: 3.49e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1622965572 642 KCHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLE 679
Cdd:cd09404     1 KCPKCGKSVYAAEERL-AGGYKWHKMCFKCGMCNKLLD 37

The second LIM domain of Lmx1a and Lmx1b; The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b 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. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. 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: 188764 Cd Length: 55 Bit Score: 36.27 E-value: 3.53e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 584 CAKCNTKIMGE--VMHALRQTWHTTCFVCAACKKPF--GNSlFHMEDGEPYCEKDY 635
Cdd:cd09378     1 CSGCLEKIAPSelVMRALENVYHLRCFCCCVCERQLqkGDE-FVLKEGQLLCKSDY 55

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: 36.12 E-value: 3.81e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09480     2 CGACGRTVYhAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCY 54

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 440556 [Multi-domain] Cd Length: 341 Bit Score: 40.24 E-value: 3.87e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622965572  40 ITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSAS-YNLSLTLQK--SKRPIPISTT 100
Cdd:COG0793    78 VIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLRGKAgTKVTLTIKRpgEGEPITVTLT 141

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: 35.89 E-value: 4.03e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKDY 635
Cdd:cd09481     2 CGACEKTVYhAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54

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: 4.07e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1622965572 541 GRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCYEQ 578
Cdd:cd09426    19 GNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEK 56

The first LIM domain of Lhx2 and Lhx9 family; The first 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: 188755 [Multi-domain] Cd Length: 54 Bit Score: 35.78 E-value: 4.10e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 525 CGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKSSLAD--VCFVEEqNNVYCERCY 576
Cdd:cd09369     1 CAGCGEKIQDRFyLLAVDRQWHASCLKCCECRLPLDSelSCFSRD-GNIYCKEDY 54

PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467181 [Multi-domain] Cd Length: 90 Bit Score: 36.85 E-value: 4.23e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572  31 GRPVPSQLQIT---PGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLqksKRP 94
Cdd:cd06695    26 EDPFSGLVRIKklfPGQPAAESgLIQEGDVILAVNGEPLKGLSYQEVLSLLRGAPPEVTLLL---CRP 90

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 40.64 E-value: 4.31e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  378 PASTYSPSPGANYSPTPYTPSPTPAYTPSPAPaytPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAE 457
Cdd:PRK12270    38 PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAA---PAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVE 114


                   ....*
gi 1622965572  458 PASRP 462
Cdd:PRK12270   115 DEVTP 119

PDZ domain 1 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467175 [Multi-domain] Cd Length: 83 Bit Score: 36.62 E-value: 4.35e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572  31 GRPVPSQLQitPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 86
Cdd:cd06687    25 GKPRVSNLR--PGGIAARSdQLNVGDYIKSVNGIRTTKLRHDEIISLLKNVGERVVL 79

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: 4.37e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSL----FHMEDGEPYC 631
Cdd:cd09393     1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREISSELsdaaFNNKDQRILC 52

PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5, and belongs to this MAGI1,2,3-like family. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467217 [Multi-domain] Cd Length: 84 Bit Score: 36.79 E-value: 4.38e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1622965572  38 LQITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 90
Cdd:cd06735    31 LRLAEDGPAQRDgRLRVGDQILEINGESTQGMTHAQAIELIRSGGSVVRLLLRR 84

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: 36.40 E-value: 4.50e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 523 PLCGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKSSLADVcFVEEQNNVYCERCY 576
Cdd:cd09462    20 PVCASCGQSIyDGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73

Chitinase [Carbohydrate transport and metabolism];

Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 40.12 E-value: 4.50e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 347 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSP------APAYTPSPAPAYT 420
Cdd:COG3469    91 STSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTtvsgteTATGGTTTTSTTT 170

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1622965572 421 PSPAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPAEPASRPP 463
Cdd:COG3469   171 TTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGLP 213

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: 35.97 E-value: 4.51e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCERCY 576
Cdd:cd09409     1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52

PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the second PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467270 [Multi-domain] Cd Length: 85 Bit Score: 36.60 E-value: 4.54e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1622965572  42 PGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYnLSLTLQ 89
Cdd:cd10834    36 PGGLAEQNGIKVGDQILAVNGVSFEDITHSKAVEVLKSQTH-LMLTIK 82

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 40.26 E-value: 4.62e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  379 ASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPnynPAPSAAYSGGPAEP 458
Cdd:PRK12270    34 ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAP---AAPPAAAAAAAPAA 110


                   ....*...
gi 1622965572  459 ASRPPWVT 466
Cdd:PRK12270   111 AAVEDEVT 118

PDZ domain of shroom2, shroom3, shroom4, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of shroom2, shroom3, shroom4, and related domains. Shroom family proteins shroom2 (also known as apical-like protein; protein APXL), shroom3 (also known as shroom-related protein), and shroom4 (also known as second homolog of apical protein) are essential regulators of cell morphology during animal development; they regulate cell architecture by directing the subcellular distribution and activation of Rho kinase (ROCK), which results in the localized activation of non-muscle myosin. The interaction between shroom and ROCK is mediated by the shroom domain 2 (SD2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This shroom2,3,4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.

Pssm-ID: 467232 [Multi-domain] Cd Length: 82 Bit Score: 36.55 E-value: 4.65e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1622965572  39 QITPGSKAA-QSQLSQGDLVVAIDGVNTDTMtHLEAQNKIKSASYNLSLTLQK 90
Cdd:cd06750    31 KIEEGGKAAsVGKLQVGDEVVNINGVPLSGS-RQEAIQLVKGSHKTLKLVVRR 82

The first LIM domain of Lhx3a; The first LIM domain of Lhx3a: Lhx3a 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. Lhx3a 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: 188850 [Multi-domain] Cd Length: 56 Bit Score: 35.91 E-value: 4.65e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622965572 523 PLCGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKSSLADVCFvEEQNNVYCErcyEQFF 580
Cdd:cd09466     2 PKCAGCDHPIFDRFiLKVQDKPWHSKCLKCVDCQAQLTDKCF-SRGGQVYCK---EDFF 56

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second 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: 188742 Cd Length: 53 Bit Score: 35.61 E-value: 4.66e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADVCF-VEEQNNVYC 572
Cdd:cd09356     1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFtVDATGQIHC 49

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 40.22 E-value: 4.70e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 327 PRPQASSYSPATAASSAPATHTSYSEGPAAPAPKPRVVTTASIRPSvyqPVPASTYSPSPGANYSPTPYTPSPTPAYTPS 406
Cdd:PRK07003  410 LAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANA---RASADSRCDERDAQPPADSGSASAPASDAPP 486

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 407 PAPAYTPSPAPAYTPSPAPTYTPSPALAYTPS---PAPNYNPAPSAAysggPAEPASRPP 463
Cdd:PRK07003  487 DAAFEPAPRAAAPSAATPAAVPDARAPAAASRedaPAAAAPPAPEAR----PPTPAAAAP 542

cytoskeleton protein RodZ;

Pssm-ID: 236776 [Multi-domain] Cd Length: 331 Bit Score: 39.62 E-value: 4.78e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 375 QPVPASTYSPSPGANYSPTPYTPSPTPayTPSPAPAYTPSPAPAYTPSPAPTYTPSPAlayTPSPAPNYNPAPSAAYSGG 454
Cdd:PRK10856  160 QSVPLDTSTTTDPATTPAPAAPVDTTP--TNSQTPAVATAPAPAVDPQQNAVVAPSQA---NVDTAATPAPAAPATPDGA 234


                  ....*.
gi 1622965572 455 PAEPAS 460
Cdd:PRK10856  235 APLPTD 240

The first LIM domain of Rga GTPase-Activating Proteins; The first LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. 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: 188780 Cd Length: 55 Bit Score: 35.80 E-value: 5.09e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 584 CAKCNTKIMGEVMHALRQT-WHTTCFVCAACKKPFG-NSLF-HMEDGEPYC 631
Cdd:cd09394     1 CVGCKESITEGHAYELGGDrWHIHCFKCYKCDKKLScDSNFlVLGDGSLIC 51

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: 35.68 E-value: 5.26e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDRPLCK 693
Cdd:cd09467     4 CAGCNQHIV--DRFIlKVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52

This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins; The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL)-like proteins. Known members of the Mical-like family includes single 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. 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: 188829 [Multi-domain] Cd Length: 53 Bit Score: 35.52 E-value: 5.72e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 584 CAKCNTKI--MGEVMhALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYC 631
Cdd:cd09445     1 CRSCGKPVykMEEII-AEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYC 49

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: 35.35 E-value: 5.76e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDRPLCKKH 695
Cdd:cd09439     1 CYFCKKRVYVMER-LSAEGLFFHRSCFKCSYCGTTLRlgAYAFDRDDGKFYCKPH 54

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 40.15 E-value: 5.79e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  354 PAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAytPSPAPTYTPSPAL 433
Cdd:PHA03307   139 RPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAAS--PRPPRRSSPISAS 216

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  434 AYTPSPAPNYNPA--PSAAYSGGPAEPASRPPWVTDDSfsqkfAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQ 511
Cdd:PHA03307   217 ASSPAPAPGRSAAddAGASSSDSSSSESSGCGWGPENE-----CPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSP 291

                          170       180
                   ....*....|....*....|..
gi 1622965572  512 RAERFPASSRTPLCGHCNNVIR 533
Cdd:PHA03307   292 RERSPSPSPSSPGSGPAPSSPR 313

The first LIM domain of Lhx2; The first LIM domain of Lhx2: Lhx2 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. 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. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 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.

Pssm-ID: 188853 Cd Length: 64 Bit Score: 35.75 E-value: 5.96e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 583 LCAKCNTKIMGEV-MHALRQTWHTTCFVCAACKKPFGNSLF-HMEDGEPYCEKDY 635
Cdd:cd09469    10 LCAGCGGKISDRYyLLAVDKQWHMRCLKCCECKLNLESELTcFSKDGSIYCKEDY 64

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 39.92 E-value: 6.32e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  267 PIEHAPVCTSQAT----TPLLPASAQPPAAAspsaaspplataaahtaitsaattapasspadSPRPQASSYSPATAASS 342
Cdd:PHA03247  2707 TPEPAPHALVSATplppGPAAARQASPALPA--------------------------------APAPPAVPAGPATPGGP 2754

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  343 APATHTSYSEGPAAPAPkPRVVTTAsirPSVYQPVPASTySPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAyTPS 422
Cdd:PHA03247  2755 ARPARPPTTAGPPAPAP-PAAPAAG---PPRRLTRPAVA-SLSESRESLPSPWDPADPPAAVLAPAAALPPAASPA-GPL 2828

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572  423 PAPTYTPSPALAYTPSPAPNYNPAPSAAYSGGPA--EPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGP 500
Cdd:PHA03247  2829 PPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVrrRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERP 2908

                          250       260
                   ....*....|....*....|...
gi 1622965572  501 QVPPLARGTVQRAERFPASSRTP 523
Cdd:PHA03247  2909 PQPQAPPPPQPQPQPPPPPQPQP 2931

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: 35.22 E-value: 6.46e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1622965572 598 ALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 632
Cdd:cd09461    17 ALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51

The first LIM domain of Lhx7 and Lhx8; The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 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. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. 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: 188767 [Multi-domain] Cd Length: 56 Bit Score: 35.34 E-value: 6.58e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 583 LCAKCNTKIMGEVMHALRQ-TWHTTCFVCAACKKPFGNSLF-HMEDGEPYCEKDY 635
Cdd:cd09381     1 VCSSCGLEIVDKYLLKVNDlCWHVRCLSCSVCRTSLGRHTScYIKDKDIFCKLDY 55

The fourth LIM domain of actin binding LIM (abLIM) proteins; The fourth 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: 188716 Cd Length: 56 Bit Score: 35.41 E-value: 6.69e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1622965572 584 CAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPF---------GNSLFHmedgePYCEK 633
Cdd:cd09330     1 CEACDKFITGKVLEAGGKHYHPTCARCSRCGQMFgegeemylqGSEIWH-----PDCRQ 54

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. 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: 273167 [Multi-domain] Cd Length: 378 Bit Score: 39.49 E-value: 6.78e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1622965572 404 TPSPAPAYTPSPAPAYTPSPAPTYTPSPALAY---TPSPAPNYNPAPSAAYSGGPAE 457
Cdd:TIGR00601  86 PPAATPTSAPTPTPSPPASPASGMSAAPASAVeekSPSEESATATAPESPSTSVPSS 142

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: 35.33 E-value: 6.79e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1622965572 643 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFY 684
Cdd:cd09468     1 CAGCNQHIL--DKFIlKVLDRHWHSSCLKCADCQMQLAERCFS 41

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: 35.28 E-value: 6.80e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 584 CAKCNTKIM-GEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCE 632
Cdd:cd09446     1 CARCGYGVYpAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50

The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3); The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. 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: 188774 Cd Length: 55 Bit Score: 35.22 E-value: 6.96e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622965572 643 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDRPLCKK 694
Cdd:cd09388     1 CAGCNRKIK--DRYlLKALDQYWHEDCLKCACCDCRLGevGSTLYTKANLILCRR 53

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. 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: 273167 [Multi-domain] Cd Length: 378 Bit Score: 39.49 E-value: 7.02e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 404 TPSPAPAYTPSPAPAYTPSPAPTYTPSPALAyTPSPAPNYNPAPSAAYSGGPAEPASRPPWVTDDSFS 471
Cdd:TIGR00601  82 GKVAPPAATPTSAPTPTPSPPASPASGMSAA-PASAVEEKSPSEESATATAPESPSTSVPSSGSDAAS 148

chromosomal replication initiator protein DnaA;

Pssm-ID: 237605 [Multi-domain] Cd Length: 617 Bit Score: 39.81 E-value: 7.03e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 347 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSPganysptpytpsptpayTPSPA-PAYTPSPAPAYTPSPAP 425
Cdd:PRK14086  101 HARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLP-----------------TARPAyPAYQQRPEPGAWPRAAD 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 426 TYTPS-PALAYTPS--PAPNYNPAPSAAY------SGGPAEPASRPPWVTDDSFSQKfaPGKSTTsisKQTLPRGGPAYT 496
Cdd:PRK14086  164 DYGWQqQRLGFPPRapYASPASYAPEQERdrepydAGRPEYDQRRRDYDHPRPDWDR--PRRDRT---DRPEPPPGAGHV 238

                         170       180
                  ....*....|....*....|....
gi 1622965572 497 PAGPQVPPLARGTVQRAERFPASS 520
Cdd:PRK14086  239 HRGGPGPPERDDAPVVPIRPSAPG 262

putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated

Pssm-ID: 235540 [Multi-domain] Cd Length: 153 Bit Score: 37.92 E-value: 7.19e-03

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1622965572 408 APAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAP 441
Cdd:PRK05641   46 SAVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAP 79

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members 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. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. 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: 188753 [Multi-domain] Cd Length: 52 Bit Score: 35.10 E-value: 7.25e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDRPLCK 693
Cdd:cd09367     1 CAGCDRPIL--DKFLlNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCR 49

translocon at the inner envelope of chloroplast subunit 62; Provisional

Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 39.52 E-value: 7.35e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 354 PAAPAPKPRVVTTASIRPSVYQPVPAS-TYSPSPGANYSPTPYTPSPTPAYTPSPAPAYT--PSPAPAYTPSPAPTYTPS 430
Cdd:PLN03209  383 PTSPIPTPPSSSPASSKSVDAVAKPAEpDVVPSPGSASNVPEVEPAQVEAKKTRPLSPYAryEDLKPPTSPSPTAPTGVS 462

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 431 PALAYTPS--PAPNYNPAPSAAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLA 506
Cdd:PLN03209  463 PSVSSTSSvpAVPDTAPATAATDAAAPPPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTA 540

The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group 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. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. 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: 188752 [Multi-domain] Cd Length: 55 Bit Score: 35.40 E-value: 7.42e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 525 CGHCNNVIRGPFL--VAMGRSWHPEEFNCAYCKSSLAD--VCFVEEqNNVYCERCY 576
Cdd:cd09366     1 CVGCGGKIHDQYIlrVAPDLEWHAACLKCAECGQYLDEtcTCFVRD-GKTYCKRDY 55

The first LIM domain of LMO4 (LIM domain only protein 4); The first LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. 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: 188772 [Multi-domain] Cd Length: 55 Bit Score: 35.09 E-value: 7.52e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 584 CAKCNTKIMGE-VMHALRQTWHTTCFVCAACKKPF---GNSLFhMEDGEPYCEKDY 635
Cdd:cd09386     1 CAGCGGKIVDRfLLHALDRYWHNGCLKCSCCQAQLgeiGSSCY-TKGGMILCKNDY 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: 35.24 E-value: 7.52e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 525 CGHCNNVIRGPFLV------AMGRSWHPEEFNCAYCKSSLADVCFVEEQNNVYCER 574
Cdd:cd09841     1 CQQCGRQICGGDIAvfasraGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYCGR 56

Uncharacterized membrane protein [Function unknown];

Pssm-ID: 444140 [Multi-domain] Cd Length: 854 Bit Score: 39.60 E-value: 7.82e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 404 TPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPNyNPAPSAAYSGGPAEPASRPPWVtdDSFSQKFA 475
Cdd:COG5373    44 ASAPAEPEPEAAAAATAAAPEAAPAPVPEAPAAPPAAAE-APAPAAAAPPAEAEPAAAPAAA--SSFEEWLG 112

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: 34.93 E-value: 8.07e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1622965572 643 CHGCDFPVEAgdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLC 692
Cdd:cd09411     1 CSGCQKPITG--RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYC 48

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 39.41 E-value: 8.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 356 APAPKPRVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAY--TPSPAPAYTPSPAPaytPSPAPTYTPSPAl 433
Cdd:PRK14950  361 VPVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATppPVPPRPVAPPVPHT---PESAPKLTRAAI- 436

                          90       100
                  ....*....|....*....|....*..
gi 1622965572 434 aytpspapnynPAPSAAYSGGPAEPAS 460
Cdd:PRK14950  437 -----------PVDEKPKYTPPAPPKE 452

ORF080 virion core protein; Provisional

Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 38.69 E-value: 8.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 370 RPSVYQPVPASTYSPSPGANYSPTPYtpsptpaytPSPAPAYT-PSPAPAYTPSPAPTyTPSPALAYTPSPAPNYNPAPS 448
Cdd:PHA02682   75 RPSGQSPLAPSPACAAPAPACPACAP---------AAPAPAVTcPAPAPACPPATAPT-CPPPAVCPAPARPAPACPPST 144

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572 449 AAYSGGPAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLpRGGPAYTPA-GPQVP 503
Cdd:PHA02682  145 RQCPPAPPLPTPKPAPAAKPIFLHNQLPPPDYPAASCPTI-ETAPAASPVlEPRIP 199

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 39.49 E-value: 8.52e-03

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622965572  367 ASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPAYTPSPAPTYTPSPALAYTPSPAPN 442
Cdd:PRK12270    34 ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPA 109

sec-independent translocase; Provisional

Pssm-ID: 135173 [Multi-domain] Cd Length: 214 Bit Score: 38.25 E-value: 8.87e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 402 AYTPSPAPAytPSPAPAYTPSPAPTYTPSPALAYTPSPAPNYNPAPSAaysggPAEPASRPPwvTDDSFSQKFAPGKSTT 481
Cdd:PRK04654  138 AHTPVPAPA--PVIAQAQPIAPAPHQTLVPAPHDTIVPAPHAAHLPSA-----PATPVSVAP--VDAGTSASPTPSEPTK 208


                  ....*
gi 1622965572 482 SISKQ 486
Cdd:PRK04654  209 IQEKQ 213

This family represents the LIM domain of CLP36; This family represents the LIM domain of CLP36. CLP36 has also been named as CLIM1, Elfin, or PDLIM1. CLP36 contains a C-terminal LIM domain and an N-terminal PDZ domain. CLP36 is highly expressed in heart and is present in many other tissues including lung, liver, spleen, and blood. CLP36 has been implicated in many processes including hypoxia and regulation of actin stress fibers. CLP36 co-localizes with alpha-actinin-2 at the Z-lines in myocardium. In addition, CLP36 binds to alpha-actinin-1 and alpha-actinin-4, and associates with F-actin filaments and stress fibers. CLP36 might be involved in not only the function of sarcomeres in muscle cells, but also in actin stress fiber-mediated cellular processes, such as cell shape, migration, polarit, and cytokinesis in non-muscle 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: 188832 Cd Length: 52 Bit Score: 34.89 E-value: 9.02e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 525 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKSSLADV--CFVEEQnnVYCER 574
Cdd:cd09448     1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKghFFVEDQ--IYCEK 50

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members 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. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. 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: 188753 [Multi-domain] Cd Length: 52 Bit Score: 34.71 E-value: 9.36e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1622965572 525 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKSSLADVCFVEEqNNVYC 572
Cdd:cd09367     1 CAGCDRPILDKFLLnVLDRAWHAKCVQCCDCKCPLTEKCFSRE-GKLYC 48

pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase]

Pssm-ID: 273566 [Multi-domain] Cd Length: 546 Bit Score: 39.09 E-value: 9.44e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622965572 430 SPALAYTPSPAPNYNPAPSAAysggpAEPASRPPwvtddsfsqkfAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLAR 507
Cdd:TIGR01348 195 TPATAPAPASAQPAAQSPAAT-----QPEPAAAP-----------AAAKAQAPAPQQAGTQNPAKVDHAAPAVRRLAR 256

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: 35.01 E-value: 9.58e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1622965572 643 CHGCDFPVEAGdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK 694
Cdd:cd09339     1 CAGCGKPITGR--CITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHP 50

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: 34.94 E-value: 9.63e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1622965572 584 CAKCNTKI-MGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEK 633
Cdd:cd09476     1 CPRCDKTVyFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHK 51

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 39.20 E-value: 9.79e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622965572 351 SEGPAAPAPKP-RVVTTASIRPSVYQPVPASTYSPSPGANYSPTPYTPSPTPAYTPSPAPAYTPSPAPaytpsPAPTYTP 429
Cdd:PRK07764  675 GAAPAAPPPAPaPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLP-----PEPDDPP 749

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1622965572 430 SPALAYTPSPAPnynPAPSAAYSGGPAEPASRPP 463
Cdd:PRK07764  750 DPAGAPAQPPPP---PAPAPAAAPAAAPPPSPPS 780