Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835591058 1230 IFVALFDYDPLTMSPNPDAADEELPFKEGQIIKVYGDKDTDGFYRGATCARRGLIPCNMVSE 1291
Cdd:cd12012      1 LFVALFDYDPLTMSPNPDAAEEELPFKEGQLIKVYGDKDADGFYLGEINGRRGLVPCNMVSE 62

Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1835591058 1356 RMVALYDYDPRESSPNVDVE------------------------GELNGQKGLVPSNFLEE 1392
Cdd:cd12013      1 RMVALFDYDPRESSPNVDAEvelsfragdiitvfgemdedgfyyGELNGQRGLVPSNFLEE 61

Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  806 PAPPQDIRIQAGpTPTAILVTWKPPtltptgTSNGANITGY-VAY--AKGQKVAEVVFPTAESTVVdllRIQNLEAK--- 879
Cdd:cd00063      1 PSPPTNLRVTDV-TSTSVTLSWTPP------EDDGGPITGYvVEYreKGSGDWKEVEVTPGSETSY---TLTGLKPGtey 70

                           90       100
                   ....*....|....*....|.
gi 1835591058  880 EITIRSLSAQGESEDSAPTAI 900
Cdd:cd00063     71 EFRVRAVNGGGESPPSESVTV 91

Fibronectin type III domain;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1835591058  712 APSQLKVDNITQTSAGLSWLPTNSNYSHVIF-------LNEEEFD---IVKAAIYKYQFFNLKPNMAYKVKLLA 775
Cdd:pfam00041    2 APSNLTVTDVTSTSLTVSWTPPPDGNGPITGyeveyrpKNSGEPWneiTVPGTTTSVTLTGLKPGTEYEVRVQA 75

Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  619 PRKITLIKQLAKSVIVGWEPPvvPPGWGNINSYNVLV-----DKDIRLSVNFGSRTKALIEKLNLATcTYRISIQSVTNR 693
Cdd:cd00063      4 PTNLRVTDVTSTSVTLSWTPP--EDDGGPITGYVVEYrekgsGDWKEVEVTPGSETSYTLTGLKPGT-EYEFRVRAVNGG 80

                   ....*..
gi 1835591058  694 GNSDELQ 700
Cdd:cd00063     81 GESPPSE 87

Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835591058 1230 IFVALFDYDPLTMSPNPDAADEELPFKEGQIIKVYGDKDTDGFYRGATCARRGLIPCNMVSE 1291
Cdd:cd12012      1 LFVALFDYDPLTMSPNPDAAEEELPFKEGQLIKVYGDKDADGFYLGEINGRRGLVPCNMVSE 62

Third Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1835591058 1356 RMVALYDYDPRESSPNVDVE------------------------GELNGQKGLVPSNFLEE 1392
Cdd:cd12013      1 RMVALFDYDPRESSPNVDAEvelsfragdiitvfgemdedgfyyGELNGQRGLVPSNFLEE 61

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058   65 AVRLRKEIKPESRI-SPAAALKKPSAkqrmrSVNGGPGQfqGINKDLATEKDME-----IKLLQVECEELKNRLCCLKEG 138
Cdd:TIGR02168  634 ALELAKKLRPGYRIvTLDGDLVRPGG-----VITGGSAK--TNSSILERRREIEeleekIEELEEKIAELEKALAELRKE 706

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  139 LmgqrpSDVEQLLKQSQKELLWLQRQLSFISTGGPTCILPSSKLRNDLPYLHPVLSQ-------------KTFDRIPFLE 205
Cdd:TIGR02168  707 L-----EELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTEleaeieeleerleEAEEELAEAE 781

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  206 EKTQVFKSDVNQEKQQWKDLEYELKDAVQEKTHLNLHYASLSQKalqydqvksdYDQLRETISKVIKERDLALKGKHQLQ 285
Cdd:TIGR02168  782 AEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRER----------LESLERRIAATERRLEDLEEQIEELS 851

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  286 AKLENLEQVLKHMREAAErrqQLELEHEQALAVLTAKQQEIELLQKAQveakkehegavQLLENTLDSMQTKVQELEEKC 365
Cdd:TIGR02168  852 EDIESLAAEIEELEELIE---ELESELEALLNERASLEEALALLRSEL-----------EELSEELRELESKRSELRREL 917

                          330       340
                   ....*....|....*....|
gi 1835591058  366 RIQSEQFNLLSKELERFRQQ 385
Cdd:TIGR02168  918 EELREKLAQLELRLEGLEVR 937

Variant SH3 domain; SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organization. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835591058 1231 FVALFDYDPltmsPNPdaadEELPFKEGQIIKVYgDKDTDGFYRGATCARRGLIPCNMVSEI 1292
Cdd:pfam07653    2 GRVIFDYVG----TDK----NGLTLKKGDVVKVL-GKDNDGWWEGETGGRVGLVPSTAVEEI 54

Variant SH3 domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1835591058  493 ARYSYNPFDgpnenpEAELPLTMGKYLYVYGDmDEDGFYEGELlDGQRGLVPSNFVE 549
Cdd:pfam14604    1 ALYPYEPKD------DDELSLQRGDVITVIEE-SEDGWWEGIN-TGRTGLVPANYVE 49

chromosome partition protein MukB;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  224 DLEYELKDAVQEK----THLNLHYASLSQKALQYDQVKSDYDQLR-----------ETISKVIKE----RDLALKGK--- 281
Cdd:PRK04863   834 DPEAELRQLNRRRveleRALADHESQEQQQRSQLEQAKEGLSALNrllprlnlladETLADRVEEireqLDEAEEAKrfv 913

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  282 HQLQAKLENLEQVLKHMREAAERRQQLELEHEQALAVLTAKQQEIELLqkAQVEAKKEH---EGAVQLLEntldsmqtKV 358
Cdd:PRK04863   914 QQHGNALAQLEPIVSVLQSDPEQFEQLKQDYQQAQQTQRDAKQQAFAL--TEVVQRRAHfsyEDAAEMLA--------KN 983

                          170       180
                   ....*....|....*....|....*..
gi 1835591058  359 QELEEKCRIQSEQfnlLSKELERFRQQ 385
Cdd:PRK04863   984 SDLNEKLRQRLEQ---AEQERTRAREQ 1007

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058   30 KQQEEEGK-LHKKERTdfTKKERNHRSEakipqkphavRLRKEIKP--ESRISPAAAlkkpsakqRMRSVNGGPGQ---F 103
Cdd:TIGR00618  472 EQQLQTKEqIHLQETR--KKAVVLARLL----------ELQEEPCPlcGSCIHPNPA--------RQDIDNPGPLTrrmQ 531

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  104 QGINKDLATEKdmEIKLLQVECEELKNRLCCLKEGLmgQRPSDVEQLLKQSQKELlwlqrqlsfistggpTCILPssKLR 183
Cdd:TIGR00618  532 RGEQTYAQLET--SEEDVYHQLTSERKQRASLKEQM--QEIQQSFSILTQCDNRS---------------KEDIP--NLQ 590

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  184 NDLPYLHPVLSQKTFDRIPFLEE--------KTQVFKSDVNQEKQQwKDLEYELKDAVQEKTHLNLHYASLSQKALQYDQ 255
Cdd:TIGR00618  591 NITVRLQDLTEKLSEAEDMLACEqhallrklQPEQDLQDVRLHLQQ-CSQELALKLTALHALQLTLTQERVREHALSIRV 669

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  256 VKSDYDQLRETISKVIKERdlalkgKHQLQAKLENLEQVLKHMREAAERRQQLELE-HEQALAVLTAK---QQEIELLQ- 330
Cdd:TIGR00618  670 LPKELLASRQLALQKMQSE------KEQLTYWKEMLAQCQTLLRELETHIEEYDREfNEIENASSSLGsdlAAREDALNq 743

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1835591058  331 -------------KAQVEAKKEHEGAVQLLENTLDSMQTKVQELEEKCRIQSEQFNLLSKELERFRQ 384
Cdd:TIGR00618  744 slkelmhqartvlKARTEAHFNNNEEVTAALQTGAELSHLAAEIQFFNRLREEDTHLLKTLEAEIGQ 810

Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058   806 PAPPQDIRIQAgPTPTAILVTWKPptltPTGTSNGANITGY-VAYAKGQKVAEVVFPTAESTVVdllRIQNLEAK---EI 881
Cdd:smart00060    1 PSPPSNLRVTD-VTSTSVTLSWEP----PPDDGITGYIVGYrVEYREEGSEWKEVNVTPSSTSY---TLTGLKPGteyEF 72

                            90
                    ....*....|.
gi 1835591058   882 TIRSLSAQGES 892
Cdd:smart00060   73 RVRAVNGAGEG 83

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  222 WKDLEYELKDAV-----------QEKTHLNLHYASLSQKALQYDQVKSDYDQLRETISKVIkerdlaLKGKHQLQAKlEN 290
Cdd:cd16269    126 SAPLEEKISQGSysvpggyqlylEDREKLVEKYRQVPRKGVKAEEVLQEFLQSKEAEAEAI------LQADQALTEK-EK 198

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  291 LEQVLKHMREAAERRQQLELEHEQALAVLTAKQQEIELLQKAQVEAKKEHEgavqlLENTLDSMQtkvQELEEKCRIQ-- 368
Cdd:cd16269    199 EIEAERAKAEAAEQERKLLEEQQRELEQKLEDQERSYEEHLRQLKEKMEEE-----RENLLKEQE---RALESKLKEQea 270

                          170       180
                   ....*....|....*....|.
gi 1835591058  369 ------SEQFNLLSKELERFR 383
Cdd:cd16269    271 lleegfKEQAELLQEEIRSLK 291

Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1835591058  712 APSQLKVDNITQTSAGLSWLPTNSNYSHV----IFLNE------EEFDIVKAAIYKYQFFNLKPNMAYKVKLLAK 776
Cdd:cd00063      3 PPTNLRVTDVTSTSVTLSWTPPEDDGGPItgyvVEYREkgsgdwKEVEVTPGSETSYTLTGLKPGTEYEFRVRAV 77

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058   13 ESSKISQPITKVENHSSKQQEEEGKLHKKERTDFTKKERNHRsEAKIPQKPH-AVRLRKEIKPESRISPAAALKKPSAK- 90
Cdd:pfam15709  156 EPRLFNQETPASISHAERELIDKAKRRKGTKTDKTKTPKRER-EGKVHGEAEaAVGKSRESKAEKKSELISKGKKTGAKr 234

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058   91 QRMRsvnggpgqfQGINKDLATEKDMEIKLLQVECEELKNRlcclkeGLMGQRPSDVEQLLK-QSQKEllwlQRQLSFIS 169
Cdd:pfam15709  235 KRTQ---------KERNLEVAAELSGPDVINSKETEDASER------GAFSSDSVVEDPWLSsKYDAE----ESQVSIDG 295

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  170 TGGPTCILPSSklrNDLPYLHPVLSQKTFDRIPFLEEKTQVFKSDVNQEKQQWKDLEYELKDAVQEKTHlnlhyaSLSQK 249
Cdd:pfam15709  296 RSSPTQTFVVT---GNMESEEERSEEDPSKALLEKREQEKASRDRLRAERAEMRRLEVERKRREQEEQR------RLQQE 366

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  250 ALQY-DQVKSDYDQLRETISKVIKERDLALKGKHQLQAKLENLEQVLKHMREAAERRQQLELeHEQALAVLTAKQQEieL 328
Cdd:pfam15709  367 QLERaEKMREELELEQQRRFEEIRLRKQRLEEERQRQEEEERKQRLQLQAAQERARQQQEEF-RRKLQELQRKKQQE--E 443

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1835591058  329 LQKAQVEAKKEHEGAVQLLENTLDSM----------QTKVQELEEKCRIQSEQFNLLSKELERFRQQ 385
Cdd:pfam15709  444 AERAEAEKQRQKELEMQLAEEQKRLMemaeeerleyQRQKQEAEEKARLEAEERRQKEEEAARLALE 510

Fibronectin type III domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  617 PYPRKITLIKQLAKSVIVGWEPPvvPPGWGNINSYNVLV------DKDIRLSVnFGSRTKALIEKLNLATcTYRISIQSV 690
Cdd:pfam00041    1 SAPSNLTVTDVTSTSLTVSWTPP--PDGNGPITGYEVEYrpknsgEPWNEITV-PGTTTSVTLTGLKPGT-EYEVRVQAV 76

                   ....*...
gi 1835591058  691 TNRGNSDE 698
Cdd:pfam00041   77 NGGGEGPP 84

Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835591058 1230 IFVALFDYDPLTMSPNPDAADEELPFKEGQIIKVYGDKDTDGFYRGATCARRGLIPCNMVSE 1291
Cdd:cd12012      1 LFVALFDYDPLTMSPNPDAAEEELPFKEGQLIKVYGDKDADGFYLGEINGRRGLVPCNMVSE 62

Src homology 3 domains of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835591058  490 LCIARYSYNPFDG-PNENPEAELPLTMGKYLYVYGDMDEDGFYEGELLDGQRGLVPSNFVEF 550
Cdd:cd11851      1 LMVALYDYNPETMsPNDDPEEELSFHAGDVVRVYGPMDEDGFYYGELEGGRKGLVPSNFVQE 62

Third Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1835591058  492 IARYSYNPFD-GPNENPEAELPLTMGKYLYVYGDMDEDGFYEGElLDGQRGLVPSNFVE 549
Cdd:cd12013      3 VALFDYDPREsSPNVDAEVELSFRAGDIITVFGEMDEDGFYYGE-LNGQRGLVPSNFLE 60

Third Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1835591058 1356 RMVALYDYDPRESSPNVDVE------------------------GELNGQKGLVPSNFLEE 1392
Cdd:cd12013      1 RMVALFDYDPRESSPNVDAEvelsfragdiitvfgemdedgfyyGELNGQRGLVPSNFLEE 61

Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins; RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  492 IARYSYNPFD-GPNENP-EAELPLTMGKYLYVYGDMDEDGFYEGElLDGQRGLVPSNFVE 549
Cdd:cd12012      3 VALFDYDPLTmSPNPDAaEEELPFKEGQLIKVYGDKDADGFYLGE-INGRRGLVPCNMVS 61

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058   65 AVRLRKEIKPESRI-SPAAALKKPSAkqrmrSVNGGPGQfqGINKDLATEKDME-----IKLLQVECEELKNRLCCLKEG 138
Cdd:TIGR02168  634 ALELAKKLRPGYRIvTLDGDLVRPGG-----VITGGSAK--TNSSILERRREIEeleekIEELEEKIAELEKALAELRKE 706

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  139 LmgqrpSDVEQLLKQSQKELLWLQRQLSFISTGGPTCILPSSKLRNDLPYLHPVLSQ-------------KTFDRIPFLE 205
Cdd:TIGR02168  707 L-----EELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTEleaeieeleerleEAEEELAEAE 781

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  206 EKTQVFKSDVNQEKQQWKDLEYELKDAVQEKTHLNLHYASLSQKalqydqvksdYDQLRETISKVIKERDLALKGKHQLQ 285
Cdd:TIGR02168  782 AEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRER----------LESLERRIAATERRLEDLEEQIEELS 851

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  286 AKLENLEQVLKHMREAAErrqQLELEHEQALAVLTAKQQEIELLQKAQveakkehegavQLLENTLDSMQTKVQELEEKC 365
Cdd:TIGR02168  852 EDIESLAAEIEELEELIE---ELESELEALLNERASLEEALALLRSEL-----------EELSEELRELESKRSELRREL 917

                          330       340
                   ....*....|....*....|
gi 1835591058  366 RIQSEQFNLLSKELERFRQQ 385
Cdd:TIGR02168  918 EELREKLAQLELRLEGLEVR 937

Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1835591058   487 KVHLCIARYSYNPfdgpnENPEaELPLTMGKYLYVYgDMDEDGFYEGELLDGQRGLVPSNFVE 549
Cdd:smart00326    1 EGPQVRALYDYTA-----QDPD-ELSFKKGDIITVL-EKSDDGWWKGRLGRGKEGLFPSNYVE 56

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  250 ALQYDQVKSDYDQLRETISKVIKERDLALKGKHQLQAKLENLEQVLKHMREAAERRQQLELEHEQALAVLTAKQQEIELL 329
Cdd:COG1196    231 LLKLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEER 310

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1835591058  330 QKAQVEAKKEHEGAVQLLENTLDSMQTKVQELEEKCRIQSEQFNLLSKELERFRQQ 385
Cdd:COG1196    311 RRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEA 366

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  220 QQWKDLEYELKDAVQEKTHLNLHYASLSQKALQYDQVKSDYDQLRETISKVIKERDL--ALKGKHQLQAKLEN----LEQ 293
Cdd:COG4717     71 KELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQLlpLYQELEALEAELAElperLEE 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  294 VLKHM---REAAERRQQLELEHEQALAVLTAKQQEIELLQKAQV----EAKKEHEGAVQLLENTLDSMQTKVQELEEkcR 366
Cdd:COG4717    151 LEERLeelRELEEELEELEAELAELQEELEELLEQLSLATEEELqdlaEELEELQQRLAELEEELEEAQEELEELEE--E 228

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1835591058  367 IQSEQFNLLSKELERfRQQTGKIDLLSGASVASSDIIGSPSKSLSQFMNGIATAIG 422
Cdd:COG4717    229 LEQLENELEAAALEE-RLKEARLLLLIAAALLALLGLGGSLLSLILTIAGVLFLVL 283

Src Homology 3 domain of metazoan osteoclast stimulating factor 1; OSTF1, also named OSF or SH3P2, is a signaling protein containing SH3 and ankyrin-repeat domains. It acts through a Src-related pathway to enhance the formation of osteoclasts and bone resorption. It also acts as a negative regulator of cell motility. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1835591058 1230 IFVALFDYDPltmspnpdAADEELPFKEGQIIKVYgDKDTDGFYRGATCARRGLIPCNMVSE 1291
Cdd:cd11772      1 VFRALYDYEA--------QHPDELSFEEGDLLYIS-DKSDPNWWKATCGGKTGLIPSNYVEE 53

Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1835591058 1230 IFVALFDYDPltmspnpdAADEELPFKEGQIIKVYgDKDTDGFYRGATC-ARRGLIPCN 1287
Cdd:cd00174      1 YARALYDYEA--------QDDDELSFKKGDIITVL-EKDDDGWWEGELNgGREGLFPAN 50

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  206 EKTQVFKSDVNQEKQ-QWKDLEYELKDAVQEKTHLNLHYASLSQK----ALQYDQVKSDYDQLRETISKVIKERDLALKG 280
Cdd:TIGR02168  210 EKAERYKELKAELRElELALLVLRLEELREELEELQEELKEAEEEleelTAELQELEEKLEELRLEVSELEEEIEELQKE 289

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591058  281 KHQLQAKLENLEQvlkHMREAAERRQQLELEHEQALAVLTAKQQEIELLQK--AQVEAKKEH-EGAVQLLENTLDSMQTK 357
Cdd:TIGR02168  290 LYALANEISRLEQ---QKQILRERLANLERQLEELEAQLEELESKLDELAEelAELEEKLEElKEELESLEAELEELEAE 366