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 1835591078 1476 IFVALFDYDPLTMSPNPDAADEELPFKEGQIIKVYGDKDTDGFYRGATCARRGLIPCNMVSE 1537
Cdd:cd12012      1 LFVALFDYDPLTMSPNPDAAEEELPFKEGQLIKVYGDKDADGFYLGEINGRRGLVPCNMVSE 62

First 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 1835591078  490 LCIARYSYNPF-DGPNENPEAELPLTMGKYLYVYGDMDEDGFYEGELLDGQRGLVPSNFVEF 550
Cdd:cd12014      1 VFVARYSYNPLrDSPNENPEAELPLNAGDYVYVYGDMDEDGFYEGELLDGRRGLVPSNFVER 62

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 1835591078  806 PAPPQDIRIQAGpTPTAILVTWKPPtltptgTSNGANITGY-VAY--AKGQKVAEVVFPTAESTVVdllRIQNLEAK--- 879
Cdd:cd00063      1 PSPPTNLRVTDV-TSTSVTLSWTPP------EDDGGPITGYvVEYreKGSGDWKEVEVTPGSETSY---TLTGLKPGtey 70

                           90       100
                   ....*....|....*....|.
gi 1835591078  880 EITIRSLSAQGESEDSAPTAI 900
Cdd:cd00063     71 EFRVRAVNGGGESPPSESVTV 91

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 1835591078   30 KQQEEEGK-LHKKERTdfTKKERNHRSEakipqkphavRLRKEIKP--ESRISPAAAlkkpsakqRMRSVNGGPGQ---F 103
Cdd:TIGR00618  472 EQQLQTKEqIHLQETR--KKAVVLARLL----------ELQEEPCPlcGSCIHPNPA--------RQDIDNPGPLTrrmQ 531

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  104 QGINKDLATEKdmEIKLLQVECEELKNRLCCLKEGLmgQRPSDVEQLLKQSQKELlwlqrqlsfistggpTCILPssKLR 183
Cdd:TIGR00618  532 RGEQTYAQLET--SEEDVYHQLTSERKQRASLKEQM--QEIQQSFSILTQCDNRS---------------KEDIP--NLQ 590

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  184 NDLPYLHPVLSQKTFDRIPFLEE--------KTQVFKSDVNQEKQQwKDLEYELKDAVQEKTHLNLHYASLSQKALQYDQ 255
Cdd:TIGR00618  591 NITVRLQDLTEKLSEAEDMLACEqhallrklQPEQDLQDVRLHLQQ-CSQELALKLTALHALQLTLTQERVREHALSIRV 669

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  256 VKSDYDQLRETISKVIKERdlalkgKHQLQAKLENLEQVLKHMREAAERRQQLELE-HEQALAVLTAK---QQEIELLQ- 330
Cdd:TIGR00618  670 LPKELLASRQLALQKMQSE------KEQLTYWKEMLAQCQTLLRELETHIEEYDREfNEIENASSSLGsdlAAREDALNq 743

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1835591078  331 -------------KAQVEAKKEHEGAVQLLENTLDSMQTKVQELEEKCRIQSEQFNLLSKELERFRQ 384
Cdd:TIGR00618  744 slkelmhqartvlKARTEAHFNNNEEVTAALQTGAELSHLAAEIQFFNRLREEDTHLLKTLEAEIGQ 810

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 1835591078  619 PRKITLIKQLAKSVIVGWEPPvvPPGWGNINSYNVLV-----DKDIRLSVNFGSRTKALIEKLNLATcTYRISIQSVTNR 693
Cdd:cd00063      4 PTNLRVTDVTSTSVTLSWTPP--EDDGGPITGYVVEYrekgsGDWKEVEVTPGSETSYTLTGLKPGT-EYEFRVRAVNGG 80

                   ....*..
gi 1835591078  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 1835591078 1476 IFVALFDYDPLTMSPNPDAADEELPFKEGQIIKVYGDKDTDGFYRGATCARRGLIPCNMVSE 1537
Cdd:cd12012      1 LFVALFDYDPLTMSPNPDAAEEELPFKEGQLIKVYGDKDADGFYLGEINGRRGLVPCNMVSE 62

First 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 1835591078  490 LCIARYSYNPF-DGPNENPEAELPLTMGKYLYVYGDMDEDGFYEGELLDGQRGLVPSNFVEF 550
Cdd:cd12014      1 VFVARYSYNPLrDSPNENPEAELPLNAGDYVYVYGDMDEDGFYEGELLDGRRGLVPSNFVER 62

Variant SH3 domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1835591078 1605 ALYDYDPREsspnvdvEAELTFCTGDIITVFGEiDEDGFYYGELNGQKGLVPSNFLE 1661
Cdd:pfam14604    1 ALYPYEPKD-------DDELSLQRGDVITVIEE-SEDGWWEGINTGRTGLVPANYVE 49

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 1835591078   65 AVRLRKEIKPESRI-SPAAALKKPSAkqrmrSVNGGPGQfqGINKDLATEKDME-----IKLLQVECEELKNRLCCLKEG 138
Cdd:TIGR02168  634 ALELAKKLRPGYRIvTLDGDLVRPGG-----VITGGSAK--TNSSILERRREIEeleekIEELEEKIAELEKALAELRKE 706

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  139 LmgqrpSDVEQLLKQSQKELLWLQRQLSFISTGGPTCILPSSKLRNDLPYLHPVLSQ-------------KTFDRIPFLE 205
Cdd:TIGR02168  707 L-----EELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTEleaeieeleerleEAEEELAEAE 781

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  206 EKTQVFKSDVNQEKQQWKDLEYELKDAVQEKTHLNLHYASLSQKalqydqvksdYDQLRETISKVIKERDLALKGKHQLQ 285
Cdd:TIGR02168  782 AEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRER----------LESLERRIAATERRLEDLEEQIEELS 851

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  286 AKLENLEQVLKHMREAAErrqQLELEHEQALAVLTAKQQEIELLQKAQveakkehegavQLLENTLDSMQTKVQELEEKC 365
Cdd:TIGR02168  852 EDIESLAAEIEELEELIE---ELESELEALLNERASLEEALALLRSEL-----------EELSEELRELESKRSELRREL 917

                          330       340
                   ....*....|....*....|
gi 1835591078  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 1835591078 1477 FVALFDYDPltmsPNPdaadEELPFKEGQIIKVYgDKDTDGFYRGATCARRGLIPCNMVSEI 1538
Cdd:pfam07653    2 GRVIFDYVG----TDK----NGLTLKKGDVVKVL-GKDNDGWWEGETGGRVGLVPSTAVEEI 54

Variant SH3 domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1835591078  493 ARYSYNPFDgpnenpEAELPLTMGKYLYVYGDmDEDGFYEGELlDGQRGLVPSNFVE 549
Cdd:pfam14604    1 ALYPYEPKD------DDELSLQRGDVITVIEE-SEDGWWEGIN-TGRTGLVPANYVE 49

chromosome partition protein MukB;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  224 DLEYELKDAVQEK----THLNLHYASLSQKALQYDQVKSDYDQLR-----------ETISKVIKE----RDLALKGK--- 281
Cdd:PRK04863   834 DPEAELRQLNRRRveleRALADHESQEQQQRSQLEQAKEGLSALNrllprlnlladETLADRVEEireqLDEAEEAKrfv 913

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  282 HQLQAKLENLEQVLKHMREAAERRQQLELEHEQALAVLTAKQQEIELLqkAQVEAKKEH---EGAVQLLEntldsmqtKV 358
Cdd:PRK04863   914 QQHGNALAQLEPIVSVLQSDPEQFEQLKQDYQQAQQTQRDAKQQAFAL--TEVVQRRAHfsyEDAAEMLA--------KN 983

                          170       180
                   ....*....|....*....|....*..
gi 1835591078  359 QELEEKCRIQSEQfnlLSKELERFRQQ 385
Cdd:PRK04863   984 SDLNEKLRQRLEQ---AEQERTRAREQ 1007

large tegument protein UL36; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  773 LLAKPHQMPWQLPLEQREKKEAFAEFSTLPAGPPAPPQDIRIQAGPTPTAILVTW-------KPPTLTPTGTSNGANITG 845
Cdd:PHA03247  2644 PTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLadpppppPTPEPAPHALVSATPLPP 2723

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  846 YVAYAKGQKVAEVVFP----TAESTVVDllriqnleAKEITIRSLSAQGESEDSAPTAIPPELLMPPTPHPRTSPKLKPL 921
Cdd:PHA03247  2724 GPAAARQASPALPAAPappaVPAGPATP--------GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESR 2795

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  922 ASAGAPDTKDEHLGP--PRKIDESWEQTPvhGHTLEPPTANFHSPAHGRRSPSPQRILPQPQGTPVSNTVAKAMAREAAQ 999
Cdd:PHA03247  2796 ESLPSPWDPADPPAAvlAPAAALPPAASP--AGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAA 2873

                          250
                   ....*....|...
gi 1835591078 1000 RVAESNRMEKRSI 1012
Cdd:PHA03247  2874 KPAAPARPPVRRL 2886

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 1835591078   806 PAPPQDIRIQAgPTPTAILVTWKPptltPTGTSNGANITGY-VAYAKGQKVAEVVFPTAESTVVdllRIQNLEAK---EI 881
Cdd:smart00060    1 PSPPSNLRVTD-VTSTSVTLSWEP----PPDDGITGYIVGYrVEYREEGSEWKEVNVTPSSTSY---TLTGLKPGteyEF 72

                            90
                    ....*....|.
gi 1835591078   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 1835591078  222 WKDLEYELKDAV-----------QEKTHLNLHYASLSQKALQYDQVKSDYDQLRETISKVIkerdlaLKGKHQLQAKlEN 290
Cdd:cd16269    126 SAPLEEKISQGSysvpggyqlylEDREKLVEKYRQVPRKGVKAEEVLQEFLQSKEAEAEAI------LQADQALTEK-EK 198

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  291 LEQVLKHMREAAERRQQLELEHEQALAVLTAKQQEIELLQKAQVEAKKEHEgavqlLENTLDSMQtkvQELEEKCRIQ-- 368
Cdd:cd16269    199 EIEAERAKAEAAEQERKLLEEQQRELEQKLEDQERSYEEHLRQLKEKMEEE-----RENLLKEQE---RALESKLKEQea 270

                          170       180
                   ....*....|....*....|.
gi 1835591078  369 ------SEQFNLLSKELERFR 383
Cdd:cd16269    271 lleegfKEQAELLQEEIRSLK 291

Fibronectin type III domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  808 PPQDIRIQaGPTPTAILVTWKPPtltptgTSNGANITGY-VAYAK---GQKVAEVVFPTAESTVVdllrIQNLEAK---E 880
Cdd:pfam00041    2 APSNLTVT-DVTSTSLTVSWTPP------PDGNGPITGYeVEYRPknsGEPWNEITVPGTTTSVT----LTGLKPGteyE 70

                           90
                   ....*....|....*
gi 1835591078  881 ITIRSLSAQGESEDS 895
Cdd:pfam00041   71 VRVQAVNGGGEGPPS 85

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 1835591078   619 PRKITLIKQLAKSVIVGWEPPVVPPGWGNINSYNVLVDKDIRLSVNF---GSRTKALIEKLNLATcTYRISIQSVTNRGN 695
Cdd:smart00060    4 PSNLRVTDVTSTSVTLSWEPPPDDGITGYIVGYRVEYREEGSEWKEVnvtPSSTSYTLTGLKPGT-EYEFRVRAVNGAGE 82

                    .
gi 1835591078   696 S 696
Cdd:smart00060   83 G 83

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 1835591078   13 ESSKISQPITKVENHSSKQQEEEGKLHKKERTDFTKKERNHRsEAKIPQKPH-AVRLRKEIKPESRISPAAALKKPSAK- 90
Cdd:pfam15709  156 EPRLFNQETPASISHAERELIDKAKRRKGTKTDKTKTPKRER-EGKVHGEAEaAVGKSRESKAEKKSELISKGKKTGAKr 234

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078   91 QRMRsvnggpgqfQGINKDLATEKDMEIKLLQVECEELKNRlcclkeGLMGQRPSDVEQLLK-QSQKEllwlQRQLSFIS 169
Cdd:pfam15709  235 KRTQ---------KERNLEVAAELSGPDVINSKETEDASER------GAFSSDSVVEDPWLSsKYDAE----ESQVSIDG 295

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  170 TGGPTCILPSSklrNDLPYLHPVLSQKTFDRIPFLEEKTQVFKSDVNQEKQQWKDLEYELKDAVQEKTHlnlhyaSLSQK 249
Cdd:pfam15709  296 RSSPTQTFVVT---GNMESEEERSEEDPSKALLEKREQEKASRDRLRAERAEMRRLEVERKRREQEEQR------RLQQE 366

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  250 ALQY-DQVKSDYDQLRETISKVIKERDLALKGKHQLQAKLENLEQVLKHMREAAERRQQLELeHEQALAVLTAKQQEieL 328
Cdd:pfam15709  367 QLERaEKMREELELEQQRRFEEIRLRKQRLEEERQRQEEEERKQRLQLQAAQERARQQQEEF-RRKLQELQRKKQQE--E 443

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1835591078  329 LQKAQVEAKKEHEGAVQLLENTLDSM----------QTKVQELEEKCRIQSEQFNLLSKELERFRQQ 385
Cdd:pfam15709  444 AERAEAEKQRQKELEMQLAEEQKRLMemaeeerleyQRQKQEAEEKARLEAEERRQKEEEAARLALE 510

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 1835591078 1476 IFVALFDYDPLTMSPNPDAADEELPFKEGQIIKVYGDKDTDGFYRGATCARRGLIPCNMVSE 1537
Cdd:cd12012      1 LFVALFDYDPLTMSPNPDAAEEELPFKEGQLIKVYGDKDADGFYLGEINGRRGLVPCNMVSE 62

First 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 1835591078  490 LCIARYSYNPF-DGPNENPEAELPLTMGKYLYVYGDMDEDGFYEGELLDGQRGLVPSNFVEF 550
Cdd:cd12014      1 VFVARYSYNPLrDSPNENPEAELPLNAGDYVYVYGDMDEDGFYEGELLDGRRGLVPSNFVER 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 1835591078  490 LCIARYSYNPFDG-PNENPEAELPLTMGKYLYVYGDMDEDGFYEGELLDGQRGLVPSNFVEF 550
Cdd:cd11851      1 LMVALYDYNPETMsPNDDPEEELSFHAGDVVRVYGPMDEDGFYYGELEGGRKGLVPSNFVQE 62

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 1835591078 1604 VALYDYDPRESSPNVD-VEAELTFCTGDIITVFGEIDEDGFYYGELNGQKGLVPSNFLEE 1662
Cdd:cd12012      3 VALFDYDPLTMSPNPDaAEEELPFKEGQLIKVYGDKDADGFYLGEINGRRGLVPCNMVSE 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 1835591078  492 IARYSYNPFD-GPNENPEAELPLTMGKYLYVYGDMDEDGFYEGElLDGQRGLVPSNFVE 549
Cdd:cd12013      3 VALFDYDPREsSPNVDAEVELSFRAGDIITVFGEMDEDGFYYGE-LNGQRGLVPSNFLE 60

First 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 1835591078 1476 IFVALFDYDPLTMSPN--PDAadeELPFKEGQIIKVYGDKDTDGFYRGATC-ARRGLIPCNMV 1535
Cdd:cd12014      1 VFVARYSYNPLRDSPNenPEA---ELPLNAGDYVYVYGDMDEDGFYEGELLdGRRGLVPSNFV 60

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 1835591078  1601 RRMVALYDYDPRESSpnvdveaELTFCTGDIITVFgEIDEDGFYYGELN-GQKGLVPSNFLE 1661
Cdd:smart00326    3 PQVRALYDYTAQDPD-------ELSFKKGDIITVL-EKSDDGWWKGRLGrGKEGLFPSNYVE 56

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 1835591078 1602 RMVALYDYDPRESSpnvdveaELTFCTGDIITVFgEIDEDGFYYGELN-GQKGLVPSNF 1659
Cdd:cd00174      1 YARALYDYEAQDDD-------ELSFKKGDIITVL-EKDDDGWWEGELNgGREGLFPANY 51

Src homology 3 domain of Nitric Oxide Synthase TRaffic INducer; Nostrin is expressed in endothelial and epithelial cells and is involved in the regulation, trafficking and targeting of endothelial NOS (eNOS). It facilitates the endocytosis of eNOS by coordinating the functions of dynamin and the Wiskott-Aldrich syndrome protein (WASP). Increased expression of Nostrin may be correlated to preeclampsia. Nostrin contains an N-terminal F-BAR domain and a C-terminal SH3 domain. 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 1835591078 1602 RMVALYDYDPREsspnvdvEAELTFCTGDIITVFgEIDEDGFYYGELNGQKGLVPSNFLEE 1662
Cdd:cd11823      1 RCKALYSYTANR-------EDELSLQPGDIIEVH-EKQDDGWWLGELNGKKGIFPATYVEE 53

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 1835591078   65 AVRLRKEIKPESRI-SPAAALKKPSAkqrmrSVNGGPGQfqGINKDLATEKDME-----IKLLQVECEELKNRLCCLKEG 138
Cdd:TIGR02168  634 ALELAKKLRPGYRIvTLDGDLVRPGG-----VITGGSAK--TNSSILERRREIEeleekIEELEEKIAELEKALAELRKE 706

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  139 LmgqrpSDVEQLLKQSQKELLWLQRQLSFISTGGPTCILPSSKLRNDLPYLHPVLSQ-------------KTFDRIPFLE 205
Cdd:TIGR02168  707 L-----EELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTEleaeieeleerleEAEEELAEAE 781

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  206 EKTQVFKSDVNQEKQQWKDLEYELKDAVQEKTHLNLHYASLSQKalqydqvksdYDQLRETISKVIKERDLALKGKHQLQ 285
Cdd:TIGR02168  782 AEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRER----------LESLERRIAATERRLEDLEEQIEELS 851

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1835591078  286 AKLENLEQVLKHMREAAErrqQLELEHEQALAVLTAKQQEIELLQKAQveakkehegavQLLENTLDSMQTKVQELEEKC 365
Cdd:TIGR02168  852 EDIESLAAEIEELEELIE---ELESELEALLNERASLEEALALLRSEL-----------EELSEELRELESKRSELRREL 917

                          330       340
                   ....*....|....*....|
gi 1835591078  366 RIQSEQFNLLSKELERFRQQ 385
Cdd:TIGR02168  918 EELREKLAQLELRLEGLEVR 937

Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins; PACSINs, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. They bind both dynamin and Wiskott-Aldrich syndrome protein (WASP), and may provide direct links between the actin cytoskeletal machinery through WASP and dynamin-dependent endocytosis. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. 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 1835591078 1602 RMVALYDYDPRESSpnvdveaELTFCTGDIITVFGEIDEDGFYYGELNGQKGLVPSNFLE 1661
Cdd:cd11843      1 PVRALYDYEGQESD-------ELSFKAGDILTKLEEEDEQGWCKGRLDGRVGLYPANYVE 53

Fifth Src homology 3 domain (or SH3E) of Intersectin; Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN proteins, ITSN1 and ITSN2, which exist in alternatively spliced short and long isoforms. The short isoforms contain two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoforms, in addition, contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. ITSN1 and ITSN2 are both widely expressed, with variations depending on tissue type and stage of development. The fifth SH3 domain (or SH3E) of ITSN1 has been shown to bind many protein partners including SGIP1, Sos1, dynamin1/2, CIN85, c-Cbl, SHIP2, N-WASP, and synaptojanin-1, among others. 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 1835591078 1602 RMVALYDYdpresspNVDVEAELTFCTGDIITVFGEiDEDGFYYGELNGQKGLVPSNFLEE 1662
Cdd:cd11840      1 QVIALFPY-------TAQNEDELSFQKGDIINVLSK-DDPDWWRGELNGQTGLFPSNYVEP 53

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.