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Conserved domains on  [gi|1278639134|gb|PJB46739|]
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peptide-binding protein [Comamonadaceae bacterium CG_4_9_14_3_um_filter_60_33]

Protein Classification

SH3 domain-containing protein( domain architecture ID 11467360)

Src Homology 3 (SH3) domain-containing protein plays 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; similar to Bacillus cereus antisigma factor

CATH:  2.30.30.40
Gene Ontology:  GO:0005515|GO:0070064
PubMed:  28510178|11256992|1639195
SCOP:  4000369

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SH3 COG3807
SH3-like domain [Function unknown];
20-160 1.76e-49

SH3-like domain [Function unknown];


:

Pssm-ID: 443020 [Multi-domain]  Cd Length: 150  Bit Score: 156.22  E-value: 1.76e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639134  20 CLVAFSLVASTAALQAREMVSVAKAEINMRAGAGTQHPTLWKLTR-GYPLEVTSRQGQWLKVRDFENDTGWVYRPLVGKT 98
Cdd:COG3807     3 LAAAAAQLGPVSGLPAPRFVSLKSDEVNLRDGPSTKYPILWVYKRrGLPVEVIAEFGNWRRVRDPEGDEGWVHQSLLSGR 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278639134  99 PHVVVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRNDWVKVqREGGLKGWIARRLLWGW 160
Cdd:COG3807    83 RTVIVTGDLANLRASPDENAAVVARLEPGVVLRLLECDGGWCKV-RADGYKGWVRQSLLWGV 143
 
Name Accession Description Interval E-value
SH3 COG3807
SH3-like domain [Function unknown];
20-160 1.76e-49

SH3-like domain [Function unknown];


Pssm-ID: 443020 [Multi-domain]  Cd Length: 150  Bit Score: 156.22  E-value: 1.76e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639134  20 CLVAFSLVASTAALQAREMVSVAKAEINMRAGAGTQHPTLWKLTR-GYPLEVTSRQGQWLKVRDFENDTGWVYRPLVGKT 98
Cdd:COG3807     3 LAAAAAQLGPVSGLPAPRFVSLKSDEVNLRDGPSTKYPILWVYKRrGLPVEVIAEFGNWRRVRDPEGDEGWVHQSLLSGR 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278639134  99 PHVVVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRNDWVKVqREGGLKGWIARRLLWGW 160
Cdd:COG3807    83 RTVIVTGDLANLRASPDENAAVVARLEPGVVLRLLECDGGWCKV-RADGYKGWVRQSLLWGV 143
SH3_3 pfam08239
Bacterial SH3 domain;
107-157 2.24e-11

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 55.72  E-value: 2.24e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1278639134 107 VANVRSDPSTRSRILGKADNGEVLRTLEHRND-WVKVQREGGLKGWIARRLL 157
Cdd:pfam08239   2 GLNVRSGPSTSSEVVGTLPKGEKVEVLEEQGGgWYKVRTYDGYEGWVSSSYL 53
SH3b smart00287
Bacterial SH3 domain homologues;
102-157 1.88e-06

Bacterial SH3 domain homologues;


Pssm-ID: 214600 [Multi-domain]  Cd Length: 63  Bit Score: 43.09  E-value: 1.88e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278639134  102 VVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRN-DWVKVQREGGLKGWIARRLL 157
Cdd:smart00287   5 VVTGDGLNVRTGPGTSSPIIGTLKKGDKVKVLGVDGqDWAKITYGSGQRGYVPGYVV 61
SH3_and_anchor TIGR04211
SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved ...
 45-112 3.28e-04

SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.


Pssm-ID: 275056 [Multi-domain]  Cd Length: 198  Bit Score: 39.22  E-value: 3.28e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278639134  45 EINMRAGAGTQHPTLWKLTRGYPLEVTSRQGQ-WLKVRDFENDTGWVYRPLVGKTPHvvVKSRVANVRS 112
Cdd:TIGR04211   7 FVYMRSGPGNQYRILGSLKSGTPVTVLERSEDgYSRVRTPKGREGWVLSRYLSDTPS--ARERLPELQQ 73
tagH PRK13545
teichoic acids export protein ATP-binding subunit; Provisional
 102-157 9.85e-04

teichoic acids export protein ATP-binding subunit; Provisional


Pssm-ID: 184130 [Multi-domain]  Cd Length: 549  Bit Score: 38.33  E-value: 9.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278639134 102 VVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRND------WVKVQREGGLKGWIARRLL 157
Cdd:PRK13545  350 IVNSNGISIREEADASSKRLAVANFGDIFTISDSNKNekkdveWIQITLSNGEIGWISTKFI 411
 
Name Accession Description Interval E-value
SH3 COG3807
SH3-like domain [Function unknown];
20-160 1.76e-49

SH3-like domain [Function unknown];


Pssm-ID: 443020 [Multi-domain]  Cd Length: 150  Bit Score: 156.22  E-value: 1.76e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639134  20 CLVAFSLVASTAALQAREMVSVAKAEINMRAGAGTQHPTLWKLTR-GYPLEVTSRQGQWLKVRDFENDTGWVYRPLVGKT 98
Cdd:COG3807     3 LAAAAAQLGPVSGLPAPRFVSLKSDEVNLRDGPSTKYPILWVYKRrGLPVEVIAEFGNWRRVRDPEGDEGWVHQSLLSGR 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278639134  99 PHVVVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRNDWVKVqREGGLKGWIARRLLWGW 160
Cdd:COG3807    83 RTVIVTGDLANLRASPDENAAVVARLEPGVVLRLLECDGGWCKV-RADGYKGWVRQSLLWGV 143
YgiM COG3103
Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family ...
 34-152 7.00e-26

Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family [General function prediction only];


Pssm-ID: 442337 [Multi-domain]  Cd Length: 119  Bit Score: 95.19  E-value: 7.00e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639134  34 QAREMVSVAKAEINMRAGAGTQHPTLWKLTRGYPLEVTSRQGQWLKVRDFENDTGWVYRPLVGKTPHVVVKSRVA-NVRS 112
Cdd:COG3103     2 AAETRYVVDADALNVRSGPGTSYRIVGTLPKGEKVTVLGRSGGWYKVRYSNGKTGWVSSRYLTVTPSARERLPDElNLRA 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1278639134 113 DPSTRSRILGKADNGEVLRTLEHRNDWVKVQREGglKGWI 152
Cdd:COG3103    82 GPSTSSEVLGLLPKGETVTVLKKSGGWFKVGYRG--TGWV 119
YgiM COG3103
Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family ...
 98-157 7.28e-14

Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family [General function prediction only];


Pssm-ID: 442337 [Multi-domain]  Cd Length: 119  Bit Score: 63.99  E-value: 7.28e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278639134  98 TPHVVVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRNDWVKVQREGGLKGWIARRLL 157
Cdd:COG3103     4 ETRYVVDADALNVRSGPGTSYRIVGTLPKGEKVTVLGRSGGWYKVRYSNGKTGWVSSRYL 63
SH3_3 pfam08239
Bacterial SH3 domain;
107-157 2.24e-11

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 55.72  E-value: 2.24e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1278639134 107 VANVRSDPSTRSRILGKADNGEVLRTLEHRND-WVKVQREGGLKGWIARRLL 157
Cdd:pfam08239   2 GLNVRSGPSTSSEVVGTLPKGEKVEVLEEQGGgWYKVRTYDGYEGWVSSSYL 53
YraI COG4991
Uncharacterized conserved protein YraI [Function unknown];
15-91 2.70e-10

Uncharacterized conserved protein YraI [Function unknown];


Pssm-ID: 444015 [Multi-domain]  Cd Length: 92  Bit Score: 53.91  E-value: 2.70e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278639134  15 KKWAQCLVAFSLVASTAALQAremVSVAKAEINMRAGAGTQHPTLWKLTRGYPLEVTSRQ--GQWLKVRdFENDTGWVY 91
Cdd:COG4991     3 RALLAAALALLLLAPAAAAAA---TAVATDDLNLRSGPGTGYPVVGTLPAGATVTVLGCTsgGGWCKVS-YGGQRGWVS 77
SH3_4 pfam06347
Bacterial SH3 domain; SH3 (src Homology-3) domains are small protein modules containing ...
 42-95 1.12e-08

Bacterial SH3 domain; SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues. They are found in a great variety of intracellular or membrane-associated proteins, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteriztic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region. Family members include probable invasion-associated protein p60 that are conceptually translated from iap genes. The iap gene, which is regarded as a virulence-associated gene in L. monocytogenes, codes for a gene product that has murein-lytic activity and is involved in cell division.


Pssm-ID: 428898 [Multi-domain]  Cd Length: 56  Bit Score: 48.88  E-value: 1.12e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1278639134  42 AKAEINMRAGAGTQHPTLWKLTRGYPLEVTSRQGQWLKVRDFENDTGWVYRPLV 95
Cdd:pfam06347   1 KKDEVNLRRGPSDKAAVAAYLEAGVPVRVVACKDNWCRVRDADGAEGWIYKSLL 54
SH3_4 pfam06347
Bacterial SH3 domain; SH3 (src Homology-3) domains are small protein modules containing ...
 108-159 4.56e-08

Bacterial SH3 domain; SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues. They are found in a great variety of intracellular or membrane-associated proteins, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteriztic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region. Family members include probable invasion-associated protein p60 that are conceptually translated from iap genes. The iap gene, which is regarded as a virulence-associated gene in L. monocytogenes, codes for a gene product that has murein-lytic activity and is involved in cell division.


Pssm-ID: 428898 [Multi-domain]  Cd Length: 56  Bit Score: 47.34  E-value: 4.56e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1278639134 108 ANVRSDPSTRSRILGKADNGEVLRTLEHRNDWVKVQREGGLKGWIARRLLWG 159
Cdd:pfam06347   5 VNLRRGPSDKAAVAAYLEAGVPVRVVACKDNWCRVRDADGAEGWIYKSLLWG 56
SH3_3 pfam08239
Bacterial SH3 domain;
46-90 1.04e-06

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 43.39  E-value: 1.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1278639134  46 INMRAGAGTQHPTLWKLTRGYPLEVTSRQ-GQWLKVRDFENDTGWV 90
Cdd:pfam08239   3 LNVRSGPSTSSEVVGTLPKGEKVEVLEEQgGGWYKVRTYDGYEGWV 48
SH3b smart00287
Bacterial SH3 domain homologues;
102-157 1.88e-06

Bacterial SH3 domain homologues;


Pssm-ID: 214600 [Multi-domain]  Cd Length: 63  Bit Score: 43.09  E-value: 1.88e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278639134  102 VVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRN-DWVKVQREGGLKGWIARRLL 157
Cdd:smart00287   5 VVTGDGLNVRTGPGTSSPIIGTLKKGDKVKVLGVDGqDWAKITYGSGQRGYVPGYVV 61
SH3_and_anchor TIGR04211
SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved ...
 45-112 3.28e-04

SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.


Pssm-ID: 275056 [Multi-domain]  Cd Length: 198  Bit Score: 39.22  E-value: 3.28e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278639134  45 EINMRAGAGTQHPTLWKLTRGYPLEVTSRQGQ-WLKVRDFENDTGWVYRPLVGKTPHvvVKSRVANVRS 112
Cdd:TIGR04211   7 FVYMRSGPGNQYRILGSLKSGTPVTVLERSEDgYSRVRTPKGREGWVLSRYLSDTPS--ARERLPELQQ 73
SH3_and_anchor TIGR04211
SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved ...
 109-157 5.22e-04

SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region.


Pssm-ID: 275056 [Multi-domain]  Cd Length: 198  Bit Score: 38.84  E-value: 5.22e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1278639134 109 NVRSDPSTRSRILGKADNGEVLRTLEHRND-WVKVQREGGLKGWIARRLL 157
Cdd:TIGR04211   9 YMRSGPGNQYRILGSLKSGTPVTVLERSEDgYSRVRTPKGREGWVLSRYL 58
tagH PRK13545
teichoic acids export protein ATP-binding subunit; Provisional
 102-157 9.85e-04

teichoic acids export protein ATP-binding subunit; Provisional


Pssm-ID: 184130 [Multi-domain]  Cd Length: 549  Bit Score: 38.33  E-value: 9.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278639134 102 VVKSRVANVRSDPSTRSRILGKADNGEVLRTLEHRND------WVKVQREGGLKGWIARRLL 157
Cdd:PRK13545  350 IVNSNGISIREEADASSKRLAVANFGDIFTISDSNKNekkdveWIQITLSNGEIGWISTKFI 411
SH3b smart00287
Bacterial SH3 domain homologues;
40-90 1.96e-03

Bacterial SH3 domain homologues;


Pssm-ID: 214600 [Multi-domain]  Cd Length: 63  Bit Score: 35.00  E-value: 1.96e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1278639134   40 SVAKAEINMRAGAGTQHPTLWKLTRGYPLEVTSRQGQ-WLKVRDFENDTGWV 90
Cdd:smart00287   5 VVTGDGLNVRTGPGTSSPIIGTLKKGDKVKVLGVDGQdWAKITYGSGQRGYV 56
YraI COG4991
Uncharacterized conserved protein YraI [Function unknown];
109-157 2.73e-03

Uncharacterized conserved protein YraI [Function unknown];


Pssm-ID: 444015 [Multi-domain]  Cd Length: 92  Bit Score: 35.43  E-value: 2.73e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1278639134 109 NVRSDPSTRSRILGKADNGEVLRTLEHRND--WVKVqREGGLKGWIARRLL 157
Cdd:COG4991    32 NLRSGPGTGYPVVGTLPAGATVTVLGCTSGggWCKV-SYGGQRGWVSARYL 81
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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