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Conserved domains on  [gi|503312836|ref|WP_013547497|]
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SH3 domain-containing C40 family peptidase [Bacteroides helcogenes]

Protein Classification

C40 family peptidase( domain architecture ID 12087778)

C40 family peptidase containing SH3 domain(s) is a cell-wall hydrolase that cleaves peptide cross-bridges between glycan chains and is essential for bacterial growth and viability; typically cleaves the linkage between D-Glu and diaminopimelic acid (or Lys) within peptidoglycan stem peptides; contains a Cys-His-His catalytic triad

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
167-381 4.93e-41

Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 144.46  E-value: 4.93e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 167 VTGEELAAWNNAEKIVVTSHYGFVYSQPDQASQPVSDVVAGNRLKWDGAKGAFYKVTYPDGRRGYISKSIAMPEKKWRSG 246
Cdd:COG0791   16 AALAAVAAAGALAAADAAVAAALVAAAAAVLAAAALLAGPAAAVAGAAAPAVGSAGAAAAAAAAKAGSSAAKSAAGASAP 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 247 LKQDAASIIRTAHTMMGIPYLWAGTSSKGVDCSGFVRTVLFMHDIIIPRDASQQAYTGRHIdiapDFSNLRPGDLIFFGR 326
Cdd:COG0791   96 PSSTAEAIVAAALSYLGTPYVWGGTSPSGFDCSGLVQYVYRQAGISLPRTSADQAAAGTPV----SRSELQPGDLVFFRT 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503312836 327 KatpelKERVVHVGIYIGNRRFIH---SQGDVHVSSLDpadelfDEYNLGRLLFASRV 381
Cdd:COG0791  172 G-----GGGISHVGIYLGNGKFIHassSGKGVRISSLD------SPYWKSRYVGARRV 218
SH3_3 pfam08239
Bacterial SH3 domain;
114-165 4.87e-11

Bacterial SH3 domain;


:

Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 57.64  E-value: 4.87e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 503312836  114 SVANLRAEPDFSSEMMTQGLMGMPIRVL--QRDGWYRIQTPDDYIAWVHRVGIH 165
Cdd:pfam08239   1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLeeQGGGWYKVRTYDGYEGWVSSSYLS 54
 
Name Accession Description Interval E-value
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
167-381 4.93e-41

Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 144.46  E-value: 4.93e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 167 VTGEELAAWNNAEKIVVTSHYGFVYSQPDQASQPVSDVVAGNRLKWDGAKGAFYKVTYPDGRRGYISKSIAMPEKKWRSG 246
Cdd:COG0791   16 AALAAVAAAGALAAADAAVAAALVAAAAAVLAAAALLAGPAAAVAGAAAPAVGSAGAAAAAAAAKAGSSAAKSAAGASAP 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 247 LKQDAASIIRTAHTMMGIPYLWAGTSSKGVDCSGFVRTVLFMHDIIIPRDASQQAYTGRHIdiapDFSNLRPGDLIFFGR 326
Cdd:COG0791   96 PSSTAEAIVAAALSYLGTPYVWGGTSPSGFDCSGLVQYVYRQAGISLPRTSADQAAAGTPV----SRSELQPGDLVFFRT 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503312836 327 KatpelKERVVHVGIYIGNRRFIH---SQGDVHVSSLDpadelfDEYNLGRLLFASRV 381
Cdd:COG0791  172 G-----GGGISHVGIYLGNGKFIHassSGKGVRISSLD------SPYWKSRYVGARRV 218
NLPC_P60 pfam00877
NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
 263-361 2.44e-24

NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.


Pssm-ID: 395705 [Multi-domain]  Cd Length: 105  Bit Score: 96.20  E-value: 2.44e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836  263 GIPYLWAGTSSKGVDCSGFVRTVLFMHDIIIPRDASQQAYTGRHiDIAPdfSNLRPGDLIFFGRKATPElkervvHVGIY 342
Cdd:pfam00877   1 GVPYRWGGGSPSGFDCSGLVRYAFAKVGIELPRSSGQQYNAGKK-TIPK--SEPQRGDLVFFGTGKGIS------HVGIY 71

                          90       100
                  ....*....|....*....|.
gi 503312836  343 IGNRRFIHSQGD--VHVSSLD 361
Cdd:pfam00877  72 LGNGQMLHASTGggVSISSLN 92
spr PRK10838
bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase;
263-383 4.00e-17

bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase;


Pssm-ID: 236773 [Multi-domain]  Cd Length: 190  Bit Score: 79.04  E-value: 4.00e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 263 GIPYLWAGTSSKGVDCSGFV-RTVLFMHDIIIPRDASQQAYTGRHIdiapDFSNLRPGDLIFFGRKATPElkervvHVGI 341
Cdd:PRK10838  79 GVRYRLGGSTKKGIDCSAFVqRTFREQFGLELPRSTYEQQEMGKSV----SRSKLRTGDLVLFRAGSTGR------HVGI 148

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 503312836 342 YIGNRRFIH---SQGdVHVSSLDpadelfDEYNLGRLLFASRVMP 383
Cdd:PRK10838 149 YIGNNQFVHastSSG-VIISSMN------EPYWKKRYNEARRVLS 186
SH3_3 pfam08239
Bacterial SH3 domain;
114-165 4.87e-11

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 57.64  E-value: 4.87e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 503312836  114 SVANLRAEPDFSSEMMTQGLMGMPIRVL--QRDGWYRIQTPDDYIAWVHRVGIH 165
Cdd:pfam08239   1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLeeQGGGWYKVRTYDGYEGWVSSSYLS 54
 
Name Accession Description Interval E-value
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
167-381 4.93e-41

Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 144.46  E-value: 4.93e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 167 VTGEELAAWNNAEKIVVTSHYGFVYSQPDQASQPVSDVVAGNRLKWDGAKGAFYKVTYPDGRRGYISKSIAMPEKKWRSG 246
Cdd:COG0791   16 AALAAVAAAGALAAADAAVAAALVAAAAAVLAAAALLAGPAAAVAGAAAPAVGSAGAAAAAAAAKAGSSAAKSAAGASAP 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 247 LKQDAASIIRTAHTMMGIPYLWAGTSSKGVDCSGFVRTVLFMHDIIIPRDASQQAYTGRHIdiapDFSNLRPGDLIFFGR 326
Cdd:COG0791   96 PSSTAEAIVAAALSYLGTPYVWGGTSPSGFDCSGLVQYVYRQAGISLPRTSADQAAAGTPV----SRSELQPGDLVFFRT 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503312836 327 KatpelKERVVHVGIYIGNRRFIH---SQGDVHVSSLDpadelfDEYNLGRLLFASRV 381
Cdd:COG0791  172 G-----GGGISHVGIYLGNGKFIHassSGKGVRISSLD------SPYWKSRYVGARRV 218
NLPC_P60 pfam00877
NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
 263-361 2.44e-24

NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.


Pssm-ID: 395705 [Multi-domain]  Cd Length: 105  Bit Score: 96.20  E-value: 2.44e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836  263 GIPYLWAGTSSKGVDCSGFVRTVLFMHDIIIPRDASQQAYTGRHiDIAPdfSNLRPGDLIFFGRKATPElkervvHVGIY 342
Cdd:pfam00877   1 GVPYRWGGGSPSGFDCSGLVRYAFAKVGIELPRSSGQQYNAGKK-TIPK--SEPQRGDLVFFGTGKGIS------HVGIY 71

                          90       100
                  ....*....|....*....|.
gi 503312836  343 IGNRRFIHSQGD--VHVSSLD 361
Cdd:pfam00877  72 LGNGQMLHASTGggVSISSLN 92
spr PRK10838
bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase;
263-383 4.00e-17

bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase;


Pssm-ID: 236773 [Multi-domain]  Cd Length: 190  Bit Score: 79.04  E-value: 4.00e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 263 GIPYLWAGTSSKGVDCSGFV-RTVLFMHDIIIPRDASQQAYTGRHIdiapDFSNLRPGDLIFFGRKATPElkervvHVGI 341
Cdd:PRK10838  79 GVRYRLGGSTKKGIDCSAFVqRTFREQFGLELPRSTYEQQEMGKSV----SRSKLRTGDLVLFRAGSTGR------HVGI 148

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 503312836 342 YIGNRRFIH---SQGdVHVSSLDpadelfDEYNLGRLLFASRVMP 383
Cdd:PRK10838 149 YIGNNQFVHastSSG-VIISSMN------EPYWKKRYNEARRVLS 186
PRK13914 PRK13914
invasion associated endopeptidase;
251-352 1.05e-12

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 69.45  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 251 AASIIRTAHTMMGIPYLWAGTSSKGVDCSGFVRTVLFMHDIIIPRDA-SQQAYTGRHIDiapdfSNLRPGDLIFFgrkat 329
Cdd:PRK13914 366 ASAIIAEAQKHLGKAYSWGGNGPTTFDCSGYTKYVFAKAGISLPRTSgAQYASTTRISE-----SQAKPGDLVFF----- 435

                         90       100
                 ....*....|....*....|...
gi 503312836 330 pELKERVVHVGIYIGNRRFIHSQ 352
Cdd:PRK13914 436 -DYGSGISHVGIYVGNGQMINAQ 457
SH3_3 pfam08239
Bacterial SH3 domain;
114-165 4.87e-11

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 57.64  E-value: 4.87e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 503312836  114 SVANLRAEPDFSSEMMTQGLMGMPIRVL--QRDGWYRIQTPDDYIAWVHRVGIH 165
Cdd:pfam08239   1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLeeQGGGWYKVRTYDGYEGWVSSSYLS 54
SH3_16 pfam18348
Bacterial dipeptidyl-peptidase Sh3 domain; This is the first of two N-terminal bacterial SH3 ...
 118-159 1.99e-10

Bacterial dipeptidyl-peptidase Sh3 domain; This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed.


Pssm-ID: 436429  Cd Length: 49  Bit Score: 55.59  E-value: 1.99e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 503312836  118 LRAEPDFSSEMMTQGLMGMPIRVL-QRDGWYRIQTP-DDYIAWV 159
Cdd:pfam18348   1 LRDSPDPDAELATQALFGEHLRVLeERDGWAWVQLCeDGYVGWL 44
YgiM COG3103
Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family ...
 106-232 2.03e-09

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: 55.13  E-value: 2.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 106 KTYGIINVSVANLRAEPDFSSEMMTQGLMGMPIRVLQRD-GWYRIQTPDDYIAWVHR--VGIHPVTGEELAAWNNaekiv 182
Cdd:COG3103    4 ETRYVVDADALNVRSGPGTSYRIVGTLPKGEKVTVLGRSgGWYKVRYSNGKTGWVSSryLTVTPSARERLPDELN----- 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 503312836 183 vtshygfVYSQPDQASQPVSDVVAGNRLKWDGAKGAFYKVTYpdGRRGYI 232
Cdd:COG3103   79 -------LRAGPSTSSEVLGLLPKGETVTVLKKSGGWFKVGY--RGTGWV 119
SH3 COG3807
SH3-like domain [Function unknown];
111-235 2.48e-08

SH3-like domain [Function unknown];


Pssm-ID: 443020 [Multi-domain]  Cd Length: 150  Bit Score: 52.60  E-value: 2.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503312836 111 INVSVANLRAEPDFSSE-MMTQGLMGMPIRVLQR-DGWYRIQTPDDYIAWVHrvgiHPVTGEELAAwnnaekiVVTSHYG 188
Cdd:COG3807   24 LKSDEVNLRDGPSTKYPiLWVYKRRGLPVEVIAEfGNWRRVRDPEGDEGWVH----QSLLSGRRTV-------IVTGDLA 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 503312836 189 FVYSQPDQASQPVSDVVAGNRLKWDGAKGAFYKVTyPDGRRGYISKS 235
Cdd:COG3807   93 NLRASPDENAAVVARLEPGVVLRLLECDGGWCKVR-ADGYKGWVRQS 138
SH3_3 pfam08239
Bacterial SH3 domain;
189-235 1.53e-05

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 42.23  E-value: 1.53e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 503312836  189 FVYSQPDQASQPVSDVVAGNRLKW-DGAKGAFYKVTYPDGRRGYISKS 235
Cdd:pfam08239   4 NVRSGPSTSSEVVGTLPKGEKVEVlEEQGGGWYKVRTYDGYEGWVSSS 51
YgiM COG3103
Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family ...
 177-235 3.39e-03

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: 37.02  E-value: 3.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 503312836 177 NAEKIVVTSHYGFVYSQPDQASQPVSDVVAGNRLKWDGAKGAFYKVTYPDGRRGYISKS 235
Cdd:COG3103    3 AETRYVVDADALNVRSGPGTSYRIVGTLPKGEKVTVLGRSGGWYKVRYSNGKTGWVSSR 61
SH3_4 pfam06347
Bacterial SH3 domain; SH3 (src Homology-3) domains are small protein modules containing ...
 116-161 7.82e-03

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: 34.63  E-value: 7.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 503312836  116 ANLRAEPDFSSEMMTQGLMGMPIRVLQ-RDGWYRIQTPDDYIAWVHR 161
Cdd:pfam06347   5 VNLRRGPSDKAAVAAYLEAGVPVRVVAcKDNWCRVRDADGAEGWIYK 51
 
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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