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Conserved domains on  [gi|2644503109|ref|WP_323458012|]
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Ig-like domain-containing protein [Cutibacterium granulosum]

Protein Classification

L,D-transpeptidase( domain architecture ID 15739075)

L,D-transpeptidase catalyzes the formation of 3->3 peptidoglycan cross-links

CATH:  2.40.440.10|2.60.40.3710
EC:  2.3.2.-
Gene Ontology:  GO:0018104|GO:0071972
PubMed:  18266857
SCOP:  4002015

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Big_10 super family cl40247
Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with ...
 53-236 1.16e-40

Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with transpeptidase domains.


The actual alignment was detected with superfamily member pfam17964:

Pssm-ID: 465591 [Multi-domain]  Cd Length: 182  Bit Score: 141.99  E-value: 1.16e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109  53 TEVEPGDSLTFTVTNGSVDKITVTNADKEDVEGTFTDG--VWKPKHPFRPSRSYEVHTTLANADPSlpaPKPLVTSISTV 130
Cdd:pfam17964   2 TGVNPGTPVTVTVAGGTLTDVTVTDSDGKEVPGKLSADgtSWTSTEPLGYGTTYTVTATAKGAGGK---ATTQTSSFTTV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 131 K-GEGNAGNILYEDMDDAGIGMPVIILFNHDVVDkdkRAAIEKAMTIEVSPEQEGSWGWLDGTHLMWRPKQYWKPGTKVS 209
Cdd:pfam17964  79 SpANTTSGTLTPLDGSTVGVGMPISINFDKPVTD---KAAVEKAITVTTSPAVEGAWHWFGDQRVDWRPKEYWPPGTKVT 155

                         170       180
                  ....*....|....*....|....*..
gi 2644503109 210 VKGDFGGLKTASNRWLLNNLTGKFSIG 236
Cdd:pfam17964 156 VDARLYGVDLGDGVYGQQDRTVTFTIG 182
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
241-362 1.42e-35

Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 126.51  E-value: 1.42e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 241 VKISTSDHRLDVFIDGKKARSMPCTTGKSGFITRSGTKVIIEREADKVMDASTIGISPGSSEYYNLEVKWALRITYTGEF 320
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAENPTWTPPAEMPAGMPGGPDNPLGPYALYLSDGGYG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2644503109 321 IHAAPWSSrSQGRaNVSHGCVGLATDDAKWLFKTCRAGDIVE 362
Cdd:COG1376    81 IHGTPWPS-SIGR-NVSHGCIRLSNEDAKWLYDRVPVGTPVV 120
 
Name Accession Description Interval E-value
Big_10 pfam17964
Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with ...
 53-236 1.16e-40

Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with transpeptidase domains.


Pssm-ID: 465591 [Multi-domain]  Cd Length: 182  Bit Score: 141.99  E-value: 1.16e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109  53 TEVEPGDSLTFTVTNGSVDKITVTNADKEDVEGTFTDG--VWKPKHPFRPSRSYEVHTTLANADPSlpaPKPLVTSISTV 130
Cdd:pfam17964   2 TGVNPGTPVTVTVAGGTLTDVTVTDSDGKEVPGKLSADgtSWTSTEPLGYGTTYTVTATAKGAGGK---ATTQTSSFTTV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 131 K-GEGNAGNILYEDMDDAGIGMPVIILFNHDVVDkdkRAAIEKAMTIEVSPEQEGSWGWLDGTHLMWRPKQYWKPGTKVS 209
Cdd:pfam17964  79 SpANTTSGTLTPLDGSTVGVGMPISINFDKPVTD---KAAVEKAITVTTSPAVEGAWHWFGDQRVDWRPKEYWPPGTKVT 155

                         170       180
                  ....*....|....*....|....*..
gi 2644503109 210 VKGDFGGLKTASNRWLLNNLTGKFSIG 236
Cdd:pfam17964 156 VDARLYGVDLGDGVYGQQDRTVTFTIG 182
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
241-362 1.42e-35

Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 126.51  E-value: 1.42e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 241 VKISTSDHRLDVFIDGKKARSMPCTTGKSGFITRSGTKVIIEREADKVMDASTIGISPGSSEYYNLEVKWALRITYTGEF 320
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAENPTWTPPAEMPAGMPGGPDNPLGPYALYLSDGGYG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2644503109 321 IHAAPWSSrSQGRaNVSHGCVGLATDDAKWLFKTCRAGDIVE 362
Cdd:COG1376    81 IHGTPWPS-SIGR-NVSHGCIRLSNEDAKWLYDRVPVGTPVV 120
LDT_IgD_like_2 cd13432
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 148-236 1.11e-33

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the repeat adjacent to the catalytic domain.


Pssm-ID: 240447  Cd Length: 99  Bit Score: 120.70  E-value: 1.11e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 148 GIGMPVIILFNHDVVDkdkRAAIEKAMTIEVSPEQEGSWGWLDGTHLMWRPKQYWKPGTKVSVKGDFGGLKTASNRWLLN 227
Cdd:cd13432    14 GVGMPVIVTFDEPVTD---RAAVEKALKVTTSPPVEGAWYWLSDREVHWRPKEYWPPGTKVTVDANLYGVDLGDGVYGQE 90


                  ....*....
gi 2644503109 228 NLTGKFSIG 236
Cdd:cd13432    91 DRSTTFTIG 99
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 240-362 2.90e-28

L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.


Pssm-ID: 341130 [Multi-domain]  Cd Length: 121  Bit Score: 107.39  E-value: 2.90e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 240 VVKISTSDHRLDVFIDGKKARSMPCTTGKSGFITRSGTKVIIEREADKVMDastiGISPGSSEYYNLEVKWALRITY--T 317
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPTWT----GPPSIPPGPYNPLGPYALRLSGpgS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2644503109 318 GEFIHAAPWssRSQGRANVSHGCVGLATDDAKWLFKTCRAGDIVE 362
Cdd:cd16913    77 GIGIHGTPW--PSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVV 119
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 238-362 3.14e-15

L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.


Pssm-ID: 461031 [Multi-domain]  Cd Length: 89  Bit Score: 70.46  E-value: 3.14e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 238 SRVVKISTSDHRLD-VFIDGKKARSMPCTTGKSGFITRSGTKVIIereadkvmdastigispgsseyynlevkwalrity 316
Cdd:pfam03734   1 DRYIVVDLSEQRLLyLYENGGLVLRYPVSVGRGDGPTPTGTFRII----------------------------------- 45

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2644503109 317 tgeFIHAAPWSSRSQGRANVSHGCVGLATDDAKWLFKTCRAGDIVE 362
Cdd:pfam03734  46 ---YIHDTGTPDLFGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVV 88
 
Name Accession Description Interval E-value
Big_10 pfam17964
Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with ...
 53-236 1.16e-40

Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with transpeptidase domains.


Pssm-ID: 465591 [Multi-domain]  Cd Length: 182  Bit Score: 141.99  E-value: 1.16e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109  53 TEVEPGDSLTFTVTNGSVDKITVTNADKEDVEGTFTDG--VWKPKHPFRPSRSYEVHTTLANADPSlpaPKPLVTSISTV 130
Cdd:pfam17964   2 TGVNPGTPVTVTVAGGTLTDVTVTDSDGKEVPGKLSADgtSWTSTEPLGYGTTYTVTATAKGAGGK---ATTQTSSFTTV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 131 K-GEGNAGNILYEDMDDAGIGMPVIILFNHDVVDkdkRAAIEKAMTIEVSPEQEGSWGWLDGTHLMWRPKQYWKPGTKVS 209
Cdd:pfam17964  79 SpANTTSGTLTPLDGSTVGVGMPISINFDKPVTD---KAAVEKAITVTTSPAVEGAWHWFGDQRVDWRPKEYWPPGTKVT 155

                         170       180
                  ....*....|....*....|....*..
gi 2644503109 210 VKGDFGGLKTASNRWLLNNLTGKFSIG 236
Cdd:pfam17964 156 VDARLYGVDLGDGVYGQQDRTVTFTIG 182
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
241-362 1.42e-35

Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 126.51  E-value: 1.42e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 241 VKISTSDHRLDVFIDGKKARSMPCTTGKSGFITRSGTKVIIEREADKVMDASTIGISPGSSEYYNLEVKWALRITYTGEF 320
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAENPTWTPPAEMPAGMPGGPDNPLGPYALYLSDGGYG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2644503109 321 IHAAPWSSrSQGRaNVSHGCVGLATDDAKWLFKTCRAGDIVE 362
Cdd:COG1376    81 IHGTPWPS-SIGR-NVSHGCIRLSNEDAKWLYDRVPVGTPVV 120
LDT_IgD_like_2 cd13432
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 148-236 1.11e-33

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the repeat adjacent to the catalytic domain.


Pssm-ID: 240447  Cd Length: 99  Bit Score: 120.70  E-value: 1.11e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 148 GIGMPVIILFNHDVVDkdkRAAIEKAMTIEVSPEQEGSWGWLDGTHLMWRPKQYWKPGTKVSVKGDFGGLKTASNRWLLN 227
Cdd:cd13432    14 GVGMPVIVTFDEPVTD---RAAVEKALKVTTSPPVEGAWYWLSDREVHWRPKEYWPPGTKVTVDANLYGVDLGDGVYGQE 90


                  ....*....
gi 2644503109 228 NLTGKFSIG 236
Cdd:cd13432    91 DRSTTFTIG 99
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 240-362 2.90e-28

L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.


Pssm-ID: 341130 [Multi-domain]  Cd Length: 121  Bit Score: 107.39  E-value: 2.90e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 240 VVKISTSDHRLDVFIDGKKARSMPCTTGKSGFITRSGTKVIIEREADKVMDastiGISPGSSEYYNLEVKWALRITY--T 317
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPTWT----GPPSIPPGPYNPLGPYALRLSGpgS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2644503109 318 GEFIHAAPWssRSQGRANVSHGCVGLATDDAKWLFKTCRAGDIVE 362
Cdd:cd16913    77 GIGIHGTPW--PSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVV 119
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 238-362 3.14e-15

L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.


Pssm-ID: 461031 [Multi-domain]  Cd Length: 89  Bit Score: 70.46  E-value: 3.14e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 238 SRVVKISTSDHRLD-VFIDGKKARSMPCTTGKSGFITRSGTKVIIereadkvmdastigispgsseyynlevkwalrity 316
Cdd:pfam03734   1 DRYIVVDLSEQRLLyLYENGGLVLRYPVSVGRGDGPTPTGTFRII----------------------------------- 45

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2644503109 317 tgeFIHAAPWSSRSQGRANVSHGCVGLATDDAKWLFKTCRAGDIVE 362
Cdd:pfam03734  46 ---YIHDTGTPDLFGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVV 88
LDT_IgD_like cd13430
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 148-217 1.50e-12

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain.


Pssm-ID: 240445  Cd Length: 98  Bit Score: 63.12  E-value: 1.50e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2644503109 148 GIGMPVIILFNHDVVDkdkRAAIEKAMTIEVSPEQEGSWGWL-DGTHLMWRPKQYWKPGTKVSVKGDFGGL 217
Cdd:cd13430    13 GVGAPVAIRFDENIAD---RGAAEKAITITTDPPVEGAFYWLpDGRRVRWRPEHFWKPGTAVDVAANTYGL 80
LDT_IgD_like_1 cd13431
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 115-219 8.11e-10

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the first (N-terminal) repeat in LdtMt2 and related proteins.


Pssm-ID: 240446  Cd Length: 95  Bit Score: 55.40  E-value: 8.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2644503109 115 PSLPAPKPLVTsISTVKGEGnagnilyedmddAGIGMPVIILFNHDVVDkdkRAAIEKAMTIEVSPEQEGSWGWLDGTHL 194
Cdd:cd13431     2 PAPPLPVPVAT-VSPADGAV------------VGVAHPVVVTFADPVAD---RAAAENAIGITVAGPVAGGFSWTDDEPL 65

                          90       100
                  ....*....|....*....|....*
gi 2644503109 195 MWRPKQYWKPGTKVSVKGdfGGLKT 219
Cdd:cd13431    66 GWTPTYFWPAHATVTVGA--GGTRT 88
 
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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