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Conserved domains on  [gi|1173748894|gb|ARE86416|]
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Putative L,D-transpeptidase YkuD [Clostridium formicaceticum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 88-196 8.70e-44

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: 144.76  E-value: 8.70e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  88 RIEVDLERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIQKTRNP------------GGPFGTRWMRINVPWGGYGI 155
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPtwtgppsippgpYNPLGPYALRLSGPGSGIGI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1173748894 156 HGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGTPVKIT 196
Cdd:cd16913    81 HGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 9-73 7.79e-23

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 88.81  E-value: 7.79e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1173748894   9 RLLDPYMEGPDVMHVQERLTTLGFYEGVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAIG 73
Cdd:COG3409     4 PTLRLGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALR 68
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 200-268 5.12e-17

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 73.40  E-value: 5.12e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1173748894 200 FSGRVLEIGVEpGPDVFEVKAILTELGYYRDEIDGIYDEAAAEAVRSFQRDFNIIADGIVGVDTYNELQ 268
Cdd:COG3409     1 ASAPTLRLGDS-GEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALR 68
 
Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 88-196 8.70e-44

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: 144.76  E-value: 8.70e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  88 RIEVDLERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIQKTRNP------------GGPFGTRWMRINVPWGGYGI 155
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPtwtgppsippgpYNPLGPYALRLSGPGSGIGI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1173748894 156 HGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGTPVKIT 196
Cdd:cd16913    81 HGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
89-195 8.42e-43

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 142.31  E-value: 8.42e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  89 IEVDLERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIQKTRNP----------------GGPFGTRWMRINvpWGG 152
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAENPtwtppaempagmpggpDNPLGPYALYLS--DGG 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1173748894 153 YGIHGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGTPVKI 195
Cdd:COG1376    79 YGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 9-73 7.79e-23

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 88.81  E-value: 7.79e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1173748894   9 RLLDPYMEGPDVMHVQERLTTLGFYEGVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAIG 73
Cdd:COG3409     4 PTLRLGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALR 68
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 87-195 4.81e-22

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: 87.40  E-value: 4.81e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  87 YRIEVDL-ERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIqktrnpggpfgtrwmrinvpwggyGIHGTDAP--ES 163
Cdd:pfam03734   2 RYIVVDLsEQRLLYLYENGGLVLRYPVSVGRGDGPTPTGTFRII------------------------YIHDTGTPdlFG 57

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1173748894 164 IGTAASHGCIRMFNEDVNALYDIVPLGTPVKI 195
Cdd:pfam03734  58 LGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 16-72 2.21e-19

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 79.48  E-value: 2.21e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1173748894  16 EGPDVMHVQERLTTLGFYEGVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAI 72
Cdd:pfam01471   1 SGEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 200-268 5.12e-17

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 73.40  E-value: 5.12e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1173748894 200 FSGRVLEIGVEpGPDVFEVKAILTELGYYRDEIDGIYDEAAAEAVRSFQRDFNIIADGIVGVDTYNELQ 268
Cdd:COG3409     1 ASAPTLRLGDS-GEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALR 68
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 212-267 2.34e-14

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 66.00  E-value: 2.34e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1173748894 212 GPDVFEVKAILTELGYYRDEIDGIYDEAAAEAVRSFQRDFNIIADGIVGVDTYNEL 267
Cdd:pfam01471   2 GEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 113-207 6.47e-11

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 61.59  E-value: 6.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894 113 AVGKPSTPT-PTGdwqiiqkTRNPGGPFGTRWMRInvpwggYGIHGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGT 191
Cdd:PRK10260  163 AAGEPLPAVvPAG-------PDNPMGLYALYIGRL------YAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGT 229

                          90       100
                  ....*....|....*....|...
gi 1173748894 192 -------PVKITGEVFSGRVLEI 207
Cdd:PRK10260  230 rvqfidePVKATTEPDGSRYIEV 252
PRK10594 PRK10594
murein L,D-transpeptidase; Provisional
 35-77 3.77e-05

murein L,D-transpeptidase; Provisional


Pssm-ID: 236723 [Multi-domain]  Cd Length: 608  Bit Score: 44.73  E-value: 3.77e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1173748894  35 GVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAIGLDPA 77
Cdd:PRK10594  303 PAVRAAYDNELVEAVKRFQAWQGLGADGVIGPRTRDWLNVTPA 345
His_Ser_Rich TIGR03979
His-Xaa-Ser repeat protein HxsA; Members of this protein share two defining regions. One is a ...
 215-267 8.42e-05

His-Xaa-Ser repeat protein HxsA; Members of this protein share two defining regions. One is a histidine/serine-rich cluster, typically H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in the context of a pair of radical SAM proteins, HxsB and HxsC, and a fourth protein HxsD. The system is predicted to perform peptide modifications, likely in the His-Xaa-Ser region, to produce some uncharacterized natural product.


Pssm-ID: 274897 [Multi-domain]  Cd Length: 186  Bit Score: 42.56  E-value: 8.42e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1173748894 215 VFEVKAILTELGYYRDEIDGIYDEAAAEAVRSFQRDFNIIADGIVGVDTYNEL 267
Cdd:TIGR03979 130 VIRVQTALVVFGYYGGIIDGVMGEATRVALKRYQMDNGLPVTGTIDTQTLNAL 182
 
Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 88-196 8.70e-44

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: 144.76  E-value: 8.70e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  88 RIEVDLERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIQKTRNP------------GGPFGTRWMRINVPWGGYGI 155
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPtwtgppsippgpYNPLGPYALRLSGPGSGIGI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1173748894 156 HGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGTPVKIT 196
Cdd:cd16913    81 HGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
89-195 8.42e-43

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 142.31  E-value: 8.42e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  89 IEVDLERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIQKTRNP----------------GGPFGTRWMRINvpWGG 152
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAENPtwtppaempagmpggpDNPLGPYALYLS--DGG 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1173748894 153 YGIHGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGTPVKI 195
Cdd:COG1376    79 YGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 9-73 7.79e-23

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 88.81  E-value: 7.79e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1173748894   9 RLLDPYMEGPDVMHVQERLTTLGFYEGVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAIG 73
Cdd:COG3409     4 PTLRLGDSGEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALR 68
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 87-195 4.81e-22

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: 87.40  E-value: 4.81e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  87 YRIEVDL-ERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIqktrnpggpfgtrwmrinvpwggyGIHGTDAP--ES 163
Cdd:pfam03734   2 RYIVVDLsEQRLLYLYENGGLVLRYPVSVGRGDGPTPTGTFRII------------------------YIHDTGTPdlFG 57

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1173748894 164 IGTAASHGCIRMFNEDVNALYDIVPLGTPVKI 195
Cdd:pfam03734  58 LGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 16-72 2.21e-19

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 79.48  E-value: 2.21e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1173748894  16 EGPDVMHVQERLTTLGFYEGVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAI 72
Cdd:pfam01471   1 SGEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
PGRP COG3409
Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope ...
 200-268 5.12e-17

Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442635 [Multi-domain]  Cd Length: 69  Bit Score: 73.40  E-value: 5.12e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1173748894 200 FSGRVLEIGVEpGPDVFEVKAILTELGYYRDEIDGIYDEAAAEAVRSFQRDFNIIADGIVGVDTYNELQ 268
Cdd:COG3409     1 ASAPTLRLGDS-GEDVRELQQRLNALGYYPGPVDGIFGPATEAAVRAFQRANGLPVDGIVGPATWAALR 68
YcbB COG2989
Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];
9-122 3.78e-15

Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442228 [Multi-domain]  Cd Length: 529  Bit Score: 74.98  E-value: 3.78e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894   9 RLLDPYMEGPDVMHVQERLTTLGFY---EGVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAIGldpavqfpVPPE 85
Cdd:COG2989   202 PTLRPGDSDPRVPALRERLAALGDLpadAPSDSDVYDAELVEAVKRFQARHGLKADGVIGPATLAALN--------VSPE 273

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1173748894  86 GY--RIEVDLERKILTLKQFSE---IIN----------------TYPVAVGKPSTPTP 122
Cdd:COG2989   274 ERirQLALNLERLRWLPRDLGDryiLVNipdfrleyvengkvvlSMRVIVGKPDRQTP 331
PG_binding_1 pfam01471
Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This ...
 212-267 2.34e-14

Putative peptidoglycan binding domain; This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally.


Pssm-ID: 460223 [Multi-domain]  Cd Length: 57  Bit Score: 66.00  E-value: 2.34e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1173748894 212 GPDVFEVKAILTELGYYRDEIDGIYDEAAAEAVRSFQRDFNIIADGIVGVDTYNEL 267
Cdd:pfam01471   2 GEDVKELQRYLNRLGYYPGPVDGYFGPSTEAAVKAFQRAFGLPVDGIVDPETLAAL 57
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 113-207 6.47e-11

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 61.59  E-value: 6.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894 113 AVGKPSTPT-PTGdwqiiqkTRNPGGPFGTRWMRInvpwggYGIHGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGT 191
Cdd:PRK10260  163 AAGEPLPAVvPAG-------PDNPMGLYALYIGRL------YAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGT 229

                          90       100
                  ....*....|....*....|...
gi 1173748894 192 -------PVKITGEVFSGRVLEI 207
Cdd:PRK10260  230 rvqfidePVKATTEPDGSRYIEV 252
PRK06132 PRK06132
hypothetical protein; Provisional
 82-199 1.14e-09

hypothetical protein; Provisional


Pssm-ID: 235709 [Multi-domain]  Cd Length: 359  Bit Score: 58.15  E-value: 1.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894  82 VPPEGY-RIEVDLERKILTLKQFSEIINTYPVAVGKPSTPTPTGDWQIIQKTR--------NPGGPFgtrwM-RINvpWG 151
Cdd:PRK06132   55 AKPQGPlVIVVSLDEQRLYVYDNGILIAVSTVSTGKRGHETPTGVFSILQKDKdhrsniysNAPMPY----MqRLT--WS 128

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1173748894 152 GYGIHGTDAPesiGTAASHGCIRMFNEDVNALYDIVPLGTPVKIT-GEV 199
Cdd:PRK06132  129 GIALHAGNLP---GYPASHGCVRLPSAFAKKLYGWTRMGTTVIISdGEV 174
YcbB COG2989
Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];
197-267 6.64e-09

Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442228 [Multi-domain]  Cd Length: 529  Bit Score: 56.10  E-value: 6.64e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1173748894 197 GEVFSGRVLEIGVEpGPDVFEVKAILTELGYY-RDEIDG--IYDEAAAEAVRSFQRDFNIIADGIVGVDTYNEL 267
Cdd:COG2989   196 PPVPAGPTLRPGDS-DPRVPALRERLAALGDLpADAPSDsdVYDAELVEAVKRFQARHGLKADGVIGPATLAAL 268
PRK10190 PRK10190
L,D-transpeptidase; Provisional
 153-207 2.61e-08

L,D-transpeptidase; Provisional


Pssm-ID: 182294 [Multi-domain]  Cd Length: 310  Bit Score: 54.10  E-value: 2.61e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1173748894 153 YGIHGTDAPESIGTAASHGCIRMFNEDVNALYDIVPLGT-------PVKITGEVFSGRVLEI 207
Cdd:PRK10190  188 YAIHGTNANFGIGLRVSQGCIRLRNDDIKYLFDNVPVGTrvqiidqPVKYTTEPDGSRWLEV 249
PRK12472 PRK12472
hypothetical protein; Provisional
 111-196 4.78e-07

hypothetical protein; Provisional


Pssm-ID: 237110 [Multi-domain]  Cd Length: 508  Bit Score: 50.64  E-value: 4.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173748894 111 PVAVGKPSTPTPTGDWQIIQKTRNPGGP-FGTRWM----RINvpWGGYGIHGTDAPesiGTAASHGCIRMFNEDVNALYD 185
Cdd:PRK12472   78 PVSTGTTGRETPAGVFAIVEKDKDHHSTmYDDAWMpnmqRIT--WNGIALHGGPLP---GYAASHGCVRMPYGFAEKLFD 152

                          90
                  ....*....|.
gi 1173748894 186 IVPLGTPVKIT 196
Cdd:PRK12472  153 KTRIGMRVIVS 163
PRK10594 PRK10594
murein L,D-transpeptidase; Provisional
 35-77 3.77e-05

murein L,D-transpeptidase; Provisional


Pssm-ID: 236723 [Multi-domain]  Cd Length: 608  Bit Score: 44.73  E-value: 3.77e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1173748894  35 GVVDGIYDDEVFEAVRSFQTDYGLNPDGIVGPDTWNAIGLDPA 77
Cdd:PRK10594  303 PAVRAAYDNELVEAVKRFQAWQGLGADGVIGPRTRDWLNVTPA 345
His_Ser_Rich TIGR03979
His-Xaa-Ser repeat protein HxsA; Members of this protein share two defining regions. One is a ...
 215-267 8.42e-05

His-Xaa-Ser repeat protein HxsA; Members of this protein share two defining regions. One is a histidine/serine-rich cluster, typically H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in the context of a pair of radical SAM proteins, HxsB and HxsC, and a fourth protein HxsD. The system is predicted to perform peptide modifications, likely in the His-Xaa-Ser region, to produce some uncharacterized natural product.


Pssm-ID: 274897 [Multi-domain]  Cd Length: 186  Bit Score: 42.56  E-value: 8.42e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1173748894 215 VFEVKAILTELGYYRDEIDGIYDEAAAEAVRSFQRDFNIIADGIVGVDTYNEL 267
Cdd:TIGR03979 130 VIRVQTALVVFGYYGGIIDGVMGEATRVALKRYQMDNGLPVTGTIDTQTLNAL 182
 
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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