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Conserved domains on  [gi|1473559321|ref|WP_118011511|]
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YdcF family protein [Holdemanella biformis]

Protein Classification

YdcF family protein( domain architecture ID 10155978)

YdcF family protein is a DUF218 domain-containing protein; similar to Streptomyces coelicolor uncharacterized protein SCO4629

CATH:  1.10.3620.10

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YdcF-like cd06259
YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found ...
 30-141 1.17e-24

YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.


:

Pssm-ID: 99750  Cd Length: 150  Bit Score: 93.53  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473559321  30 YALLLGCPAHDDGTMSSSQiKRCDLAIKAYQQNLYDTLIISGSNVKNEFI-EAKVMHAYIQnKMDIPT---ILETNARNT 105
Cdd:cd06259     2 AIVVLGGGVNGDGPSPILA-ERLDAAAELYRAGPAPKLIVSGGQGPGEGYsEAEAMARYLI-ELGVPAeaiLLEDRSTNT 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1473559321 106 FENFKFSKDIIQKQD---VLILTSQTHAKRACAIARQFF 141
Cdd:cd06259    80 YENARFSAELLRERGirsVLLVTSAYHMPRALLIFRKAG 118
 
Name Accession Description Interval E-value
YdcF-like cd06259
YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found ...
 30-141 1.17e-24

YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.


Pssm-ID: 99750  Cd Length: 150  Bit Score: 93.53  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473559321  30 YALLLGCPAHDDGTMSSSQiKRCDLAIKAYQQNLYDTLIISGSNVKNEFI-EAKVMHAYIQnKMDIPT---ILETNARNT 105
Cdd:cd06259     2 AIVVLGGGVNGDGPSPILA-ERLDAAAELYRAGPAPKLIVSGGQGPGEGYsEAEAMARYLI-ELGVPAeaiLLEDRSTNT 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1473559321 106 FENFKFSKDIIQKQD---VLILTSQTHAKRACAIARQFF 141
Cdd:cd06259    80 YENARFSAELLRERGirsVLLVTSAYHMPRALLIFRKAG 118
ElyC COG1434
Lipid carrier protein ElyC involved in cell wall biogenesis, DUF218 family [Cell wall/membrane ...
 7-140 8.87e-22

Lipid carrier protein ElyC involved in cell wall biogenesis, DUF218 family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441043  Cd Length: 212  Bit Score: 87.77  E-value: 8.87e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473559321   7 ILILACIYIYFFPFI-----------PKRKKHYTYALLLGCpAHDDGTMSSSQIKRCDLAIKAYQQNLYDTLIISGSNVK 75
Cdd:COG1434    18 LLLLALLLLLLLSPVgfwllrpleryADPPQPADAIVVLGG-GVYDGRPSPVLLERLDAAARLYRQGPAPRIIVSGGQGP 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1473559321  76 NEFI-EAKVMHAYIQnKMDIP---TILETNARNTFENFKFSKDIIQKQD---VLILTSQTHAKRACAIARQF 140
Cdd:COG1434    97 GEGVsEAEVMARYLL-ALGVPaerILLEDRSRNTWENARFSAALLRERGirrVILVTSAYHMPRALALFRRA 167
DUF218 pfam02698
DUF218 domain; This large family of proteins contains several highly conserved charged amino ...
 30-145 1.79e-18

DUF218 domain; This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA, which is involved in Vancomycin resistance. This protein may be involved in murein synthesis.


Pssm-ID: 460654  Cd Length: 138  Bit Score: 76.91  E-value: 1.79e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473559321  30 YALLLGCpahddgTMSSSQIKRCDLAIKAYQQNLYdtLIISG-SNVKNEFIEAKVMHAYIQnKMDIPT---ILETNARNT 105
Cdd:pfam02698   2 AIVVLGA------ALSPVLAARLDAAAELYREGPP--IIVSGgQGGGEPYSEAEAMARYLL-ELGVPEeriILEDRSRNT 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1473559321 106 FENFKFSKDIIQK--QDVLILTSQTHAKRACAIARQFFSDYG 145
Cdd:pfam02698  73 YENARFSAELLKEriRRILLVTSAFHMPRALLLFRRAGLDVG 114
 
Name Accession Description Interval E-value
YdcF-like cd06259
YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found ...
 30-141 1.17e-24

YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis.


Pssm-ID: 99750  Cd Length: 150  Bit Score: 93.53  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473559321  30 YALLLGCPAHDDGTMSSSQiKRCDLAIKAYQQNLYDTLIISGSNVKNEFI-EAKVMHAYIQnKMDIPT---ILETNARNT 105
Cdd:cd06259     2 AIVVLGGGVNGDGPSPILA-ERLDAAAELYRAGPAPKLIVSGGQGPGEGYsEAEAMARYLI-ELGVPAeaiLLEDRSTNT 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1473559321 106 FENFKFSKDIIQKQD---VLILTSQTHAKRACAIARQFF 141
Cdd:cd06259    80 YENARFSAELLRERGirsVLLVTSAYHMPRALLIFRKAG 118
ElyC COG1434
Lipid carrier protein ElyC involved in cell wall biogenesis, DUF218 family [Cell wall/membrane ...
 7-140 8.87e-22

Lipid carrier protein ElyC involved in cell wall biogenesis, DUF218 family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 441043  Cd Length: 212  Bit Score: 87.77  E-value: 8.87e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473559321   7 ILILACIYIYFFPFI-----------PKRKKHYTYALLLGCpAHDDGTMSSSQIKRCDLAIKAYQQNLYDTLIISGSNVK 75
Cdd:COG1434    18 LLLLALLLLLLLSPVgfwllrpleryADPPQPADAIVVLGG-GVYDGRPSPVLLERLDAAARLYRQGPAPRIIVSGGQGP 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1473559321  76 NEFI-EAKVMHAYIQnKMDIP---TILETNARNTFENFKFSKDIIQKQD---VLILTSQTHAKRACAIARQF 140
Cdd:COG1434    97 GEGVsEAEVMARYLL-ALGVPaerILLEDRSRNTWENARFSAALLRERGirrVILVTSAYHMPRALALFRRA 167
DUF218 pfam02698
DUF218 domain; This large family of proteins contains several highly conserved charged amino ...
 30-145 1.79e-18

DUF218 domain; This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA, which is involved in Vancomycin resistance. This protein may be involved in murein synthesis.


Pssm-ID: 460654  Cd Length: 138  Bit Score: 76.91  E-value: 1.79e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473559321  30 YALLLGCpahddgTMSSSQIKRCDLAIKAYQQNLYdtLIISG-SNVKNEFIEAKVMHAYIQnKMDIPT---ILETNARNT 105
Cdd:pfam02698   2 AIVVLGA------ALSPVLAARLDAAAELYREGPP--IIVSGgQGGGEPYSEAEAMARYLL-ELGVPEeriILEDRSRNT 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1473559321 106 FENFKFSKDIIQK--QDVLILTSQTHAKRACAIARQFFSDYG 145
Cdd:pfam02698  73 YENARFSAELLKEriRRILLVTSAFHMPRALLLFRRAGLDVG 114
 
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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