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Conserved domains on  [gi|2559423420|ref|WP_304761777|]
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VOC family protein [Sediminibacterium sp.]

Protein Classification

VOC family protein( domain architecture ID 10008083)

vicinal oxygen chelate (VOC) family protein uses a metal center to coordinate a substrate, intermediate, or transition state through vicinal oxygen atoms

CATH:  3.10.180.70
Gene Ontology:  GO:0046872|GO:0003824
PubMed:  21820381|11076500

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG3865 COG3865
Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General ...
 3-155 2.75e-61

Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General function prediction only];


:

Pssm-ID: 443074  Cd Length: 156  Bit Score: 185.74  E-value: 2.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   3 TQKITPSIWVETtDAKAVADYYLSIFKDGKLKEHHKY-TNPPEVGGGDFETAVIEIAGMELSILAAGPFQKFNESVSLVI 81
Cdd:COG3865     1 MQKITPCLWFDG-QAEEAAEFYVSVFPDSRITAVTRYpEDGPGGPAGSVLTVEFTLAGQPFMALNGGPLFKFNEAVSFQV 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2559423420  82 NTKDQDETDYYWDALIKnGGQESSCGWCKDKYGLSWQVVPVEYFSLINSADPMIKEKAMKNTMLQKKIILAELK 155
Cdd:COG3865    80 NCEDQAEVDRLWDALSA-GGEESQCGWLKDRFGLSWQIVPRRLGELLADPDPAKAQRAMQAMMQMKKIDIAALE 152
 
Name Accession Description Interval E-value
COG3865 COG3865
Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General ...
 3-155 2.75e-61

Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General function prediction only];


Pssm-ID: 443074  Cd Length: 156  Bit Score: 185.74  E-value: 2.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   3 TQKITPSIWVETtDAKAVADYYLSIFKDGKLKEHHKY-TNPPEVGGGDFETAVIEIAGMELSILAAGPFQKFNESVSLVI 81
Cdd:COG3865     1 MQKITPCLWFDG-QAEEAAEFYVSVFPDSRITAVTRYpEDGPGGPAGSVLTVEFTLAGQPFMALNGGPLFKFNEAVSFQV 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2559423420  82 NTKDQDETDYYWDALIKnGGQESSCGWCKDKYGLSWQVVPVEYFSLINSADPMIKEKAMKNTMLQKKIILAELK 155
Cdd:COG3865    80 NCEDQAEVDRLWDALSA-GGEESQCGWLKDRFGLSWQIVPRRLGELLADPDPAKAQRAMQAMMQMKKIDIAALE 152
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 4-120 4.87e-41

3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region approximately 100 residues long within a number of bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases (EC:2.1.1.64). Note that some family members contain more than one copy of this region, and that many members are hypothetical proteins.


Pssm-ID: 399756  Cd Length: 116  Bit Score: 133.20  E-value: 4.87e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   4 QKITPSIWVETtDAKAVADYYLSIFKDGKLKEHHKYTNPPEVGGGDFETAVIEIAGMELSILAAGPFQKFNESVSLVINT 83
Cdd:pfam06983   1 QKITPCLWFDG-QAEEAAEFYVSLFPNSEIGSVNRYPEDGPGKPGSVLTVEFTLNGQPFIALNGGPNFKFNEAVSFQVTC 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2559423420  84 KDQDETDYYWDALIKNGGQESSCGWCKDKYGLSWQVV 120
Cdd:pfam06983  80 KDQEEVDRYWNALSENGGPESQCGWLKDKFGVSWQIV 116
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 6-120 8.55e-28

Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to bleomycin resistance proteins, glyoxalase I, and type I extradiol dioxygenases.


Pssm-ID: 319899  Cd Length: 129  Bit Score: 100.04  E-value: 8.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   6 ITPSIWVeTTDAKAVADYYLSIFKDGKLKEHHKYTNPPEVGGGDFE----TAVIEIAGMELSILAAGPFQK--FNESVSL 79
Cdd:cd06588     1 ITPYLWF-NGNAEEALEFYAEVFPGGEILSLTRYGEGPPDFPEGDEgkvmHAEFTLGGQTLMASDDGPGFPftFGNAISL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2559423420  80 VINTKDQDETDYYWDALIKNGGQE---------SSCGWCKDKYGLSWQVV 120
Cdd:cd06588    80 SVDCDSQEEADRLFEKLSEGGEVLmplqetfwgARYGWVKDKFGVSWQIN 129
 
Name Accession Description Interval E-value
COG3865 COG3865
Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General ...
 3-155 2.75e-61

Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General function prediction only];


Pssm-ID: 443074  Cd Length: 156  Bit Score: 185.74  E-value: 2.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   3 TQKITPSIWVETtDAKAVADYYLSIFKDGKLKEHHKY-TNPPEVGGGDFETAVIEIAGMELSILAAGPFQKFNESVSLVI 81
Cdd:COG3865     1 MQKITPCLWFDG-QAEEAAEFYVSVFPDSRITAVTRYpEDGPGGPAGSVLTVEFTLAGQPFMALNGGPLFKFNEAVSFQV 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2559423420  82 NTKDQDETDYYWDALIKnGGQESSCGWCKDKYGLSWQVVPVEYFSLINSADPMIKEKAMKNTMLQKKIILAELK 155
Cdd:COG3865    80 NCEDQAEVDRLWDALSA-GGEESQCGWLKDRFGLSWQIVPRRLGELLADPDPAKAQRAMQAMMQMKKIDIAALE 152
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 4-120 4.87e-41

3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region approximately 100 residues long within a number of bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases (EC:2.1.1.64). Note that some family members contain more than one copy of this region, and that many members are hypothetical proteins.


Pssm-ID: 399756  Cd Length: 116  Bit Score: 133.20  E-value: 4.87e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   4 QKITPSIWVETtDAKAVADYYLSIFKDGKLKEHHKYTNPPEVGGGDFETAVIEIAGMELSILAAGPFQKFNESVSLVINT 83
Cdd:pfam06983   1 QKITPCLWFDG-QAEEAAEFYVSLFPNSEIGSVNRYPEDGPGKPGSVLTVEFTLNGQPFIALNGGPNFKFNEAVSFQVTC 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2559423420  84 KDQDETDYYWDALIKNGGQESSCGWCKDKYGLSWQVV 120
Cdd:pfam06983  80 KDQEEVDRYWNALSENGGPESQCGWLKDKFGVSWQIV 116
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 6-120 8.55e-28

Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to bleomycin resistance proteins, glyoxalase I, and type I extradiol dioxygenases.


Pssm-ID: 319899  Cd Length: 129  Bit Score: 100.04  E-value: 8.55e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   6 ITPSIWVeTTDAKAVADYYLSIFKDGKLKEHHKYTNPPEVGGGDFE----TAVIEIAGMELSILAAGPFQK--FNESVSL 79
Cdd:cd06588     1 ITPYLWF-NGNAEEALEFYAEVFPGGEILSLTRYGEGPPDFPEGDEgkvmHAEFTLGGQTLMASDDGPGFPftFGNAISL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2559423420  80 VINTKDQDETDYYWDALIKNGGQE---------SSCGWCKDKYGLSWQVV 120
Cdd:cd06588    80 SVDCDSQEEADRLFEKLSEGGEVLmplqetfwgARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
5-119 2.83e-03

Zn-dependent glyoxalase, PhnB family [Energy production and conversion];


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 35.60  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559423420   5 KITPSIWVEttDAKAVADYYLSIFkdGkLKEHHKYTNPpevgGGDFETAVIEIAGMELSILAAGPFQKFNE--SVSLVIN 82
Cdd:COG2764     1 SVTPYLVVD--DAEEALEFYEDVF--G-FEVVFRMTDP----DGKIMHAELRIGGSVLMLSDAPPDSPAAEgnGVSLSLY 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2559423420  83 TkdqDETDYYWDALIKNGGQE----------SSCGWCKDKYGLSWQV 119
Cdd:COG2764    72 V---DDVDALFARLVAAGATVvmplqdtfwgDRFGMVRDPFGVLWMI 115
 
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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