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Conserved domains on  [gi|500336228|gb|EOO55116|]
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PhnB protein [Bacillus cereus BAG1X2-2]

Protein Classification

VOC family protein( domain architecture ID 10159541)

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

CATH:  3.10.180.10
PubMed:  21820381

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 5-136 3.07e-47

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: 148.96  E-value: 3.07e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   5 INPYLVLDGSGQEAVQFYKEAL-DAKVEVMQTFGDMPENPeypiPAEAKERVLHATLKVGNTDLMISDTFPGQGHAIGSQ 83
Cdd:cd06588    1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPPDF----PEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 500336228  84 VTIAIQISNAEKAKEVFDKLQEGGEVIMPLQETFWSPAYGQVKDKFNIEWQIT 136
Cdd:cd06588   77 ISLSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
 
Name Accession Description Interval E-value
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 5-136 3.07e-47

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: 148.96  E-value: 3.07e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   5 INPYLVLDGSGQEAVQFYKEAL-DAKVEVMQTFGDMPENPeypiPAEAKERVLHATLKVGNTDLMISDTFPGQGHAIGSQ 83
Cdd:cd06588    1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPPDF----PEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 500336228  84 VTIAIQISNAEKAKEVFDKLQEGGEVIMPLQETFWSPAYGQVKDKFNIEWQIT 136
Cdd:cd06588   77 ISLSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
5-137 6.39e-32

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 109.56  E-value: 6.39e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   5 INPYLVLDGSgQEAVQFYKEALDAKVEVMQTFGDmpenpeypipaeakERVLHATLKVGNTDLMISDTFPGQGHAIGSQV 84
Cdd:COG2764    2 VTPYLVVDDA-EEALEFYEDVFGFEVVFRMTDPD--------------GKIMHAELRIGGSVLMLSDAPPDSPAAEGNGV 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 500336228  85 TIAIqisNAEKAKEVFDKLQ-EGGEVIMPLQETFWSPAYGQVKDKFNIEWQITT 137
Cdd:COG2764   67 SLSL---YVDDVDALFARLVaAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINT 117
PRK10148 PRK10148
VOC family metalloprotein YjdN;
5-135 2.10e-24

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 91.50  E-value: 2.10e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   5 INPYLVLDGSGQEAVQFYKEALDAKVEVMQTFGDMP---ENPEYPIPAEAK---ERVLHATLKVGNTDLMISDTFPGqGH 78
Cdd:PRK10148   3 LSPYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPksaQDSEEGCPSGMQfpdTAIAHANVRIAGSDIMMSDAIPS-GK 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 500336228  79 AIGSQVTIAIQISNAEKAKEVFDKLQEGGEVIMPLQETFWSPAYGQVKDKFNIEWQI 135
Cdd:PRK10148  82 AHYSGFTLVLDTQDVEEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMI 138
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
4-135 1.70e-09

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 52.07  E-value: 1.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228    4 GINPYLVLDGSGQEAVQFYKEALDAKVEVmqtfgdmpenpEYPIPAEAKERvlHATLKVGNTDLMISDT-FPGQGHAIGS 82
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVE-----------ETDAGEEGGLR--SAFFLAGGRVLELLLNeTPPPAAAGFG 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 500336228   83 QVTIAIQISNAEKAKEVFDKLQE-GGEVIMPLQETFWSPAYGQVKDKFNIEWQI 135
Cdd:pfam00903  68 GHHIAFIAFSVDDVDAAYDRLKAaGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
 
Name Accession Description Interval E-value
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 5-136 3.07e-47

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: 148.96  E-value: 3.07e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   5 INPYLVLDGSGQEAVQFYKEAL-DAKVEVMQTFGDMPENPeypiPAEAKERVLHATLKVGNTDLMISDTFPGQGHAIGSQ 83
Cdd:cd06588    1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPPDF----PEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 500336228  84 VTIAIQISNAEKAKEVFDKLQEGGEVIMPLQETFWSPAYGQVKDKFNIEWQIT 136
Cdd:cd06588   77 ISLSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
5-137 6.39e-32

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 109.56  E-value: 6.39e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   5 INPYLVLDGSgQEAVQFYKEALDAKVEVMQTFGDmpenpeypipaeakERVLHATLKVGNTDLMISDTFPGQGHAIGSQV 84
Cdd:COG2764    2 VTPYLVVDDA-EEALEFYEDVFGFEVVFRMTDPD--------------GKIMHAELRIGGSVLMLSDAPPDSPAAEGNGV 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 500336228  85 TIAIqisNAEKAKEVFDKLQ-EGGEVIMPLQETFWSPAYGQVKDKFNIEWQITT 137
Cdd:COG2764   67 SLSL---YVDDVDALFARLVaAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINT 117
PRK10148 PRK10148
VOC family metalloprotein YjdN;
5-135 2.10e-24

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 91.50  E-value: 2.10e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   5 INPYLVLDGSGQEAVQFYKEALDAKVEVMQTFGDMP---ENPEYPIPAEAK---ERVLHATLKVGNTDLMISDTFPGqGH 78
Cdd:PRK10148   3 LSPYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPksaQDSEEGCPSGMQfpdTAIAHANVRIAGSDIMMSDAIPS-GK 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 500336228  79 AIGSQVTIAIQISNAEKAKEVFDKLQEGGEVIMPLQETFWSPAYGQVKDKFNIEWQI 135
Cdd:PRK10148  82 AHYSGFTLVLDTQDVEEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMI 138
VOC_like cd07246
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 4-137 8.27e-16

uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping


Pssm-ID: 319910 [Multi-domain]  Cd Length: 124  Bit Score: 68.48  E-value: 8.27e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   4 GINPYLVLDGSGqEAVQFYKEALDAKvEVMQTFGDMPenpeypipaeakeRVLHATLKVGNTDLMISDTFPGQGHAI--- 80
Cdd:cd07246    2 TVSPYLVVEDAA-AAIAFYKKAFGAE-ELGRTTQEDG-------------RVGHAELRIGGTVVMVADENPERGALSptk 66

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228  81 --GSQVTIAIQISNAEKAkevFDK-LQEGGEVIMPLQETFWSPAYGQVKDKFNIEWQITT 137
Cdd:cd07246   67 lgGTPVIFHLYVEDVDAT---FARaVAAGAVVVEPVEDQFWGDRVGKVKDPFGHVWWLAT 123
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
4-135 1.70e-09

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 52.07  E-value: 1.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228    4 GINPYLVLDGSGQEAVQFYKEALDAKVEVmqtfgdmpenpEYPIPAEAKERvlHATLKVGNTDLMISDT-FPGQGHAIGS 82
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVE-----------ETDAGEEGGLR--SAFFLAGGRVLELLLNeTPPPAAAGFG 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 500336228   83 QVTIAIQISNAEKAKEVFDKLQE-GGEVIMPLQETFWSPAYGQVKDKFNIEWQI 135
Cdd:pfam00903  68 GHHIAFIAFSVDDVDAAYDRLKAaGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 4-136 4.82e-06

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: 43.06  E-value: 4.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228    4 GINPYLVLDGSGQEAVQFYKEAL-DAKVEVMQTFGDmpenpEYPIPAEAkerVLHATLKVGNTDLMISD---TFPgQGHA 79
Cdd:pfam06983   2 KITPCLWFDGQAEEAAEFYVSLFpNSEIGSVNRYPE-----DGPGKPGS---VLTVEFTLNGQPFIALNggpNFK-FNEA 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 500336228   80 IGSQVTIAIQisnaEKAKEVFDKLQEGGEvimplQETfwspAYGQVKDKFNIEWQIT 136
Cdd:pfam06983  73 VSFQVTCKDQ----EEVDRYWNALSENGG-----PES----QCGWLKDKFGVSWQIV 116
ASKHA_NBD_LGK cd24051
nucleotide-binding domain (NBD) of levoglucosan kinase (LGK) and similar proteins; LGK (EC 2.7. ...
 2-126 5.95e-03

nucleotide-binding domain (NBD) of levoglucosan kinase (LGK) and similar proteins; LGK (EC 2.7.1.232) catalyzes the transfer of a phosphate group from ATP to levoglucosan (1,6-anhydro-beta-D-glucopyranose, LG) to yield glucose 6-phosphate in the presence of magnesium ion and ATP. In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O-6 atom.


Pssm-ID: 466901  Cd Length: 409  Bit Score: 35.60  E-value: 5.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500336228   2 ILGINPYLVLDGSGQEAVQFYKEALDAKVEVmqtfgDMPENPEYPIPAEAKERVLHATLKVGNTDLMISDTFPGQGHAIG 81
Cdd:cd24051    3 VLGLNSGTSMDGIDCALCHFTQKTPDAPMEF-----ELIEYGEVPLAQPIKQRVMSMILEDTTSPSELSEVNVILGETFA 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 500336228  82 SqvtiAIQISNAEK--AKEVFDKLQEGGEVIMpLQETfwsPAYGQVK 126
Cdd:cd24051   78 D----AVRQFAAERnvDLSDIDAIASHGQTIW-LLSM---PEEGQVK 116
 
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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