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Conserved domains on  [gi|1816261921|ref|WP_163353179|]
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pyridoxamine 5'-phosphate oxidase family protein [Desulfovibrio sp. JC010]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein( domain architecture ID 10472314)

pyridoxamine 5'-phosphate oxidase family protein may catalyze an FMN-mediated redox reaction, similar to Aspergillus flavus pyridoxamine 5'-phosphate oxidase family protein ustO that is part of the gene cluster that mediates the biosynthesis of the secondary metabolite ustiloxin B, an antimitotic tetrapeptide

CATH:  2.30.110.10
EC:  1.-.-.-
Gene Ontology:  GO:0010181|GO:0016491
PubMed:  26434506|32951820
SCOP:  4002129

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YzzA super family cl39142
General stress protein 26 (function unknown) [Function unknown];
12-140 1.71e-12

General stress protein 26 (function unknown) [Function unknown];


The actual alignment was detected with superfamily member COG3871:

Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 60.33  E-value: 1.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816261921  12 ELISENSILVLATQGEDG-VHTSLMAYAGSADCNEIYMISSRNSRKWKNLSRYPQVSLLIDDRDQKlsgrrneiKALTIK 90
Cdd:COG3871    13 ELLEDIRTAMLATVDADGrPHSRPMWFQVDVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDD--------RYVSVE 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1816261921  91 GTfipvVDKTEEKAILKQIagaVPAIASAF--SGPEN---SIIRVKAESFLLLDG 140
Cdd:COG3871    85 GT----AEIVDDRAKIDEL---WNPLAEAWfpDGPDDpdlVLLRVTPERAEYWDS 132
 
Name Accession Description Interval E-value
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
12-140 1.71e-12

General stress protein 26 (function unknown) [Function unknown];


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 60.33  E-value: 1.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816261921  12 ELISENSILVLATQGEDG-VHTSLMAYAGSADCNEIYMISSRNSRKWKNLSRYPQVSLLIDDRDQKlsgrrneiKALTIK 90
Cdd:COG3871    13 ELLEDIRTAMLATVDADGrPHSRPMWFQVDVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDD--------RYVSVE 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1816261921  91 GTfipvVDKTEEKAILKQIagaVPAIASAF--SGPEN---SIIRVKAESFLLLDG 140
Cdd:COG3871    85 GT----AEIVDDRAKIDEL---WNPLAEAWfpDGPDDpdlVLLRVTPERAEYWDS 132
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 10-86 6.15e-10

Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both pfam01243 and pfam10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown.


Pssm-ID: 426149 [Multi-domain]  Cd Length: 88  Bit Score: 52.64  E-value: 6.15e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1816261921  10 CQELISENSILVLATQGEDG-VHTSLMAYAGSADCNEIYMISSRNSRKWKNLSRYPQVSLLIDDRDQklsGRRNEIKA 86
Cdd:pfam01243   5 IREFLAEPNAVVLATVDKDGrPNVRPVGLKYGFDTVGILFATNTDSRKARNLEENPRVALLFGDPEL---RRGVRIEG 79
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 12-74 4.88e-06

PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomyces, make F420. The Partial Phylogenetic Profiling algorithm identifies this members of this protein family as high-scoring proteins to the F420 biosynthesis profile. A member of this family, Rv1155, was crytallized after expression in Escherichia coli, which does not synthesize F420; the crystal structure shown to resemble FMN-binding proteins, but with a recognizable empty cleft corresponding to, yet differing profounding from, the FMN site of pyridoxine 5'-phosphate oxidase. We propose that this protein family consists of F420-binding enzymes. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274679 [Multi-domain]  Cd Length: 126  Bit Score: 43.05  E-value: 4.88e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1816261921  12 ELISENSILVLATQGEDG-VHTSLMAYAGSADcnEIYMISSRNSRKWKNLSRYPQVSLLIDDRD 74
Cdd:TIGR03618   3 DLLSERRLAVLATIRPDGrPQLSPVWFALDGD--ELVFSTTAGRAKARNLRRDPRVSLSVLDPD 64
 
Name Accession Description Interval E-value
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
12-140 1.71e-12

General stress protein 26 (function unknown) [Function unknown];


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 60.33  E-value: 1.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816261921  12 ELISENSILVLATQGEDG-VHTSLMAYAGSADCNEIYMISSRNSRKWKNLSRYPQVSLLIDDRDQKlsgrrneiKALTIK 90
Cdd:COG3871    13 ELLEDIRTAMLATVDADGrPHSRPMWFQVDVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDD--------RYVSVE 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1816261921  91 GTfipvVDKTEEKAILKQIagaVPAIASAF--SGPEN---SIIRVKAESFLLLDG 140
Cdd:COG3871    85 GT----AEIVDDRAKIDEL---WNPLAEAWfpDGPDDpdlVLLRVTPERAEYWDS 132
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 9-134 3.96e-12

Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5'-phosphate oxidase superfamily [Defense mechanisms];


Pssm-ID: 442690 [Multi-domain]  Cd Length: 144  Bit Score: 59.94  E-value: 3.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816261921   9 DCQELISENSILVLATQGEDGVHTSLMAYAgsADCNEIYMISSRNSRKWKNLSRYPQVSLLIDDRDqklSGRRNEIKALT 88
Cdd:COG3467    12 EIRALLDEARVGRLATVDDGRPYVVPVNYV--YDGDTIYFHTAKEGRKLDNLRRNPRVCFEVDELD---GLHSTNYRSVV 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1816261921  89 IKGTFIPVVDKTEEKAILKQIAGA-VPAIASAFSGPE---NSIIRVKAES 134
Cdd:COG3467    87 VFGRAEEVEDPEEKARALRLLLEKyAPGRWRPFSDKEldaTAVIRIDPEE 136
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 10-86 6.15e-10

Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both pfam01243 and pfam10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown.


Pssm-ID: 426149 [Multi-domain]  Cd Length: 88  Bit Score: 52.64  E-value: 6.15e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1816261921  10 CQELISENSILVLATQGEDG-VHTSLMAYAGSADCNEIYMISSRNSRKWKNLSRYPQVSLLIDDRDQklsGRRNEIKA 86
Cdd:pfam01243   5 IREFLAEPNAVVLATVDKDGrPNVRPVGLKYGFDTVGILFATNTDSRKARNLEENPRVALLFGDPEL---RRGVRIEG 79
HugZ COG0748
Putative heme iron utilization protein, contains PNPOx domain [Inorganic ion transport and ...
 9-137 2.66e-07

Putative heme iron utilization protein, contains PNPOx domain [Inorganic ion transport and metabolism];


Pssm-ID: 440511 [Multi-domain]  Cd Length: 221  Bit Score: 48.03  E-value: 2.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816261921   9 DCQELISENSILVLATQGEDGV-HTSLMAYAGSADcNEIYMISSRNSRKWKNLSRYPQVSLLIDDRDQK----LSGRRne 83
Cdd:COG0748    11 EARTLLRSARSGALATLDADGYpFASYAPFALDDD-GSPYILISGLAEHTRNLLADPRASLLLIEDESKagdpLARPR-- 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1816261921  84 ikaLTIKGTFIPVVDKTEEKAILKQIAGAVPAIASAFSGPENSIIRVKAESFLL 137
Cdd:COG0748    88 ---LTLQGRAERVEDSEEWEAARARYLARFPKAALYADLPDFSLFRLTPERGRL 138
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 12-74 4.88e-06

PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomyces, make F420. The Partial Phylogenetic Profiling algorithm identifies this members of this protein family as high-scoring proteins to the F420 biosynthesis profile. A member of this family, Rv1155, was crytallized after expression in Escherichia coli, which does not synthesize F420; the crystal structure shown to resemble FMN-binding proteins, but with a recognizable empty cleft corresponding to, yet differing profounding from, the FMN site of pyridoxine 5'-phosphate oxidase. We propose that this protein family consists of F420-binding enzymes. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274679 [Multi-domain]  Cd Length: 126  Bit Score: 43.05  E-value: 4.88e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1816261921  12 ELISENSILVLATQGEDG-VHTSLMAYAGSADcnEIYMISSRNSRKWKNLSRYPQVSLLIDDRD 74
Cdd:TIGR03618   3 DLLSERRLAVLATIRPDGrPQLSPVWFALDGD--ELVFSTTAGRAKARNLRRDPRVSLSVLDPD 64
 
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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