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Conserved domains on  [gi|517296928|ref|WP_018485746|]
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MULTISPECIES: pyridoxamine 5'-phosphate oxidase family protein [Rhizobium]

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
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 7-91 4.12e-09

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: 50.33  E-value: 4.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517296928    7 KKVILEFLRRHTLAVIATSHADGKPEAAVIDFsVRDNLEIVFDTF--EQTRKFENLSDRGSVALVVGWDKN-ITVQYEGD 83
Cdd:pfam01243   2 TEEIREFLAEPNAVVLATVDKDGRPNVRPVGL-KYGFDTVGILFAtnTDSRKARNLEENPRVALLFGDPELrRGVRIEGT 80


                  ....*...
gi 517296928   84 AMKVSASD 91
Cdd:pfam01243  81 AEIVTDGE 88
 
Name Accession Description Interval E-value
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 7-91 4.12e-09

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: 50.33  E-value: 4.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517296928    7 KKVILEFLRRHTLAVIATSHADGKPEAAVIDFsVRDNLEIVFDTF--EQTRKFENLSDRGSVALVVGWDKN-ITVQYEGD 83
Cdd:pfam01243   2 TEEIREFLAEPNAVVLATVDKDGRPNVRPVGL-KYGFDTVGILFAtnTDSRKARNLEENPRVALLFGDPELrRGVRIEGT 80


                  ....*...
gi 517296928   84 AMKVSASD 91
Cdd:pfam01243  81 AEIVTDGE 88
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 11-84 1.15e-05

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: 41.90  E-value: 1.15e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 517296928   11 LEFLRRHTLAVIATSHADGKPEAAVIDFsVRDNLEIVFDTFEQTRKFENLSDRGSVALVV----GWDKniTVQYEGDA 84
Cdd:TIGR03618   2 RDLLSERRLAVLATIRPDGRPQLSPVWF-ALDGDELVFSTTAGRAKARNLRRDPRVSLSVldpdGPYR--YVEIEGTA 76
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
10-128 2.14e-05

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 41.46  E-value: 2.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517296928  10 ILEFLRRHTLAVIATSHADGKPEAAVIDFSV-RDNLEIVFDTFEQTRKFENLSDRGSVALVVGWDKNIT-VQYEGDAmkv 87
Cdd:COG3871   11 LWELLEDIRTAMLATVDADGRPHSRPMWFQVdVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRyVSVEGTA--- 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 517296928  88 SASDVQEYQKAHLESVpVEReFVEKGA-----VLFKVVPRWIRYSD 128
Cdd:COG3871   88 EIVDDRAKIDELWNPL-AEA-WFPDGPddpdlVLLRVTPERAEYWD 131
 
Name Accession Description Interval E-value
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 7-91 4.12e-09

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: 50.33  E-value: 4.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517296928    7 KKVILEFLRRHTLAVIATSHADGKPEAAVIDFsVRDNLEIVFDTF--EQTRKFENLSDRGSVALVVGWDKN-ITVQYEGD 83
Cdd:pfam01243   2 TEEIREFLAEPNAVVLATVDKDGRPNVRPVGL-KYGFDTVGILFAtnTDSRKARNLEENPRVALLFGDPELrRGVRIEGT 80


                  ....*...
gi 517296928   84 AMKVSASD 91
Cdd:pfam01243  81 AEIVTDGE 88
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 11-84 1.15e-05

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: 41.90  E-value: 1.15e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 517296928   11 LEFLRRHTLAVIATSHADGKPEAAVIDFsVRDNLEIVFDTFEQTRKFENLSDRGSVALVV----GWDKniTVQYEGDA 84
Cdd:TIGR03618   2 RDLLSERRLAVLATIRPDGRPQLSPVWF-ALDGDELVFSTTAGRAKARNLRRDPRVSLSVldpdGPYR--YVEIEGTA 76
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
10-128 2.14e-05

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 41.46  E-value: 2.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517296928  10 ILEFLRRHTLAVIATSHADGKPEAAVIDFSV-RDNLEIVFDTFEQTRKFENLSDRGSVALVVGWDKNIT-VQYEGDAmkv 87
Cdd:COG3871   11 LWELLEDIRTAMLATVDADGRPHSRPMWFQVdVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRyVSVEGTA--- 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 517296928  88 SASDVQEYQKAHLESVpVEReFVEKGA-----VLFKVVPRWIRYSD 128
Cdd:COG3871   88 EIVDDRAKIDELWNPL-AEA-WFPDGPddpdlVLLRVTPERAEYWD 131
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 10-70 8.22e-05

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: 39.91  E-value: 8.22e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517296928  10 ILEFLRRHTLAVIATSHaDGKPEAAVIDFsVRDNLEIVFDTFEQTRKFENLSDRGSVALVV 70
Cdd:COG3467   13 IRALLDEARVGRLATVD-DGRPYVVPVNY-VYDGDTIYFHTAKEGRKLDNLRRNPRVCFEV 71
 
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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