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Conserved domains on  [gi|503443382|ref|WP_013678043|]
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MULTISPECIES: pyridoxamine 5'-phosphate oxidase family protein [Pseudonocardia]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein( domain architecture ID 707177)

pyridoxamine 5'-phosphate oxidase family protein may catalyze an FMN-mediated redox reaction

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rv1155_F420 super family cl25688
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 13-120 6.17e-16

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]


The actual alignment was detected with superfamily member TIGR03618:

Pssm-ID: 274679 [Multi-domain]  Cd Length: 126  Bit Score: 69.63  E-value: 6.17e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   13 AQALLDATSAAHLAYTGRDGTPRVVPVGYFWTGEEFVVSTADTAPKVAAVRARPDVALAIDGGGTPGSaqSLSIRGRAEV 92
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYR--YVEIEGTAEV 78

                          90       100
                  ....*....|....*....|....*....
gi 503443382   93 RIVDGLVPEYVAA-ARKSMGAEAADEFER 120
Cdd:TIGR03618  79 SPDPDAVRDLVDRlAERYRGAAGEDEYRR 107
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 13-120 6.17e-16

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: 69.63  E-value: 6.17e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   13 AQALLDATSAAHLAYTGRDGTPRVVPVGYFWTGEEFVVSTADTAPKVAAVRARPDVALAIDGGGTPGSaqSLSIRGRAEV 92
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYR--YVEIEGTAEV 78

                          90       100
                  ....*....|....*....|....*....
gi 503443382   93 RIVDGLVPEYVAA-ARKSMGAEAADEFER 120
Cdd:TIGR03618  79 SPDPDAVRDLVDRlAERYRGAAGEDEYRR 107
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 3-139 5.23e-13

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: 62.63  E-value: 5.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   3 RQDVLTELTAAQ--ALLDATSAAHLAYTgRDGTPRVVPVGYFWTGEEFVVSTADTAPKVAAVRARPDVALAIDG--GGTP 78
Cdd:COG3467    1 MRRKDRELDREEirALLDEARVGRLATV-DDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLRRNPRVCFEVDEldGLHS 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503443382  79 GSAQSLSIRGRAEVrIVDGlvPEYVAAARKSMGAEAADEFERNCRRMYERMARIAIVPAWA 139
Cdd:COG3467   80 TNYRSVVVFGRAEE-VEDP--EEKARALRLLLEKYAPGRWRPFSDKELDATAVIRIDPEEI 137
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 12-92 9.98e-07

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: 44.55  E-value: 9.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   12 AAQALLDATSAAHLAYTGRDGTPRVVPVGYFWTGEE--FVVSTADTAPKVAAVRARPDVALAIDGggtPGSAQSLSIRGR 89
Cdd:pfam01243   4 EIREFLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGD---PELRRGVRIEGT 80


                  ...
gi 503443382   90 AEV 92
Cdd:pfam01243  81 AEI 83
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 13-120 6.17e-16

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: 69.63  E-value: 6.17e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   13 AQALLDATSAAHLAYTGRDGTPRVVPVGYFWTGEEFVVSTADTAPKVAAVRARPDVALAIDGGGTPGSaqSLSIRGRAEV 92
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYR--YVEIEGTAEV 78

                          90       100
                  ....*....|....*....|....*....
gi 503443382   93 RIVDGLVPEYVAA-ARKSMGAEAADEFER 120
Cdd:TIGR03618  79 SPDPDAVRDLVDRlAERYRGAAGEDEYRR 107
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 3-139 5.23e-13

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: 62.63  E-value: 5.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   3 RQDVLTELTAAQ--ALLDATSAAHLAYTgRDGTPRVVPVGYFWTGEEFVVSTADTAPKVAAVRARPDVALAIDG--GGTP 78
Cdd:COG3467    1 MRRKDRELDREEirALLDEARVGRLATV-DDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLRRNPRVCFEVDEldGLHS 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503443382  79 GSAQSLSIRGRAEVrIVDGlvPEYVAAARKSMGAEAADEFERNCRRMYERMARIAIVPAWA 139
Cdd:COG3467   80 TNYRSVVVFGRAEE-VEDP--EEKARALRLLLEKYAPGRWRPFSDKELDATAVIRIDPEEI 137
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
15-92 4.75e-12

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 59.56  E-value: 4.75e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382  15 ALLDATSAAHLAYTGRDGTPRVVPVGYFW--TGEEFVVSTADTAPKVAAVRARPDVALAIDGggtPGSAQSLSIRGRAEV 92
Cdd:COG3871   13 ELLEDIRTAMLATVDADGRPHSRPMWFQVdvDDGTLWFFTSRDSAKVRNIRRDPRVSLSFAD---PGDDRYVSVEGTAEI 89
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 12-92 9.98e-07

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: 44.55  E-value: 9.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   12 AAQALLDATSAAHLAYTGRDGTPRVVPVGYFWTGEE--FVVSTADTAPKVAAVRARPDVALAIDGggtPGSAQSLSIRGR 89
Cdd:pfam01243   4 EIREFLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGD---PELRRGVRIEGT 80


                  ...
gi 503443382   90 AEV 92
Cdd:pfam01243  81 AEI 83
Pyridox_ox_2 pfam12900
Pyridoxamine 5'-phosphate oxidase; Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein ...
 12-110 4.34e-04

Pyridoxamine 5'-phosphate oxidase; Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyzes the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This entry contains several pyridoxamine 5'-phosphate oxidases, and related proteins.


Pssm-ID: 432864  Cd Length: 143  Bit Score: 38.54  E-value: 4.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503443382   12 AAQALLDATSAAHLAYTGrDGTPRVVPVGYFWTGEEFVVSTADTAPKVAAVRARPD--VALAIDGGGTPGSAQSLS---- 85
Cdd:pfam12900   4 ECHALLDSGPVGRLAFVD-DGAPYILPVNYVVDGDTLYFHGATGSKLAAALRGAPVcvVVFEVDGLVLARSAFHHSmnwr 82

                          90       100
                  ....*....|....*....|....*...
gi 503443382   86 ---IRGRAEVrIVDglvPEYVAAARKSM 110
Cdd:pfam12900  83 svvVRGTAEL-VTD---PEEKAAALEAL 106
 
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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