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Conserved domains on  [gi|384468473|gb|EIE52903|]
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pyridoxamine 5'-phosphate oxidase, FMN-binding protein [Citreicella sp. 357]

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 ...
 10-137 1.22e-10

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: 55.76  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473   10 LLSMPLMANLATMCAEG-PRNAPVWFIWEDDAIWMLGDRDGSSVRRLEEDPRCAVEIvrfDRGKGILLHLGMRGTATVEP 88
Cdd:TIGR03618   4 LLSERRLAVLATIRPDGrPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSV---LDPDGPYRYVEIEGTAEVSP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 384468473   89 M---RPELFGRLLEKYLGADRSKWNSWfigniaRIDDPSGRLIRLEPQSFYT 137
Cdd:TIGR03618  81 DpdaVRDLVDRLAERYRGAAGEDEYRR------PMVDPRRVVVRVTPERVYG 126
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 10-137 1.22e-10

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: 55.76  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473   10 LLSMPLMANLATMCAEG-PRNAPVWFIWEDDAIWMLGDRDGSSVRRLEEDPRCAVEIvrfDRGKGILLHLGMRGTATVEP 88
Cdd:TIGR03618   4 LLSERRLAVLATIRPDGrPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSV---LDPDGPYRYVEIEGTAEVSP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 384468473   89 M---RPELFGRLLEKYLGADRSKWNSWfigniaRIDDPSGRLIRLEPQSFYT 137
Cdd:TIGR03618  81 DpdaVRDLVDRLAERYRGAAGEDEYRR------PMVDPRRVVVRVTPERVYG 126
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
16-136 4.31e-10

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 54.55  E-value: 4.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473  16 MANLATMCAEG-PRNAPVWFIWE--DDAIWMLGDRDGSSVRRLEEDPRCAVEIVRFDRGKGILLhlgmRGTATVEPMRpE 92
Cdd:COG3871   20 TAMLATVDADGrPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRYVSV----EGTAEIVDDR-A 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 384468473  93 LFGRLLEKYLGAdrskwnsWFIGNiarIDDPSGRLIRLEPQSFY 136
Cdd:COG3871   95 KIDELWNPLAEA-------WFPDG---PDDPDLVLLRVTPERAE 128
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 8-86 1.44e-05

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: 41.47  E-value: 1.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473    8 QQLLSMPLMANLATMCAEG-PRNAPVWFIWEDDA--IWMLGDRDGSSVRRLEEDPRCAVEIVRFDRGKGILLHlgmrGTA 84
Cdd:pfam01243   6 REFLAEPNAVVLATVDKDGrPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGDPELRRGVRIE----GTA 81


                  ..
gi 384468473   85 TV 86
Cdd:pfam01243  82 EI 83
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 10-137 1.22e-10

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: 55.76  E-value: 1.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473   10 LLSMPLMANLATMCAEG-PRNAPVWFIWEDDAIWMLGDRDGSSVRRLEEDPRCAVEIvrfDRGKGILLHLGMRGTATVEP 88
Cdd:TIGR03618   4 LLSERRLAVLATIRPDGrPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSV---LDPDGPYRYVEIEGTAEVSP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 384468473   89 M---RPELFGRLLEKYLGADRSKWNSWfigniaRIDDPSGRLIRLEPQSFYT 137
Cdd:TIGR03618  81 DpdaVRDLVDRLAERYRGAAGEDEYRR------PMVDPRRVVVRVTPERVYG 126
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
16-136 4.31e-10

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 54.55  E-value: 4.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473  16 MANLATMCAEG-PRNAPVWFIWE--DDAIWMLGDRDGSSVRRLEEDPRCAVEIVRFDRGKGILLhlgmRGTATVEPMRpE 92
Cdd:COG3871   20 TAMLATVDADGrPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRYVSV----EGTAEIVDDR-A 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 384468473  93 LFGRLLEKYLGAdrskwnsWFIGNiarIDDPSGRLIRLEPQSFY 136
Cdd:COG3871   95 KIDELWNPLAEA-------WFPDG---PDDPDLVLLRVTPERAE 128
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 9-126 6.05e-10

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: 54.16  E-value: 6.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473   9 QLLSMPLMANLATMCAEGPRNAPVWFIWEDDAIWMLGDRDGSSVRRLEEDPRCAVEIVRFD-----RGKGILLhlgmRGT 83
Cdd:COG3467   15 ALLDEARVGRLATVDDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLRRNPRVCFEVDELDglhstNYRSVVV----FGR 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 384468473  84 ATV---EPMRPELFGRLLEKYLGADRSKWNSWFIGNIA----RIDDPSGR 126
Cdd:COG3467   91 AEEvedPEEKARALRLLLEKYAPGRWRPFSDKELDATAviriDPEEISGK 140
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 8-86 1.44e-05

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: 41.47  E-value: 1.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 384468473    8 QQLLSMPLMANLATMCAEG-PRNAPVWFIWEDDA--IWMLGDRDGSSVRRLEEDPRCAVEIVRFDRGKGILLHlgmrGTA 84
Cdd:pfam01243   6 REFLAEPNAVVLATVDKDGrPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGDPELRRGVRIE----GTA 81


                  ..
gi 384468473   85 TV 86
Cdd:pfam01243  82 EI 83
 
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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