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Conserved domains on  [gi|501276100|ref|WP_012319118|]
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pyridoxamine 5'-phosphate oxidase family protein [Methylobacterium radiotolerans]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein( domain architecture ID 12177348)

pyridoxamine 5'-phosphate oxidase family protein binds FMN and FAD; similar to Bacillus subtilis general stress protein 26 that is induced by heat shock, salt stress, oxidative stress, glucose limitation and oxygen limitation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pyrid_ox_like pfam16242
Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is ...
 10-157 3.28e-65

Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is mainly found in general stress proteins in various Xanthomonas species. It is composed of a six-stranded antiparallel beta-barrel flanked by five alpha-helices and can bind to FMN and FAD, suggesting that it may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant.


:

Pssm-ID: 435234 [Multi-domain]  Cd Length: 149  Bit Score: 196.01  E-value: 3.28e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   10 EGAKKLFELIKDVKIAMMTTVDSDGTLNSRPMWNNDADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSSQNYVSVTG 89
Cdd:pfam16242   1 DAVEKLWELIKDIRTAMLTTTTAGGGLHSRPMATQEVEFDGDLWFFTDKDSDKVDEIREDPQVNVAFSDPSKNNYVSVSG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501276100   90 KAEIVRDQSIIDAKWNESLKTWFPNGKDDPEVALIRVHPEKGEYWDSPNSTMLHLYGYVKASLTGESP 157
Cdd:pfam16242  81 TAEVVRDRAKIDELWNPVAKAWFPEGKDDPNITLLKVTPKEAEYWDSPGGKLKFGIKMAKAAVTGKKP 148
 
Name Accession Description Interval E-value
Pyrid_ox_like pfam16242
Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is ...
 10-157 3.28e-65

Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is mainly found in general stress proteins in various Xanthomonas species. It is composed of a six-stranded antiparallel beta-barrel flanked by five alpha-helices and can bind to FMN and FAD, suggesting that it may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant.


Pssm-ID: 435234 [Multi-domain]  Cd Length: 149  Bit Score: 196.01  E-value: 3.28e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   10 EGAKKLFELIKDVKIAMMTTVDSDGTLNSRPMWNNDADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSSQNYVSVTG 89
Cdd:pfam16242   1 DAVEKLWELIKDIRTAMLTTTTAGGGLHSRPMATQEVEFDGDLWFFTDKDSDKVDEIREDPQVNVAFSDPSKNNYVSVSG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501276100   90 KAEIVRDQSIIDAKWNESLKTWFPNGKDDPEVALIRVHPEKGEYWDSPNSTMLHLYGYVKASLTGESP 157
Cdd:pfam16242  81 TAEVVRDRAKIDELWNPVAKAWFPEGKDDPNITLLKVTPKEAEYWDSPGGKLKFGIKMAKAAVTGKKP 148
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
8-136 1.41e-57

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 176.28  E-value: 1.41e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   8 DHEGAKKLFELIKDVKIAMMTTVDSDGTLNSRPMWNNDADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSSQNYVSV 87
Cdd:COG3871    4 DEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVDVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRYVSV 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 501276100  88 TGKAEIVRDQSIIDAKWNESLKTWFPNGKDDPEVALIRVHPEKGEYWDS 136
Cdd:COG3871   84 EGTAEIVDDRAKIDELWNPLAEAWFPDGPDDPDLVLLRVTPERAEYWDS 132
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 24-130 7.07e-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: 7.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   24 IAMMTTVDSDGTLNSRPMWNndADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSS-QNYVSVTGKAEIVRD------ 96
Cdd:TIGR03618  10 LAVLATIRPDGRPQLSPVWF--ALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGpYRYVEIEGTAEVSPDpdavrd 87

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 501276100   97 --QSIIDAKWNESLKTWFPNGKDDPEVALIRVHPEK 130
Cdd:TIGR03618  88 lvDRLAERYRGAAGEDEYRRPMVDPRRVVVRVTPER 123
 
Name Accession Description Interval E-value
Pyrid_ox_like pfam16242
Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is ...
 10-157 3.28e-65

Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is mainly found in general stress proteins in various Xanthomonas species. It is composed of a six-stranded antiparallel beta-barrel flanked by five alpha-helices and can bind to FMN and FAD, suggesting that it may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant.


Pssm-ID: 435234 [Multi-domain]  Cd Length: 149  Bit Score: 196.01  E-value: 3.28e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   10 EGAKKLFELIKDVKIAMMTTVDSDGTLNSRPMWNNDADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSSQNYVSVTG 89
Cdd:pfam16242   1 DAVEKLWELIKDIRTAMLTTTTAGGGLHSRPMATQEVEFDGDLWFFTDKDSDKVDEIREDPQVNVAFSDPSKNNYVSVSG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501276100   90 KAEIVRDQSIIDAKWNESLKTWFPNGKDDPEVALIRVHPEKGEYWDSPNSTMLHLYGYVKASLTGESP 157
Cdd:pfam16242  81 TAEVVRDRAKIDELWNPVAKAWFPEGKDDPNITLLKVTPKEAEYWDSPGGKLKFGIKMAKAAVTGKKP 148
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
8-136 1.41e-57

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 176.28  E-value: 1.41e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   8 DHEGAKKLFELIKDVKIAMMTTVDSDGTLNSRPMWNNDADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSSQNYVSV 87
Cdd:COG3871    4 DEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVDVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRYVSV 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 501276100  88 TGKAEIVRDQSIIDAKWNESLKTWFPNGKDDPEVALIRVHPEKGEYWDS 136
Cdd:COG3871   84 EGTAEIVDDRAKIDELWNPLAEAWFPDGPDDPDLVLLRVTPERAEYWDS 132
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 13-96 7.01e-17

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: 71.13  E-value: 7.01e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   13 KKLFELIKDVKIAMMTTVDSDGTLNSRPMWNNDADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSSQNYVSVTGKAE 92
Cdd:pfam01243   3 EEIREFLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTVGILFATNTDSRKARNLEENPRVALLFGDPELRRGVRIEGTAE 82


                  ....
gi 501276100   93 IVRD 96
Cdd:pfam01243  83 IVTD 86
COG5015 COG5015
Pyridoxamine 5'-phosphate oxidase (PNPOx-like) family protein [General function prediction ...
 13-135 3.21e-12

Pyridoxamine 5'-phosphate oxidase (PNPOx-like) family protein [General function prediction only];


Pssm-ID: 444039 [Multi-domain]  Cd Length: 130  Bit Score: 60.24  E-value: 3.21e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100  13 KKLFELIKDVKIAMMTTVDsDGTLNSRPMWNNDADENGdLWFFTKLHSPKTAEISKDNQINLAYSDPSSQnYVSVTGKAE 92
Cdd:COG5015    1 EEILKFLKENPVFYLATVD-GGQPRVRPFGFVFEDEGK-LYFCTSNQKDVYKQLKANPKVEICAMKKDGE-WIRLSGKAV 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 501276100  93 IVRDQSIIDAKW--NESLKTWFPNGkDDPEVALIRVHPEKGEYWD 135
Cdd:COG5015   78 FVDDRELKEKILeeNPFLKEIYPSA-DDPIFEVFYLEDGEAEFYD 121
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 24-130 7.07e-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: 7.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100   24 IAMMTTVDSDGTLNSRPMWNndADENGDLWFFTKLHSPKTAEISKDNQINLAYSDPSS-QNYVSVTGKAEIVRD------ 96
Cdd:TIGR03618  10 LAVLATIRPDGRPQLSPVWF--ALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGpYRYVEIEGTAEVSPDpdavrd 87

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 501276100   97 --QSIIDAKWNESLKTWFPNGKDDPEVALIRVHPEK 130
Cdd:TIGR03618  88 lvDRLAERYRGAAGEDEYRRPMVDPRRVVVRVTPER 123
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 48-130 3.40e-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: 41.45  E-value: 3.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100  48 ENGDLWFFTKLHSPKTAEISKDNQINL---AYSDPSSQNYVSV--TGKAEIVRDQSIIDAKWNESLKTWFP------NGK 116
Cdd:COG3467   43 DGDTIYFHTAKEGRKLDNLRRNPRVCFevdELDGLHSTNYRSVvvFGRAEEVEDPEEKARALRLLLEKYAPgrwrpfSDK 122

                         90
                 ....*....|....
gi 501276100 117 DDPEVALIRVHPEK 130
Cdd:COG3467  123 ELDATAVIRIDPEE 136
PdxH COG0259
Pyridoxine/pyridoxamine 5'-phosphate oxidase [Coenzyme transport and metabolism]; Pyridoxine ...
 27-94 1.67e-03

Pyridoxine/pyridoxamine 5'-phosphate oxidase [Coenzyme transport and metabolism]; Pyridoxine/pyridoxamine 5'-phosphate oxidase is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis


Pssm-ID: 440029  Cd Length: 212  Bit Score: 37.48  E-value: 1.67e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501276100  27 MT--TVDSDGTLNSRPMWNNDADENGdLWFFTKLHSPKTAEISKDNQINLAYSDPSSQNYVSVTGKAEIV 94
Cdd:COG0259   47 MTlaTVDADGRPSARTVLLKGVDERG-FVFYTNYESRKGRELAANPRAALTFFWPELERQVRIEGRVEKV 115
 
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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