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Conserved domains on  [gi|2443763097|ref|WP_273305085|]
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pyridoxamine 5'-phosphate oxidase family protein [Barnesiella viscericola]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein( domain architecture ID 10007424)

pyridoxamine 5'-phosphate oxidase family protein similar to Deinococcus radiodurans antibiotic resistance protein NimA

CATH:  2.30.110.10
EC:  1.-.-.-
Gene Ontology:  GO:0016491
PubMed:  18540048|26434506
SCOP:  4002129

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 9-159 1.89e-41

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: 135.43  E-value: 1.89e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097   9 RRQDRLLDESQARALLQSGEYGVLSLIDtEGRPYGIPINYVWDGqEHIYLHCAPEGKKLNAIRRQAEVSFCVVGRTHVvs 88
Cdd:COG3467     2 RRKDRELDREEIRALLDEARVGRLATVD-DGRPYVVPVNYVYDG-DTIYFHTAKEGRKLDNLRRNPRVCFEVDELDGL-- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2443763097  89 hkFTTGYESIVMKCRAQIGLSVDERHHALRLLLEKYSPDDLavgLKYAEKSFHRTEIIRLDIREYSGKQKR 159
Cdd:COG3467    78 --HSTNYRSVVVFGRAEEVEDPEEKARALRLLLEKYAPGRW---RPFSDKELDATAVIRIDPEEISGKRRA 143
 
Name Accession Description Interval E-value
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 9-159 1.89e-41

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: 135.43  E-value: 1.89e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097   9 RRQDRLLDESQARALLQSGEYGVLSLIDtEGRPYGIPINYVWDGqEHIYLHCAPEGKKLNAIRRQAEVSFCVVGRTHVvs 88
Cdd:COG3467     2 RRKDRELDREEIRALLDEARVGRLATVD-DGRPYVVPVNYVYDG-DTIYFHTAKEGRKLDNLRRNPRVCFEVDELDGL-- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2443763097  89 hkFTTGYESIVMKCRAQIGLSVDERHHALRLLLEKYSPDDLavgLKYAEKSFHRTEIIRLDIREYSGKQKR 159
Cdd:COG3467    78 --HSTNYRSVVVFGRAEEVEDPEEKARALRLLLEKYAPGRW---RPFSDKELDATAVIRIDPEEISGKRRA 143
Pyridox_ox_2 pfam12900
Pyridoxamine 5'-phosphate oxidase; Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein ...
 16-157 5.22e-21

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: 83.23  E-value: 5.22e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097  16 DESQARALLQSGEYGVLSLIDtEGRPYGIPINYVWDGqEHIYLHCAPEGKKLNAIRrQAEVSFCVVGRTHVVSHK----F 91
Cdd:pfam12900   1 DREECHALLDSGPVGRLAFVD-DGAPYILPVNYVVDG-DTLYFHGATGSKLAAALR-GAPVCVVVFEVDGLVLARsafhH 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2443763097  92 TTGYESIVMKCRAQIGLSVDERHHALRLLLEKYSPDDLAVGLKYAEKSFHRTEIIRLDIREYSGKQ 157
Cdd:pfam12900  78 SMNWRSVVVRGTAELVTDPEEKAAALEALTDRIVPGRWDNLRPPTRKELAATAVLRITPDEISGRR 143
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 20-124 3.10e-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: 43.82  E-value: 3.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097  20 ARALLQSGEYGVLSLIDTEGRPYGIPINYVWDGqEHIYLHCAPEGKKLNAIRRQAEVSFCVVGRTHVVSHkfttgyesIV 99
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDG-DELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYRY--------VE 71

                          90       100
                  ....*....|....*....|....*
gi 2443763097 100 MKCRAQIGLSVDERHHALRLLLEKY 124
Cdd:TIGR03618  72 IEGTAEVSPDPDAVRDLVDRLAERY 96
 
Name Accession Description Interval E-value
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 9-159 1.89e-41

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: 135.43  E-value: 1.89e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097   9 RRQDRLLDESQARALLQSGEYGVLSLIDtEGRPYGIPINYVWDGqEHIYLHCAPEGKKLNAIRRQAEVSFCVVGRTHVvs 88
Cdd:COG3467     2 RRKDRELDREEIRALLDEARVGRLATVD-DGRPYVVPVNYVYDG-DTIYFHTAKEGRKLDNLRRNPRVCFEVDELDGL-- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2443763097  89 hkFTTGYESIVMKCRAQIGLSVDERHHALRLLLEKYSPDDLavgLKYAEKSFHRTEIIRLDIREYSGKQKR 159
Cdd:COG3467    78 --HSTNYRSVVVFGRAEEVEDPEEKARALRLLLEKYAPGRW---RPFSDKELDATAVIRIDPEEISGKRRA 143
Pyridox_ox_2 pfam12900
Pyridoxamine 5'-phosphate oxidase; Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein ...
 16-157 5.22e-21

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: 83.23  E-value: 5.22e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097  16 DESQARALLQSGEYGVLSLIDtEGRPYGIPINYVWDGqEHIYLHCAPEGKKLNAIRrQAEVSFCVVGRTHVVSHK----F 91
Cdd:pfam12900   1 DREECHALLDSGPVGRLAFVD-DGAPYILPVNYVVDG-DTLYFHGATGSKLAAALR-GAPVCVVVFEVDGLVLARsafhH 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2443763097  92 TTGYESIVMKCRAQIGLSVDERHHALRLLLEKYSPDDLAVGLKYAEKSFHRTEIIRLDIREYSGKQ 157
Cdd:pfam12900  78 SMNWRSVVVRGTAELVTDPEEKAAALEALTDRIVPGRWDNLRPPTRKELAATAVLRITPDEISGRR 143
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 20-124 3.10e-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: 43.82  E-value: 3.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097  20 ARALLQSGEYGVLSLIDTEGRPYGIPINYVWDGqEHIYLHCAPEGKKLNAIRRQAEVSFCVVGRTHVVSHkfttgyesIV 99
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDG-DELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYRY--------VE 71

                          90       100
                  ....*....|....*....|....*
gi 2443763097 100 MKCRAQIGLSVDERHHALRLLLEKY 124
Cdd:TIGR03618  72 IEGTAEVSPDPDAVRDLVDRLAERY 96
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 19-81 6.64e-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: 39.54  E-value: 6.64e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2443763097  19 QARALLQSGEYGVLSLIDTEGRPYGIPINYVW-DGQEHIYLHCAPEGKKLNAIRRQAEVSFCVV 81
Cdd:pfam01243   4 EIREFLAEPNAVVLATVDKDGRPNVRPVGLKYgFDTVGILFATNTDSRKARNLEENPRVALLFG 67
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
16-128 6.31e-04

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 37.61  E-value: 6.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443763097  16 DESQARALLQSGEYGVLSLIDTEGRPYGIPINYVWD-GQEHIYLHCAPEGKKLNAIRRQAEVSFCVVGRTHvvshkfttg 94
Cdd:COG3871     7 LEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVDvDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGD--------- 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2443763097  95 YESIVMKCRAQIglsVDERHHALRL---LLEKY---SPDD 128
Cdd:COG3871    78 DRYVSVEGTAEI---VDDRAKIDELwnpLAEAWfpdGPDD 114
 
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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