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Conserved domains on  [gi|1573948858|gb|RZE33067|]
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pyridoxamine 5'-phosphate oxidase family protein [Streptomyces albidoflavus]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein( domain architecture ID 10583942)

pyridoxamine 5'-phosphate oxidase family protein may catalyze an FMN-mediated redox reaction, similar to Mycobacterium tuberculosis uncharacterized protein Rv0080, which is a member of the dormancy regulon and is induced in response to reduced oxygen tension, as well as low levels of nitric oxide and carbon monoxide

CATH:  2.30.110.10
EC:  1.-.-.-
Gene Ontology:  GO:0016491|GO:0010181
PubMed:  26434506|32951820
SCOP:  4002129

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pyridox_ox_2 pfam12900
Pyridoxamine 5'-phosphate oxidase; Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein ...
 31-175 1.26e-56

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: 176.45  E-value: 1.26e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573948858  31 DRETVHAILDEGTVCHLGFVRDGAPVVLPTLYTRIGEHLYVHGSTGSRPLHSARGeagLPVCVTVTHLDALVLARSAFHH 110
Cdd:pfam12900   1 DREECHALLDSGPVGRLAFVDDGAPYILPVNYVVDGDTLYFHGATGSKLAAALRG---APVCVVVFEVDGLVLARSAFHH 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1573948858 111 SLNYRSVVAHGTAHQVTDPAEKAAALDALVDQVVPGRSADCRPADAKELAATAVLRLELAEVSAK 175
Cdd:pfam12900  78 SMNWRSVVVRGTAELVTDPEEKAAALEALTDRIVPGRWDNLRPPTRKELAATAVLRITPDEISGR 142
 
Name Accession Description Interval E-value
Pyridox_ox_2 pfam12900
Pyridoxamine 5'-phosphate oxidase; Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein ...
 31-175 1.26e-56

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: 176.45  E-value: 1.26e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573948858  31 DRETVHAILDEGTVCHLGFVRDGAPVVLPTLYTRIGEHLYVHGSTGSRPLHSARGeagLPVCVTVTHLDALVLARSAFHH 110
Cdd:pfam12900   1 DREECHALLDSGPVGRLAFVDDGAPYILPVNYVVDGDTLYFHGATGSKLAAALRG---APVCVVVFEVDGLVLARSAFHH 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1573948858 111 SLNYRSVVAHGTAHQVTDPAEKAAALDALVDQVVPGRSADCRPADAKELAATAVLRLELAEVSAK 175
Cdd:pfam12900  78 SMNWRSVVVRGTAELVTDPEEKAAALEALTDRIVPGRWDNLRPPTRKELAATAVLRITPDEISGR 142
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 23-179 6.67e-45

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: 146.61  E-value: 6.67e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573948858  23 RSRDRASyDRETVHAILDEGTVCHLGFVRDGAPVVLPTLYTRIGEHLYVHGSTGSRPLHSARgeAGLPVCVTVTHLDALv 102
Cdd:COG3467     2 RRKDREL-DREEIRALLDEARVGRLATVDDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLR--RNPRVCFEVDELDGL- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1573948858 103 larsafhHSLNYRSVVAHGTAHQVTDPAEKAAALDALVDQVVPGRSadcRPADAKELAATAVLRLELAEVSAKSRTG 179
Cdd:COG3467    78 -------HSTNYRSVVVFGRAEEVEDPEEKARALRLLLEKYAPGRW---RPFSDKELDATAVIRIDPEEISGKRRAG 144
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 37-158 2.09e-03

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: 36.89  E-value: 2.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573948858  37 AILDEGTVCHLGFVR-DGAPVVLPTLYTRIGEHLYVHGSTGSRPLHSARGEAGLPVCVTVTHLdalvlarsafhhslNYR 115
Cdd:TIGR03618   3 DLLSERRLAVLATIRpDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDG--------------PYR 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1573948858 116 SVVAHGTAHQVTDPAEKAAALDALVDQ-VVPGRSADCRPADAKE 158
Cdd:TIGR03618  69 YVEIEGTAEVSPDPDAVRDLVDRLAERyRGAAGEDEYRRPMVDP 112
 
Name Accession Description Interval E-value
Pyridox_ox_2 pfam12900
Pyridoxamine 5'-phosphate oxidase; Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein ...
 31-175 1.26e-56

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: 176.45  E-value: 1.26e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573948858  31 DRETVHAILDEGTVCHLGFVRDGAPVVLPTLYTRIGEHLYVHGSTGSRPLHSARGeagLPVCVTVTHLDALVLARSAFHH 110
Cdd:pfam12900   1 DREECHALLDSGPVGRLAFVDDGAPYILPVNYVVDGDTLYFHGATGSKLAAALRG---APVCVVVFEVDGLVLARSAFHH 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1573948858 111 SLNYRSVVAHGTAHQVTDPAEKAAALDALVDQVVPGRSADCRPADAKELAATAVLRLELAEVSAK 175
Cdd:pfam12900  78 SMNWRSVVVRGTAELVTDPEEKAAALEALTDRIVPGRWDNLRPPTRKELAATAVLRITPDEISGR 142
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 23-179 6.67e-45

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: 146.61  E-value: 6.67e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573948858  23 RSRDRASyDRETVHAILDEGTVCHLGFVRDGAPVVLPTLYTRIGEHLYVHGSTGSRPLHSARgeAGLPVCVTVTHLDALv 102
Cdd:COG3467     2 RRKDREL-DREEIRALLDEARVGRLATVDDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLR--RNPRVCFEVDELDGL- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1573948858 103 larsafhHSLNYRSVVAHGTAHQVTDPAEKAAALDALVDQVVPGRSadcRPADAKELAATAVLRLELAEVSAKSRTG 179
Cdd:COG3467    78 -------HSTNYRSVVVFGRAEEVEDPEEKARALRLLLEKYAPGRW---RPFSDKELDATAVIRIDPEEISGKRRAG 144
FMN_bind_2 pfam04299
Putative FMN-binding domain; In Bacillus subtilis, family member PAI 2/ORF-2 was found to be ...
 113-158 1.62e-03

Putative FMN-binding domain; In Bacillus subtilis, family member PAI 2/ORF-2 was found to be essential for growth. The SUPERFAMILY database finds that this domain is related to FMN-binding domains, suggesting this protein is also FMN-binding.


Pssm-ID: 461254  Cd Length: 166  Bit Score: 37.90  E-value: 1.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1573948858 113 NYRSVVAHGTAHQVTDPAEKAAALDALVDQVVPGRSADCRPADAKE 158
Cdd:pfam04299 102 NYAAVHAYGRARIIDDPEELRAQLERLTDRFEAGRPSPWKVDDAPE 147
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 37-158 2.09e-03

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: 36.89  E-value: 2.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573948858  37 AILDEGTVCHLGFVR-DGAPVVLPTLYTRIGEHLYVHGSTGSRPLHSARGEAGLPVCVTVTHLdalvlarsafhhslNYR 115
Cdd:TIGR03618   3 DLLSERRLAVLATIRpDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDG--------------PYR 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1573948858 116 SVVAHGTAHQVTDPAEKAAALDALVDQ-VVPGRSADCRPADAKE 158
Cdd:TIGR03618  69 YVEIEGTAEVSPDPDAVRDLVDRLAERyRGAAGEDEYRRPMVDP 112
 
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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