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Conserved domains on  [gi|499883306|ref|WP_011564040|]
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PPOX class F420-dependent oxidoreductase [Rubrobacter xylanophilus]

Protein Classification

PPOX class F420-dependent oxidoreductase( domain architecture ID 11497257)

PPOX class F420-dependent oxidoreductase similar to Mycobacterium tuberculosis F420H(2)-dependent biliverdin reductase, which catalyzes the reduction of biliverdin-IXalpha at the C10 position to form bilirubin-IXalpha, a potent antioxidant

CATH:  2.30.110.10
EC:  1.-.-.-
Gene Ontology:  GO:0016491|GO:0070967
PubMed:  15620716
SCOP:  4002129

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 12-133 1.10e-52

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: 162.46  E-value: 1.10e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306   12 HRDLLESRALAHVATIGPKGEPQCNPVWFDWDGRHIKFSQTTARQKYRNVRRDPRVALSIVDPENPYRYLEIRGIVEKIE 91
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYRYVEIEGTAEVSP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 499883306   92 D-DPDHGFINAMAKKYLGV---EEYPHHRPGDERVVVYVRPEHTTH 133
Cdd:TIGR03618  81 DpDAVRDLVDRLAERYRGAageDEYRRPMVDPRRVVVRVTPERVYG 126
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 12-133 1.10e-52

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: 162.46  E-value: 1.10e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306   12 HRDLLESRALAHVATIGPKGEPQCNPVWFDWDGRHIKFSQTTARQKYRNVRRDPRVALSIVDPENPYRYLEIRGIVEKIE 91
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYRYVEIEGTAEVSP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 499883306   92 D-DPDHGFINAMAKKYLGV---EEYPHHRPGDERVVVYVRPEHTTH 133
Cdd:TIGR03618  81 DpDAVRDLVDRLAERYRGAageDEYRRPMVDPRRVVVRVTPERVYG 126
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
2-130 1.87e-24

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 90.76  E-value: 1.87e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306   2 TETATLIPESHRDLLESRALAHVATIGPKGEPQCNPVWFDWD--GRHIKFSQTTARQKYRNVRRDPRVALSIVDPENpYR 79
Cdd:COG3871    1 TTDDEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGD-DR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499883306  80 YLEIRGIVEKIED-DPDHGFINAMAKKYlgveeYPHHRPGDERVVVYVRPEH 130
Cdd:COG3871   80 YVSVEGTAEIVDDrAKIDELWNPLAEAW-----FPDGPDDPDLVLLRVTPER 126
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 8-94 5.09e-18

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: 73.05  E-value: 5.09e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306    8 IPESHRDLLESRALAHVATIGPKGEPQCNPVWF--DWDGRHIKFSQTTARQKYRNVRRDPRVALSIVDPENpYRYLEIRG 85
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDGRPNVRPVGLkyGFDTVGILFATNTDSRKARNLEENPRVALLFGDPEL-RRGVRIEG 79


                  ....*....
gi 499883306   86 IVEKIEDDP 94
Cdd:pfam01243  80 TAEIVTDGE 88
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 12-133 1.10e-52

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: 162.46  E-value: 1.10e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306   12 HRDLLESRALAHVATIGPKGEPQCNPVWFDWDGRHIKFSQTTARQKYRNVRRDPRVALSIVDPENPYRYLEIRGIVEKIE 91
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYRYVEIEGTAEVSP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 499883306   92 D-DPDHGFINAMAKKYLGV---EEYPHHRPGDERVVVYVRPEHTTH 133
Cdd:TIGR03618  81 DpDAVRDLVDRLAERYRGAageDEYRRPMVDPRRVVVRVTPERVYG 126
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
2-130 1.87e-24

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 90.76  E-value: 1.87e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306   2 TETATLIPESHRDLLESRALAHVATIGPKGEPQCNPVWFDWD--GRHIKFSQTTARQKYRNVRRDPRVALSIVDPENpYR 79
Cdd:COG3871    1 TTDDEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGD-DR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499883306  80 YLEIRGIVEKIED-DPDHGFINAMAKKYlgveeYPHHRPGDERVVVYVRPEH 130
Cdd:COG3871   80 YVSVEGTAEIVDDrAKIDELWNPLAEAW-----FPDGPDDPDLVLLRVTPER 126
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 13-132 1.34e-18

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: 76.11  E-value: 1.34e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306  13 RDLLESRALAHVATIgPKGEPQCNPVWFDWDGRHIKFSQTTARQKYRNVRRDPRVALSIVDPENP----YRYLEIRGIVE 88
Cdd:COG3467   14 RALLDEARVGRLATV-DDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLRRNPRVCFEVDELDGLhstnYRSVVVFGRAE 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 499883306  89 KIEDDPDH-GFINAMAKKYLGVEEYPHHRPGDERVVVY-VRPEHTT 132
Cdd:COG3467   93 EVEDPEEKaRALRLLLEKYAPGRWRPFSDKELDATAVIrIDPEEIS 138
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 8-94 5.09e-18

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: 73.05  E-value: 5.09e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306    8 IPESHRDLLESRALAHVATIGPKGEPQCNPVWF--DWDGRHIKFSQTTARQKYRNVRRDPRVALSIVDPENpYRYLEIRG 85
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDGRPNVRPVGLkyGFDTVGILFATNTDSRKARNLEENPRVALLFGDPEL-RRGVRIEG 79


                  ....*....
gi 499883306   86 IVEKIEDDP 94
Cdd:pfam01243  80 TAEIVTDGE 88
Rv3369 TIGR03667
PPOX class probable F420-dependent enzyme, Rv3369 family; A Genome Properties metabolic ...
 16-131 3.77e-13

PPOX class probable F420-dependent enzyme, Rv3369 family; 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 Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 132706  Cd Length: 130  Bit Score: 61.71  E-value: 3.77e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306   16 LESRALAHVATIGPKGEPQCNPVWFDWDGRHIK-FSQTTArQKYRNVRRDPRVALSIVDPENPYRYLEIRGIVEKIEDDP 94
Cdd:TIGR03667  11 LREESIVWLTTVRRSGQPQPVPVWFLWDGTEFLiYSRPQA-AKLRNIRRNPRVSLHLNSDGRGGDVVVFTGTAEVVADAP 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 499883306   95 DHGFINAMAKKY------LGVEEYPHHRpgDERVVVYVRPEHT 131
Cdd:TIGR03667  90 PAREIPAYLAKYredaarIGMTPERFAA--DYSVPLRVTPERL 130
HugZ COG0748
Putative heme iron utilization protein, contains PNPOx domain [Inorganic ion transport and ...
 13-96 3.07e-05

Putative heme iron utilization protein, contains PNPOx domain [Inorganic ion transport and metabolism];


Pssm-ID: 440511 [Multi-domain]  Cd Length: 221  Bit Score: 41.87  E-value: 3.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306  13 RDLLESRALAHVATIGPKGEPQCN--PVWFDWDGRHIKFSQTTArQKYRNVRRDPRVALSIVDPE----NPY--RYLEIR 84
Cdd:COG0748   13 RTLLRSARSGALATLDADGYPFASyaPFALDDDGSPYILISGLA-EHTRNLLADPRASLLLIEDEskagDPLarPRLTLQ 91

                         90
                 ....*....|..
gi 499883306  85 GIVEKIEDDPDH 96
Cdd:COG0748   92 GRAERVEDSEEW 103
COG3576 COG3576
Predicted flavin-nucleotide-binding protein, pyridoxine 5'-phosphate oxidase superfamily ...
 8-95 3.49e-05

Predicted flavin-nucleotide-binding protein, pyridoxine 5'-phosphate oxidase superfamily [General function prediction only];


Pssm-ID: 442796  Cd Length: 189  Bit Score: 41.35  E-value: 3.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499883306   8 IPESHRDLLESRALAHVATIGPKGEPQCNP---------------VWF-DWDG--RHIKFsqttarqkyRNVRRDPRVAL 69
Cdd:COG3576   28 LTPHERAFIAASPFFFLATVDADGWPDVSPrggppgfvrvlddrtLAFpDRRGnrRYDSL---------GNILENPRVGL 98

                         90       100
                 ....*....|....*....|....*.
gi 499883306  70 SIVDPENPYRyLEIRGIVEkIEDDPD 95
Cdd:COG3576   99 LFLDPGRRER-LRVNGRAR-IVTDPA 122
 
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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