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Conserved domains on  [gi|1056812636|ref|WP_068232417|]
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PPOX class F420-dependent oxidoreductase [Mycobacterium sp. E3198]

Protein Classification

PPOX class F420-dependent oxidoreductase( domain architecture ID 10022755)

PPOX class F420-dependent oxidoreductase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rv2061_F420 TIGR03666
PPOX class probable F420-dependent enzyme, Rv2061 family; A Genome Properties metabolic ...
 1-128 5.59e-73

PPOX class probable F420-dependent enzyme, Rv2061 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: 274712  Cd Length: 132  Bit Score: 213.36  E-value: 5.59e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636   1 MTPTFADLAKAQYILLTTFTKDGRPKPVPIWAAADGDRLLVITQEKSWKVKRIRNTPRVTLATCTMQGKPTSEAVEGTAA 80
Cdd:TIGR03666   2 MTPTFADLARARYALLTTFRKDGTPVPTPVWAAVDGDKLLVRTKEDSWKVKRIRNNPRVTLAPCDRRGRPTGPVVPGRAR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1056812636  81 ILDKSQTAAVYDAIGKRYGIVGKVFNFVSKLRGGMQNNVGLELKVAAS 128
Cdd:TIGR03666  82 ILDGAETARARDLLARRYGLQGRLFPLFSKLRRGRDRNVGLELTPAGD 129
 
Name Accession Description Interval E-value
Rv2061_F420 TIGR03666
PPOX class probable F420-dependent enzyme, Rv2061 family; A Genome Properties metabolic ...
 1-128 5.59e-73

PPOX class probable F420-dependent enzyme, Rv2061 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: 274712  Cd Length: 132  Bit Score: 213.36  E-value: 5.59e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636   1 MTPTFADLAKAQYILLTTFTKDGRPKPVPIWAAADGDRLLVITQEKSWKVKRIRNTPRVTLATCTMQGKPTSEAVEGTAA 80
Cdd:TIGR03666   2 MTPTFADLARARYALLTTFRKDGTPVPTPVWAAVDGDKLLVRTKEDSWKVKRIRNNPRVTLAPCDRRGRPTGPVVPGRAR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1056812636  81 ILDKSQTAAVYDAIGKRYGIVGKVFNFVSKLRGGMQNNVGLELKVAAS 128
Cdd:TIGR03666  82 ILDGAETARARDLLARRYGLQGRLFPLFSKLRRGRDRNVGLELTPAGD 129
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
8-98 4.57e-11

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 56.10  E-value: 4.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636   8 LAKAQYILLTTFTKDGRPKPVPIWAAAD--GDRLLVITQEKSWKVKRIRNTPRVTLATCTmQGKPTSEAVEGTAAIL-DK 84
Cdd:COG3871    15 LEDIRTAMLATVDADGRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFAD-PGDDRYVSVEGTAEIVdDR 93

                          90
                  ....*....|....
gi 1056812636  85 SQTAAVYDAIGKRY 98
Cdd:COG3871    94 AKIDELWNPLAEAW 107
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 1-83 4.97e-11

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: 54.95  E-value: 4.97e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636   1 MTPTFAD-LAKAQYILLTTFTKDGRPKPVPIWAAADGDR--LLVITQEKSWKVKRIRNTPRVTLATCTmQGKPTSEAVEG 77
Cdd:pfam01243   1 LTEEIREfLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGD-PELRRGVRIEG 79


                  ....*.
gi 1056812636  78 TAAILD 83
Cdd:pfam01243  80 TAEIVT 85
 
Name Accession Description Interval E-value
Rv2061_F420 TIGR03666
PPOX class probable F420-dependent enzyme, Rv2061 family; A Genome Properties metabolic ...
 1-128 5.59e-73

PPOX class probable F420-dependent enzyme, Rv2061 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: 274712  Cd Length: 132  Bit Score: 213.36  E-value: 5.59e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636   1 MTPTFADLAKAQYILLTTFTKDGRPKPVPIWAAADGDRLLVITQEKSWKVKRIRNTPRVTLATCTMQGKPTSEAVEGTAA 80
Cdd:TIGR03666   2 MTPTFADLARARYALLTTFRKDGTPVPTPVWAAVDGDKLLVRTKEDSWKVKRIRNNPRVTLAPCDRRGRPTGPVVPGRAR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1056812636  81 ILDKSQTAAVYDAIGKRYGIVGKVFNFVSKLRGGMQNNVGLELKVAAS 128
Cdd:TIGR03666  82 ILDGAETARARDLLARRYGLQGRLFPLFSKLRRGRDRNVGLELTPAGD 129
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
8-98 4.57e-11

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 56.10  E-value: 4.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636   8 LAKAQYILLTTFTKDGRPKPVPIWAAAD--GDRLLVITQEKSWKVKRIRNTPRVTLATCTmQGKPTSEAVEGTAAIL-DK 84
Cdd:COG3871    15 LEDIRTAMLATVDADGRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFAD-PGDDRYVSVEGTAEIVdDR 93

                          90
                  ....*....|....
gi 1056812636  85 SQTAAVYDAIGKRY 98
Cdd:COG3871    94 AKIDELWNPLAEAW 107
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 1-83 4.97e-11

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: 54.95  E-value: 4.97e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636   1 MTPTFAD-LAKAQYILLTTFTKDGRPKPVPIWAAADGDR--LLVITQEKSWKVKRIRNTPRVTLATCTmQGKPTSEAVEG 77
Cdd:pfam01243   1 LTEEIREfLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGD-PELRRGVRIEG 79


                  ....*.
gi 1056812636  78 TAAILD 83
Cdd:pfam01243  80 TAEIVT 85
Rv3369 TIGR03667
PPOX class probable F420-dependent enzyme, Rv3369 family; A Genome Properties metabolic ...
 8-81 1.77e-10

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: 54.39  E-value: 1.77e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1056812636   8 LAKAQYILLTTFTKDGRPKPVPIWAAADGDRLLVITQEKSWKVKRIRNTPRVTLA-TCTMQGKPTSeAVEGTAAI 81
Cdd:TIGR03667  11 LREESIVWLTTVRRSGQPQPVPVWFLWDGTEFLIYSRPQAAKLRNIRRNPRVSLHlNSDGRGGDVV-VFTGTAEV 84
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 16-98 1.15e-09

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: 52.30  E-value: 1.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636  16 LTTFTKDGRPKPVPIWAAADGDRLLVITQEKSWKVKRIRNTPRVTLaTCTMQGKPTSEA-VEGTAAILDksQTAAVYD-- 92
Cdd:TIGR03618  13 LATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSL-SVLDPDGPYRYVeIEGTAEVSP--DPDAVRDlv 89


                  ....*..
gi 1056812636  93 -AIGKRY 98
Cdd:TIGR03618  90 dRLAERY 96
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 19-98 3.75e-07

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: 46.07  E-value: 3.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1056812636  19 FTKDGRPKPVPIWAAADGDRLLVITQEKSWKVKRIRNTPRVTLATCTMQGKPTSEA----VEGTAAIL-DKSQTAAVYDA 93
Cdd:COG3467    27 TVDDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLRRNPRVCFEVDELDGLHSTNYrsvvVFGRAEEVeDPEEKARALRL 106


                  ....*
gi 1056812636  94 IGKRY 98
Cdd:COG3467   107 LLEKY 111
 
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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