NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15607263|ref|NP_214635|]
View 

hypothetical protein Rv0121c [Mycobacterium tuberculosis H37Rv]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein; nitroreductase family deazaflavin-dependent oxidoreductase( domain architecture ID 10022757)

pyridoxamine 5'-phosphate oxidase family protein may utilize either FMN or F420 as a cofactor| nitroreductase family deazaflavin-dependent oxidoreductase similar to Mycobacterium tuberculosis deazaflavin-dependent nitroreductase and F420H(2)-dependent quinone reductase

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Rv0121_F420 TIGR03668
PPOX class probable F420-dependent enzyme, Rv0121 family; A Genome Properties metabolic ...
 2-143 1.15e-73

PPOX class probable F420-dependent enzyme, Rv0121 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: 132707  Cd Length: 141  Bit Score: 216.24  E-value: 1.15e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263     2 GEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEatGADVIYTAVDAKRKTTQRLRRLANLEHNPRASVLVD 81
Cdd:TIGR03668   1 LEFEARTRFAQARVARLATVSPDGEPHLVPVVFAVGAGAVAA--GDAVIYTAVDAKPKTTPRLRRLRNIEENPRVSLLVD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15607263    82 SYADDWTQLWWVRADGVAAIHRDG-EVMRAAYRLLRAKYAQYQSVPLNGPVIAIAVQRWASWH 143
Cdd:TIGR03668  79 RYDDDWTRLWWVRADGRAEILRPGeEEHAAAVRLLRAKYHQYQAVPLEGPVIAIRVERWASWG 141
 
Name Accession Description Interval E-value
Rv0121_F420 TIGR03668
PPOX class probable F420-dependent enzyme, Rv0121 family; A Genome Properties metabolic ...
 2-143 1.15e-73

PPOX class probable F420-dependent enzyme, Rv0121 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: 132707  Cd Length: 141  Bit Score: 216.24  E-value: 1.15e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263     2 GEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEatGADVIYTAVDAKRKTTQRLRRLANLEHNPRASVLVD 81
Cdd:TIGR03668   1 LEFEARTRFAQARVARLATVSPDGEPHLVPVVFAVGAGAVAA--GDAVIYTAVDAKPKTTPRLRRLRNIEENPRVSLLVD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15607263    82 SYADDWTQLWWVRADGVAAIHRDG-EVMRAAYRLLRAKYAQYQSVPLNGPVIAIAVQRWASWH 143
Cdd:TIGR03668  79 RYDDDWTRLWWVRADGRAEILRPGeEEHAAAVRLLRAKYHQYQAVPLEGPVIAIRVERWASWG 141
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 11-142 2.10e-14

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: 65.71  E-value: 2.10e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263  11 AQSPVARLATStPDGTPHLVPVVFALGArrpaeatgaDVIYTAvdakrkTTQRLRRLANLEHNPRASVLVDSYADDWTQL 90
Cdd:COG3467  18 DEARVGRLATV-DDGRPYVVPVNYVYDG---------DTIYFH------TAKEGRKLDNLRRNPRVCFEVDELDGLHSTN 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15607263  91 WW-VRADGVAAIHRDGEVMRAAYRLLRAKYAQYQSVPLNGP------VIAIAVQRWASW 142
Cdd:COG3467  82 YRsVVVFGRAEEVEDPEEKARALRLLLEKYAPGRWRPFSDKeldataVIRIDPEEISGK 140
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 4-106 7.86e-13

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: 59.96  E-value: 7.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263     4 FDPKLR--FAQSPVARLATSTPDGTPHLVPVVFALGARRpaeatgaDVIYTAvdakrkTTQRLRRLANLEHNPRASVLVd 81
Cdd:pfam01243   1 LTEEIRefLAEPNAVVLATVDKDGRPNVRPVGLKYGFDT-------VGILFA------TNTDSRKARNLEENPRVALLF- 66

                          90       100
                  ....*....|....*....|....*
gi 15607263    82 syaDDWTQLWWVRADGVAAIHRDGE 106
Cdd:pfam01243  67 ---GDPELRRGVRIEGTAEIVTDGE 88
 
Name Accession Description Interval E-value
Rv0121_F420 TIGR03668
PPOX class probable F420-dependent enzyme, Rv0121 family; A Genome Properties metabolic ...
 2-143 1.15e-73

PPOX class probable F420-dependent enzyme, Rv0121 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: 132707  Cd Length: 141  Bit Score: 216.24  E-value: 1.15e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263     2 GEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEatGADVIYTAVDAKRKTTQRLRRLANLEHNPRASVLVD 81
Cdd:TIGR03668   1 LEFEARTRFAQARVARLATVSPDGEPHLVPVVFAVGAGAVAA--GDAVIYTAVDAKPKTTPRLRRLRNIEENPRVSLLVD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15607263    82 SYADDWTQLWWVRADGVAAIHRDG-EVMRAAYRLLRAKYAQYQSVPLNGPVIAIAVQRWASWH 143
Cdd:TIGR03668  79 RYDDDWTRLWWVRADGRAEILRPGeEEHAAAVRLLRAKYHQYQAVPLEGPVIAIRVERWASWG 141
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 11-142 2.10e-14

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: 65.71  E-value: 2.10e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263  11 AQSPVARLATStPDGTPHLVPVVFALGArrpaeatgaDVIYTAvdakrkTTQRLRRLANLEHNPRASVLVDSYADDWTQL 90
Cdd:COG3467  18 DEARVGRLATV-DDGRPYVVPVNYVYDG---------DTIYFH------TAKEGRKLDNLRRNPRVCFEVDELDGLHSTN 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15607263  91 WW-VRADGVAAIHRDGEVMRAAYRLLRAKYAQYQSVPLNGP------VIAIAVQRWASW 142
Cdd:COG3467  82 YRsVVVFGRAEEVEDPEEKARALRLLLEKYAPGRWRPFSDKeldataVIRIDPEEISGK 140
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 4-106 7.86e-13

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: 59.96  E-value: 7.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263     4 FDPKLR--FAQSPVARLATSTPDGTPHLVPVVFALGARRpaeatgaDVIYTAvdakrkTTQRLRRLANLEHNPRASVLVd 81
Cdd:pfam01243   1 LTEEIRefLAEPNAVVLATVDKDGRPNVRPVGLKYGFDT-------VGILFA------TNTDSRKARNLEENPRVALLF- 66

                          90       100
                  ....*....|....*....|....*
gi 15607263    82 syaDDWTQLWWVRADGVAAIHRDGE 106
Cdd:pfam01243  67 ---GDPELRRGVRIEGTAEIVTDGE 88
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
18-142 6.20e-09

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 51.09  E-value: 6.20e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263  18 LATSTPDGTPHLVPVVFALGArrpaeatGADVIYTAVDAKRkttqrlRRLANLEHNPRASVLVdSYADDWTqlwWVRADG 97
Cdd:COG3871  23 LATVDADGRPHSRPMWFQVDV-------DDGTLWFFTSRDS------AKVRNIRRDPRVSLSF-ADPGDDR---YVSVEG 85

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 15607263  98 VAAIHRDGEVMRAAYRLLRAKYAQyqsvplNGP------VIAIAVQRWASW 142
Cdd:COG3871  86 TAEIVDDRAKIDELWNPLAEAWFP------DGPddpdlvLLRVTPERAEYW 130
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 13-120 2.20e-07

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: 46.52  E-value: 2.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263    13 SPVARLATSTPDGTPHLVPVVFALgarrpaeatGADVIYTAVDAKRkttqrlRRLANLEHNPRASVLVDSyADDWTQlwW 92
Cdd:TIGR03618   8 RRLAVLATIRPDGRPQLSPVWFAL---------DGDELVFSTTAGR------AKARNLRRDPRVSLSVLD-PDGPYR--Y 69

                          90       100
                  ....*....|....*....|....*...
gi 15607263    93 VRADGVAAIHRDGEVMRAAYRLLRAKYA 120
Cdd:TIGR03618  70 VEIEGTAEVSPDPDAVRDLVDRLAERYR 97
PPOX_MSMEG_5819 TIGR04023
PPOX class F420-dependent enzyme, MSMEG_5819/OxyR family; A Genome Properties metabolic ...
 11-143 1.51e-04

PPOX class F420-dependent enzyme, MSMEG_5819/OxyR 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. This subfamily within the PPOX family occurs in at least 19 distinct species of F420 producers and is likely to bind F420 rather than FMN. The member OxyR was shown to use F420 to catalyze a C5a-C11a reduction in oxytetracycline biosynthesis. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274925  Cd Length: 115  Bit Score: 38.86  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15607263    11 AQSPVARLATSTPDGTPHLVPVVFALGArrpaeATGadVIYTAVDAKRKTtqrlRRLANLEHNPRASVLVDSYADdwTQL 90
Cdd:TIGR04023  10 ASQRLGRLATVDPDGQPQVVPVGFEYDG-----TLG--TIDIGGYNMSAT----RKFRNVAANGKVALVVDDLAS--TDP 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 15607263    91 WWVRAdgvAAIHRDGEVMRAayrllrakyaqyQSVPLNGPVIAIAVQRWASWH 143
Cdd:TIGR04023  77 WRVRG---IEIRGTAEALTD------------GGPPGPGPYIRIHPRRIWSWG 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH