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Conserved domains on  [gi|873551503|emb|CRY79185|]
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Uncharacterized stress protein (general stress protein 26) [Nocardia farcinica]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein; nitroreductase family deazaflavin-dependent oxidoreductase( domain architecture ID 10022756)

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

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List of domain hits

 Name Accession Description Interval E-value
Rv3369 TIGR03667
PPOX class probable F420-dependent enzyme, Rv3369 family; A Genome Properties metabolic ...
 15-144 1.72e-76

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: 223.11  E-value: 1.72e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   15 TEFGAKVAERLEREQVVWLTTVGPTGTPQPNPVWFQWRDGEFLLFSQPDTPKIRNIRRNPRVSVHFNSTVHGGDVVVFTG 94
Cdd:TIGR03667   1 TEFTAKVARRLREESIVWLTTVRRSGQPQPVPVWFLWDGTEFLIYSRPQAAKLRNIRRNPRVSLHLNSDGRGGDVVVFTG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 873551503   95 TARIAEDRPTEQEIAAFTAKYTEGLRDIPMTAEQFYADYSVPLRIAPDRL 144
Cdd:TIGR03667  81 TAEVVADAPPAREIPAYLAKYREDAARIGMTPERFAADYSVPLRVTPERL 130
 
Name Accession Description Interval E-value
Rv3369 TIGR03667
PPOX class probable F420-dependent enzyme, Rv3369 family; A Genome Properties metabolic ...
 15-144 1.72e-76

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: 223.11  E-value: 1.72e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   15 TEFGAKVAERLEREQVVWLTTVGPTGTPQPNPVWFQWRDGEFLLFSQPDTPKIRNIRRNPRVSVHFNSTVHGGDVVVFTG 94
Cdd:TIGR03667   1 TEFTAKVARRLREESIVWLTTVRRSGQPQPVPVWFLWDGTEFLIYSRPQAAKLRNIRRNPRVSLHLNSDGRGGDVVVFTG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 873551503   95 TARIAEDRPTEQEIAAFTAKYTEGLRDIPMTAEQFYADYSVPLRIAPDRL 144
Cdd:TIGR03667  81 TAEVVADAPPAREIPAYLAKYREDAARIGMTPERFAADYSVPLRVTPERL 130
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
12-143 1.91e-24

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 91.15  E-value: 1.91e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503  12 DTGTEFGAKVAERLEREQVVWLTTVGPTGTPQPNPVWFQW--RDGEFLLFSQPDTPKIRNIRRNPRVSVHFNSTvHGGDV 89
Cdd:COG3871    2 TDDEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVdvDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADP-GDDRY 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 873551503  90 VVFTGTARIAEDRPTEQEIA-AFTAKYTEGLRDIPmtaeqfyaDYSVpLRIAPDR 143
Cdd:COG3871   81 VSVEGTAEIVDDRAKIDELWnPLAEAWFPDGPDDP--------DLVL-LRVTPER 126
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 17-103 6.21e-14

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: 63.04  E-value: 6.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   17 FGAKVAERLEREQVVWLTTVGPTGTPQPNPVWFQWRDGE--FLLFSQPDTPKIRNIRRNPRVSVHFNStVHGGDVVVFTG 94
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGD-PELRRGVRIEG 79


                  ....*....
gi 873551503   95 TARIAEDRP 103
Cdd:pfam01243  80 TAEIVTDGE 88
 
Name Accession Description Interval E-value
Rv3369 TIGR03667
PPOX class probable F420-dependent enzyme, Rv3369 family; A Genome Properties metabolic ...
 15-144 1.72e-76

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: 223.11  E-value: 1.72e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   15 TEFGAKVAERLEREQVVWLTTVGPTGTPQPNPVWFQWRDGEFLLFSQPDTPKIRNIRRNPRVSVHFNSTVHGGDVVVFTG 94
Cdd:TIGR03667   1 TEFTAKVARRLREESIVWLTTVRRSGQPQPVPVWFLWDGTEFLIYSRPQAAKLRNIRRNPRVSLHLNSDGRGGDVVVFTG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 873551503   95 TARIAEDRPTEQEIAAFTAKYTEGLRDIPMTAEQFYADYSVPLRIAPDRL 144
Cdd:TIGR03667  81 TAEVVADAPPAREIPAYLAKYREDAARIGMTPERFAADYSVPLRVTPERL 130
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
12-143 1.91e-24

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 91.15  E-value: 1.91e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503  12 DTGTEFGAKVAERLEREQVVWLTTVGPTGTPQPNPVWFQW--RDGEFLLFSQPDTPKIRNIRRNPRVSVHFNSTvHGGDV 89
Cdd:COG3871    2 TDDEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVdvDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADP-GDDRY 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 873551503  90 VVFTGTARIAEDRPTEQEIA-AFTAKYTEGLRDIPmtaeqfyaDYSVpLRIAPDR 143
Cdd:COG3871   81 VSVEGTAEIVDDRAKIDELWnPLAEAWFPDGPDDP--------DLVL-LRVTPER 126
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 33-146 1.83e-16

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: 70.40  E-value: 1.83e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   33 LTTVGPTGTPQPNPVWFQWRDGEFLLFSQPDTPKIRNIRRNPRVSVHFNSTVHGGDVVVFTGTARIAED----RPTEQEI 108
Cdd:TIGR03618  13 LATIRPDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSVLDPDGPYRYVEIEGTAEVSPDpdavRDLVDRL 92

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 873551503  109 AA-FTAKYTEGLRDIPMTAEQfyadySVPLRIAPDRLRG 146
Cdd:TIGR03618  93 AErYRGAAGEDEYRRPMVDPR-----RVVVRVTPERVYG 126
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 17-103 6.21e-14

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: 63.04  E-value: 6.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   17 FGAKVAERLEREQVVWLTTVGPTGTPQPNPVWFQWRDGE--FLLFSQPDTPKIRNIRRNPRVSVHFNStVHGGDVVVFTG 94
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTvgILFATNTDSRKARNLEENPRVALLFGD-PELRRGVRIEG 79


                  ....*....
gi 873551503   95 TARIAEDRP 103
Cdd:pfam01243  80 TAEIVTDGE 88
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 19-146 2.71e-13

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: 62.63  E-value: 2.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503  19 AKVAERLEREQVVWLTTVgPTGTPQPNPVWFQWRDGEFLLFSQPDTPKIRNIRRNPRVSV-----HFNSTVHGGDVVVFt 93
Cdd:COG3467   11 EEIRALLDEARVGRLATV-DDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLRRNPRVCFevdelDGLHSTNYRSVVVF- 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 873551503  94 GTARIAEDRPTEQEI-AAFTAKYTEGLRDIPMTAEqfYADYSVpLRIAPDRLRG 146
Cdd:COG3467   89 GRAEEVEDPEEKARAlRLLLEKYAPGRWRPFSDKE--LDATAV-IRIDPEEISG 139
Pyrid_ox_like pfam16242
Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is ...
 19-121 1.51e-10

Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is mainly found in general stress proteins in various Xanthomonas species. It is composed of a six-stranded antiparallel beta-barrel flanked by five alpha-helices and can bind to FMN and FAD, suggesting that it may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant.


Pssm-ID: 435234 [Multi-domain]  Cd Length: 149  Bit Score: 55.79  E-value: 1.51e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   19 AKVAERLEREQVVWLTTVGPTGTPQPNPVWFQWR--DGEFLLFSQPDTPKIRNIRRNPRVSVHFNSTVHgGDVVVFTGTA 96
Cdd:pfam16242   4 EKLWELIKDIRTAMLTTTTAGGGLHSRPMATQEVefDGDLWFFTDKDSDKVDEIREDPQVNVAFSDPSK-NNYVSVSGTA 82

                          90       100
                  ....*....|....*....|....*..
gi 873551503   97 RIAEDRPTEQEI--AAFTAKYTEGLRD 121
Cdd:pfam16242  83 EVVRDRAKIDELwnPVAKAWFPEGKDD 109
Rv2061_F420 TIGR03666
PPOX class probable F420-dependent enzyme, Rv2061 family; A Genome Properties metabolic ...
 23-115 8.50e-08

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: 48.10  E-value: 8.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   23 ERLEREQVVWLTTVGPTGTPQPNPVWFQWRDGEFLLFSQPDTPKIRNIRRNPRVSVHfNSTVHG---GDVVvfTGTARIA 99
Cdd:TIGR03666   7 ADLARARYALLTTFRKDGTPVPTPVWAAVDGDKLLVRTKEDSWKVKRIRNNPRVTLA-PCDRRGrptGPVV--PGRARIL 83

                          90
                  ....*....|....*.
gi 873551503  100 EDRPTEQEIAAFTAKY 115
Cdd:TIGR03666  84 DGAETARARDLLARRY 99
F420H2_quin_red pfam04075
F420H(2)-dependent quinone reductase; This family of proteins is found in the genera ...
 16-133 9.35e-05

F420H(2)-dependent quinone reductase; This family of proteins is found in the genera Mycobacterium and Streptomyces. Member protein Rv3547 has been characterized as a deazaflavin-dependent nitroreductase. Rv1558 is an F420H(2)-dependent quinone reductase involved in oxidative stress protection.


Pssm-ID: 281995  Cd Length: 129  Bit Score: 39.74  E-value: 9.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873551503   16 EFGAKVAERLEREQVVWLTTVGP-TGTPQPNPVWFQWRDGEFLLFSQ----PDTPK-IRNIRRNPRVSVHFNStvhggdv 89
Cdd:pfam04075  11 RTGGTVGRRLPGVPVLLLTTTGRkTGQPRTTPLGGVRDGDSYLVVASkggaPRHPGwYYNLKANPRVRVQIGG------- 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 873551503   90 VVFTGTARIAEDRPTEQeiaaftakytegLRDIPMTAEQFYADY 133
Cdd:pfam04075  84 RWLDGTARLAPDDERAR------------LWQLPVLNSPGYAVY 115
 
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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