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Conserved domains on  [gi|1359345029|gb|PRT13938|]
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general stress protein [Bacillus toyonensis]

Protein Classification

pyridoxamine 5'-phosphate oxidase family protein( domain architecture ID 11467517)

pyridoxamine 5'-phosphate oxidase family protein binds FMN and FAD; similar to Bacillus subtilis general stress protein 26 that is induced by heat shock, salt stress, oxidative stress, glucose limitation and oxygen limitation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
3-127 7.66e-35

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


:

Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 117.34  E-value: 7.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   3 LKEKIATIIQGQRTGVLSTVR-NEKPHSAFMMFFHE--DFVLYVATDRQSKKITDIENNPNVHVLLGREGkklDEDYIEV 79
Cdd:COG3871     7 LEEKLWELLEDIRTAMLATVDaDGRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPG---DDRYVSV 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1359345029  80 EGLASIEEDSTLKNKFWNNSLKRWL-LGPEDPNYVLIKINPDTIYYIDG 127
Cdd:COG3871    84 EGTAEIVDDRAKIDELWNPLAEAWFpDGPDDPDLVLLRVTPERAEYWDS 132
 
Name Accession Description Interval E-value
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
3-127 7.66e-35

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 117.34  E-value: 7.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   3 LKEKIATIIQGQRTGVLSTVR-NEKPHSAFMMFFHE--DFVLYVATDRQSKKITDIENNPNVHVLLGREGkklDEDYIEV 79
Cdd:COG3871     7 LEEKLWELLEDIRTAMLATVDaDGRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPG---DDRYVSV 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1359345029  80 EGLASIEEDSTLKNKFWNNSLKRWL-LGPEDPNYVLIKINPDTIYYIDG 127
Cdd:COG3871    84 EGTAEIVDDRAKIDELWNPLAEAWFpDGPDDPDLVLLRVTPERAEYWDS 132
Pyrid_ox_like pfam16242
Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is ...
 4-129 2.06e-19

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: 78.52  E-value: 2.06e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   4 KEKIATIIQGQRTGVLSTV-RNEKPHSAFMMFFHEDF--VLYVATDRQSKKITDIENNPNVHVLLGREGKKldeDYIEVE 80
Cdd:pfam16242   3 VEKLWELIKDIRTAMLTTTtAGGGLHSRPMATQEVEFdgDLWFFTDKDSDKVDEIREDPQVNVAFSDPSKN---NYVSVS 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1359345029  81 GLASIEEDSTLKNKFWNNSLKRWLL-GPEDPNYVLIKINPDTIYYIDGAG 129
Cdd:pfam16242  80 GTAEVVRDRAKIDELWNPVAKAWFPeGKDDPNITLLKVTPKEAEYWDSPG 129
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 8-88 1.71e-06

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: 44.21  E-value: 1.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   8 ATIIQGQRTGVLSTVR-NEKPHSAFMMFFHEDFVLYVATDRQSKKITDIENNPNVHVLLgregkkLDED----YIEVEGL 82
Cdd:TIGR03618   2 RDLLSERRLAVLATIRpDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSV------LDPDgpyrYVEIEGT 75


                  ....*.
gi 1359345029  83 ASIEED 88
Cdd:TIGR03618  76 AEVSPD 81
 
Name Accession Description Interval E-value
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
3-127 7.66e-35

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 117.34  E-value: 7.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   3 LKEKIATIIQGQRTGVLSTVR-NEKPHSAFMMFFHE--DFVLYVATDRQSKKITDIENNPNVHVLLGREGkklDEDYIEV 79
Cdd:COG3871     7 LEEKLWELLEDIRTAMLATVDaDGRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPG---DDRYVSV 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1359345029  80 EGLASIEEDSTLKNKFWNNSLKRWL-LGPEDPNYVLIKINPDTIYYIDG 127
Cdd:COG3871    84 EGTAEIVDDRAKIDELWNPLAEAWFpDGPDDPDLVLLRVTPERAEYWDS 132
Pyrid_ox_like pfam16242
Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is ...
 4-129 2.06e-19

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: 78.52  E-value: 2.06e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   4 KEKIATIIQGQRTGVLSTV-RNEKPHSAFMMFFHEDF--VLYVATDRQSKKITDIENNPNVHVLLGREGKKldeDYIEVE 80
Cdd:pfam16242   3 VEKLWELIKDIRTAMLTTTtAGGGLHSRPMATQEVEFdgDLWFFTDKDSDKVDEIREDPQVNVAFSDPSKN---NYVSVS 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1359345029  81 GLASIEEDSTLKNKFWNNSLKRWLL-GPEDPNYVLIKINPDTIYYIDGAG 129
Cdd:pfam16242  80 GTAEVVRDRAKIDELWNPVAKAWFPeGKDDPNITLLKVTPKEAEYWDSPG 129
NimA COG3467
Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5 ...
 4-122 1.91e-11

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: 57.62  E-value: 1.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   4 KEKIATIIQGQRTGVLSTVRNEKPHSAFMMFFHEDFVLYVATDRQSKKITDIENNPNVHVLLGREGKKLDEDY--IEVEG 81
Cdd:COG3467    10 REEIRALLDEARVGRLATVDDGRPYVVPVNYVYDGDTIYFHTAKEGRKLDNLRRNPRVCFEVDELDGLHSTNYrsVVVFG 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1359345029  82 LASIEEDSTLKNKFWNNSLKRWLLGPEDP-------NYVLIKINPDTI 122
Cdd:COG3467    90 RAEEVEDPEEKARALRLLLEKYAPGRWRPfsdkeldATAVIRIDPEEI 137
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 3-88 1.92e-10

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: 53.79  E-value: 1.92e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   3 LKEKIATIIQGQRTGVLSTVRNE-KPHSAFMMFFHED--FVLYVATDRQSKKITDIENNPNVHVLLGREGkklDEDYIEV 79
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDgRPNVRPVGLKYGFdtVGILFATNTDSRKARNLEENPRVALLFGDPE---LRRGVRI 77


                  ....*....
gi 1359345029  80 EGLASIEED 88
Cdd:pfam01243  78 EGTAEIVTD 86
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 8-88 1.71e-06

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: 44.21  E-value: 1.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1359345029   8 ATIIQGQRTGVLSTVR-NEKPHSAFMMFFHEDFVLYVATDRQSKKITDIENNPNVHVLLgregkkLDED----YIEVEGL 82
Cdd:TIGR03618   2 RDLLSERRLAVLATIRpDGRPQLSPVWFALDGDELVFSTTAGRAKARNLRRDPRVSLSV------LDPDgpyrYVEIEGT 75


                  ....*.
gi 1359345029  83 ASIEED 88
Cdd:TIGR03618  76 AEVSPD 81
 
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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