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Conserved domains on  [gi|394268550|gb|EJE13106|]
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hypothetical protein HMPREF9981_00291 [Staphylococcus epidermidis NIHLM020]

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];
2-128 1.33e-27

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


:

Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 98.85  E-value: 1.33e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394268550   2 NKQQVTKAIEKVLNSSKIGVLSTAHHN-KPNSRYMVFYND--DLNLYTKTNINSLKVEEIENNPDAHILLGYNEttNNSF 78
Cdd:COG3871    3 DDEELEEKLWELLEDIRTAMLATVDADgRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPG--DDRY 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 394268550  79 VEIDATIEVVKNQKVIDWLWETQDKTFF-NSKEDPELCVLKVIPRSIKLMN 128
Cdd:COG3871   81 VSVEGTAEIVDDRAKIDELWNPLAEAWFpDGPDDPDLVLLRVTPERAEYWD 131
 
Name Accession Description Interval E-value
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
2-128 1.33e-27

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 98.85  E-value: 1.33e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394268550   2 NKQQVTKAIEKVLNSSKIGVLSTAHHN-KPNSRYMVFYND--DLNLYTKTNINSLKVEEIENNPDAHILLGYNEttNNSF 78
Cdd:COG3871    3 DDEELEEKLWELLEDIRTAMLATVDADgRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPG--DDRY 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 394268550  79 VEIDATIEVVKNQKVIDWLWETQDKTFF-NSKEDPELCVLKVIPRSIKLMN 128
Cdd:COG3871   81 VSVEGTAEIVDDRAKIDELWNPLAEAWFpDGPDDPDLVLLRVTPERAEYWD 131
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 6-88 4.80e-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: 4.80e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394268550    6 VTKAIEKVLNSSKIGVLSTAHHN-KPNSRYM--VFYNDDLNLYTKTNINSLKVEEIENNPDAHILLGYNEttNNSFVEID 82
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDgRPNVRPVglKYGFDTVGILFATNTDSRKARNLEENPRVALLFGDPE--LRRGVRIE 78


                  ....*.
gi 394268550   83 ATIEVV 88
Cdd:pfam01243  79 GTAEIV 84
 
Name Accession Description Interval E-value
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
2-128 1.33e-27

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


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 98.85  E-value: 1.33e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394268550   2 NKQQVTKAIEKVLNSSKIGVLSTAHHN-KPNSRYMVFYND--DLNLYTKTNINSLKVEEIENNPDAHILLGYNEttNNSF 78
Cdd:COG3871    3 DDEELEEKLWELLEDIRTAMLATVDADgRPHSRPMWFQVDvdDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPG--DDRY 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 394268550  79 VEIDATIEVVKNQKVIDWLWETQDKTFF-NSKEDPELCVLKVIPRSIKLMN 128
Cdd:COG3871   81 VSVEGTAEIVDDRAKIDELWNPLAEAWFpDGPDDPDLVLLRVTPERAEYWD 131
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 6-88 4.80e-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: 4.80e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394268550    6 VTKAIEKVLNSSKIGVLSTAHHN-KPNSRYM--VFYNDDLNLYTKTNINSLKVEEIENNPDAHILLGYNEttNNSFVEID 82
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDgRPNVRPVglKYGFDTVGILFATNTDSRKARNLEENPRVALLFGDPE--LRRGVRIE 78


                  ....*.
gi 394268550   83 ATIEVV 88
Cdd:pfam01243  79 GTAEIV 84
Pyrid_ox_like pfam16242
Pyridoxamine 5'-phosphate oxidase like; This domain, approximately 140 residues in length, is ...
 8-123 6.56e-14

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: 64.27  E-value: 6.56e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394268550    8 KAIEKV---LNSSKIGVLSTAHH-NKPNSRYMVFY--NDDLNLYTKTNINSLKVEEIENNPDAHilLGYNETTNNSFVEI 81
Cdd:pfam16242   1 DAVEKLwelIKDIRTAMLTTTTAgGGLHSRPMATQevEFDGDLWFFTDKDSDKVDEIREDPQVN--VAFSDPSKNNYVSV 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 394268550   82 DATIEVVKNQKVIDWLWETQDKTFF-NSKEDPELCVLKVIPRS 123
Cdd:pfam16242  79 SGTAEVVRDRAKIDELWNPVAKAWFpEGKDDPNITLLKVTPKE 121
 
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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