YRC Public Data Repository - Protein Structure Prediction

Protein:	PDX3
Organism:	Saccharomyces cerevisiae
Length:	228 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for PDX3.

Description	E-value	Query Range	Subject Range
gi\|3396098 - gi\|3396098\|gb\|AAC28862.1\| pyridoxamine 5'-phosphate oxidase [Schizophyllum commune]	9.0E-82	[2..228]	[10..229]
gi\|207347761 - gi\|207347761\|gb\|EDZ73835.1\| YBR035Cp-like protein [Saccharomyces cerevisiae AWRI1631] gi\|190408798 - gi\|190408798\|gb\|EDV12063.1\| pyridoxine phosphate oxidase [Saccharomyces cerevisiae RM11-1a] PDX3 - Pyridoxine (pyridoxamine) phosphate oxidase, has homologs in E. coli and Myxococcus xanthus; transcr... PDX3_YEAST - Pyridoxamine 5'-phosphate oxidase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PDX3 P... gi\|151946426 - gi\|151946426\|gb\|EDN64648.1\| pyridoxine (pyridoxiamine) phosphate oxidase [Saccharomyces cerevisiae Y...	6.0E-81	[1..228]	[1..228]
PPOX1_ARATH - Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic OS=Arabidopsis thaliana GN=PPOX1 PE=1 ...	6.0E-80	[11..228]	[314..530]
PDXH_SHIFL - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Shigella flexneri GN=pdxH PE=3 SV=2 gi\|83569261, gi\|... - gi\|83569261\|ref\|ZP_00920718.1\| COG0259: Pyridoxamine-phosphate oxidase [Shigella dysenteriae 1012], ... PDXH_ECOLI - Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx) - Escherichia coli gi\|24113028, gi\|... - gi\|24113028\|ref\|NP_707538.1\| pyridoxamine 5'-phosphate oxidase [Shigella flexneri 2a str. 301], gi\|2... gi\|30063153, gi\|... - gi\|30063153\|ref\|NP_837324.1\| pyridoxamine 5'-phosphate oxidase [Shigella flexneri 2a str. 2457T], gi... gi\|188491170, gi... - gi\|75512929\|ref\|ZP_00735410.1\| COG0259: Pyridoxamine-phosphate oxidase [Escherichia coli 53638], gi\|... EG11487 - pyridoxine 5'-phosphate oxidase / Pyridoxine /pyridoxamine phosphate (PNP /PMP) oxidase; isoniazid res... gi\|89108480, gi\|... - gi\|89108480\|ref\|AP_002260.1\| pyridoxine 5'-phosphate oxidase [Escherichia coli str. K-12 substr. W31... gi\|194436464, gi... - gi\|83587973\|ref\|ZP_00926599.1\| COG0259: Pyridoxamine-phosphate oxidase [Escherichia coli 101-1], gi\|... PDXH_SHIF8 - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Shigella flexneri serotype 5b (strain 8401) GN=pdxH ... PDXH_ECOHS - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli O9:H4 (strain HS) GN=pdxH PE=3 SV=1 PDXH_ECOLU - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)... EG11487 - pyridoxine 5'-phosphate oxidase / Pyridoxine /pyridoxamine phosphate (PNP /PMP) oxidase; isoniazid res... PDXH_ECOLC - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Croo... PDXH_SHIBS - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Shigella boydii serotype 4 (strain Sb227) GN=pdxH PE... sp\|B7URX9\|PDXH_ECO27 - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN... PDXH_SHIDS - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=pd... PDXH_ECODH - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli (strain K12 / DH10B) GN=pdxH PE=3 S... PDXH_ECO27 - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN... gi\|124529205, gi... - gi\|124529205\|ref\|ZP_01700280.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli B], gi\|124499979... PDXH_ECOBW - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=p... gi\|251785096, gi... - gi\|251785096\|ref\|YP_002999400.1\| hypothetical protein B21_01598 [Escherichia coli BL21], gi\|24237736... gi\|254288489, gi... - gi\|254288489\|ref\|YP_003054237.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli BL21(DE3)], gi\|... gi\|254161700, gi... - gi\|254161700\|ref\|YP_003044808.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli B str. REL606],...	2.0E-78	[1..228]	[1..218]
PDXH_ECO5E - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=p... gi\|208821813, gi... - gi\|208821813\|ref\|ZP_03262133.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4... gi\|217328903, gi... - gi\|217328903\|ref\|ZP_03444984.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. TW1... gi\|195939028 - gi\|195939028\|ref\|ZP_03084410.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4... gi\|189370944, gi... - gi\|189370944\|gb\|EDU89360.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC869],... gi\|254793255, gi... - gi\|254793255\|ref\|YP_003078092.1\| pyridoxine 5'-phosphate oxidase [Escherichia coli O157:H7 str. TW14... PDXH_ECO57 - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Escherichia coli O157:H7 GN=pdxH PE=3 SV=1 gi\|208731057, gi... - gi\|208816714\|ref\|ZP_03257834.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4... gi\|25284781, gi\|... - pir\|\|G85770 pyridoxinephosphate oxidase [imported] - Escherichia coli (strain O157:H7, substrain ED... gi\|208810284, gi... - gi\|208810284\|ref\|ZP_03252160.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4... gi\|189360014, gi... - gi\|189360014\|gb\|EDU78433.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4486]... gi\|12515630, gi\|... - gi\|15802052\|ref\|NP_288074.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 EDL933], gi... gi\|189364999, gi... - gi\|189364999\|gb\|EDU83415.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4501]... gi\|188999208, gi... - gi\|188999208\|gb\|EDU68194.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4076]... gi\|187768649, gi... - gi\|187768649\|gb\|EDU32493.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4196]... gi\|189354268, gi... - gi\|189354268\|gb\|EDU72687.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4401]... gi\|188013553, gi... - gi\|188013553\|gb\|EDU51675.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. EC4113]... gi\|15831601, gi\|... - gi\|15831601\|ref\|NP_310374.1\| pyridoxamine 5'-phosphate oxidase [Escherichia coli O157:H7 str. Sakai]...	3.0E-78	[1..228]	[1..218]
PNPO_MOUSE - Pyridoxine-5'-phosphate oxidase OS=Mus musculus GN=Pnpo PE=1 SV=1	7.0E-78	[9..228]	[29..261]
PDXH_SALTI - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella typhi GN=pdxH PE=3 SV=1 gi\|213586446 - gi\|213586446\|ref\|ZP_03368272.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... gi\|29141775, gi\|... - gi\|29141775\|ref\|NP_805117.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica ... gi\|213649177 - gi\|213649177\|ref\|ZP_03379230.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... gi\|213981250 - gi\|213981250\|ref\|ZP_03408509.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... gi\|214000282 - gi\|214000282\|ref\|ZP_03411017.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... gi\|16760465 - gi\|16760465\|ref\|NP_456082.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica ... gi\|213051638 - gi\|213051638\|ref\|ZP_03344516.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... gi\|213425989 - gi\|213425989\|ref\|ZP_03358739.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... PDXH_SALTI - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella typhi GN=pdxH PE=3 SV=1	9.0E-78	[1..228]	[1..218]
gi\|168235520, gi... - gi\|197290951\|gb\|EDY30304.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... gi\|168229822, gi... - gi\|205335225\|gb\|EDZ21989.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... gi\|205346937, gi... - gi\|205346937\|gb\|EDZ33568.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... PDXH_SALCH - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella choleraesuis GN=pdxH PE=3 SV=1 gi\|205339325, gi... - gi\|205339325\|gb\|EDZ26089.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... PDXH_SALTY - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella typhimurium GN=pdxH PE=3 SV=1 lcl\|NC_016856.1_... - [gene=pdxH] [protein=pyridoxamine 5'-phosphate oxidase] [protein_id=YP_005237318.1] [location=153268... gi\|205327836, gi... - gi\|205327836\|gb\|EDZ14600.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... gi\|205323536, gi... - gi\|205323536\|gb\|EDZ11375.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... PDXH_SALPB - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)... PDXH_SALEP - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella enteritidis PT4 (strain P125109) GN=pdxH ... PDXH_SALG2 - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) G... PDXH_SALPC - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella paratyphi C (strain RKS4594) GN=pdxH PE=3... PDXH_SALDC - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella dublin (strain CT_02021853) GN=pdxH PE=3 ... PDXH_SALPK - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella paratyphi A (strain AKU_12601) GN=pdxH PE... gi\|204927951, gi... - gi\|204927951\|ref\|ZP_03219152.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... gi\|199602693, gi... - gi\|200390248\|ref\|ZP_03216859.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... PDXH_SALSV - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella schwarzengrund (strain CVM19633) GN=pdxH ... gi\|194458771, gi... - gi\|194472407\|ref\|ZP_03078391.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... gi\|197265568, gi... - gi\|197265568\|ref\|ZP_03165642.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri... PDXH_SALA4 - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella agona (strain SL483) GN=pdxH PE=3 SV=1 gi\|168819198, gi... - gi\|205343887\|gb\|EDZ30651.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... gi\|168463141, gi... - gi\|195634425\|gb\|EDX52777.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enterica s... PDXH_SALTY - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC... PDXH_SALHS - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella heidelberg (strain SL476) GN=pdxH PE=3 SV... PDXH_SALNS - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella newport (strain SL254) GN=pdxH PE=3 SV=1 PDXH_SALTY - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella typhimurium GN=pdxH PE=3 SV=1 PDXH_SALCH - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella choleraesuis GN=pdxH PE=3 SV=1 PDXH_SALPA - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella paratyphi A GN=pdxH PE=3 SV=1 PDXH_SALPB - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)... PDXH_SALCH - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella choleraesuis (strain SC-B67) GN=pdxH PE=3... PDXH_SALPA - Pyridoxine/pyridoxamine 5'-phosphate oxidase OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) G... gi\|238913151 - gi\|238913151\|ref\|ZP_04656988.1\| pyridoxamine 5'-phosphate oxidase [Salmonella enterica subsp. enteri...	2.0E-77	[1..228]	[1..218]
PDXH_ECOLI - (P0AFI7) Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx) PDXH_SHIFL - (P0AFI8) Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) (PNP/PMP oxidase) (PNPOx)	2.0E-77	[2..228]	[1..217]
PDX3_SCHPO - Probable pyridoxamine 5'-phosphate oxidase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN... SPAC1093.02 - pyridoxamine 5'-phosphate oxidase	7.0E-77	[1..228]	[1..231]

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Predicted Domain #1

Region A:
Residues: [1-139]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTKQAEETQK PIIFAPETYQ YDKFTLNEKQ LTDDPIDLFT KWFNEAKEDP RETLPEAITF  60
   61 SSAELPSGRV SSRILLFKEL DHRGFTIYSN WGTSRKAHDI ATNPNAAIVF FWKDLQRQVR 120
  121 VEGITEHVNR ETSERYFKT

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [183-228]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PDYWGGLRIV PLEIEFWQGR PSRLHDRFVY RRKTENDPWK VVRLAP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1311.69897
Match:	1ci0A_
Description:	Pyridoxine 5'-phoshate oxidase (PNP oxidase)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
pyridoxamine-phosphate oxidase activity	3.81533880638523	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor	1.18444956617957	bayes_pls_golite062009
catalytic activity	0.660906721832294	bayes_pls_golite062009
oxidoreductase activity	0.0268904833845668	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [140-182]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RPRGSKIGAW ASRQSDVIKN REELDELTQK NTERFKDAED IPC

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1311.69897
Match:	1ci0A_
Description:	Pyridoxine 5'-phoshate oxidase (PNP oxidase)
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: