YRC Public Data Repository - Protein Structure Prediction

Protein:	SER33
Organism:	Saccharomyces cerevisiae
Length:	469 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 SER33.

Description	E-value	Query Range	Subject Range
SER33 - 3-phosphoglycerate dehydrogenase, catalyzes the first step in serine and glycine biosynthesis; isozy... SER33_YEAST - D-3-phosphoglycerate dehydrogenase 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SER...	0.0	[1..469]	[1..469]
SERA_SCHPO - Putative D-3-phosphoglycerate dehydrogenase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) G... SPCC364.07 - D-3 phosphoglycerate dehydrogenase	0.0	[15..469]	[7..466]
SERA_HAEIN - D-3-phosphoglycerate dehydrogenase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 /... SERA_HAEIN - D-3-phosphoglycerate dehydrogenase OS=Haemophilus influenzae GN=serA PE=3 SV=1	0.0	[51..469]	[4..410]
gi\|15603536, gi\|... - gi\|15603536\|ref\|NP_246610.1\| D-3-phosphoglycerate dehydrogenase [Pasteurella multocida subsp. multoc...	0.0	[50..469]	[3..410]
gi\|149367076, gi... - gi\|149367076\|ref\|ZP_01889109.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis CA88-4125], gi\|1... gi\|145597906, gi... - gi\|145597906\|ref\|YP_001161982.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis Pestoides F], g... Q666Q8\|Q666Q8_YERPS - D-3-phosphoglycerate dehydrogenase - Yersinia pseudotuberculosis gi\|162351285, gi... - gi\|77635842\|ref\|ZP_00797922.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [Y... gi\|229837603, gi... - gi\|229837603\|ref\|ZP_04457765.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis Pestoides A], gi... gi\|77630166, gi\|... - gi\|77630166\|ref\|ZP_00792752.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [Y... gi\|229840827, gi... - gi\|229840827\|ref\|ZP_04460986.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis biovar Orientali... gi\|166212868, gi... - gi\|166212868\|ref\|ZP_02238903.1\| phosphoglycerate dehydrogenase [Yersinia pestis biovar Antiqua str. ... gi\|229690923, gi... - gi\|229842613\|ref\|ZP_04462768.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis biovar Orientali... gi\|165990784, gi... - gi\|166010298\|ref\|ZP_02231196.1\| phosphoglycerate dehydrogenase [Yersinia pestis biovar Antiqua str. ... gi\|166963027, gi... - gi\|167419033\|ref\|ZP_02310786.1\| phosphoglycerate dehydrogenase [Yersinia pestis biovar Orientalis st... gi\|167399894, gi... - gi\|167399894\|ref\|ZP_02305412.1\| phosphoglycerate dehydrogenase [Yersinia pestis biovar Antiqua str. ... gi\|169749642, gi... - gi\|170023108\|ref\|YP_001719613.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pseudotuberculosis YPI... gi\|167425272, gi... - gi\|167425272\|ref\|ZP_02317025.1\| phosphoglycerate dehydrogenase [Yersinia pestis biovar Mediaevalis s... gi\|186699647, gi... - gi\|186896621\|ref\|YP_001873733.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pseudotuberculosis PB1... gi\|51597499, gi\|... - gi\|51597499\|ref\|YP_071690.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pseudotuberculosis IP 3295... gi\|25283924 - pir\|\|AC0112 phosphoglycerate dehydrogenase (EC 1.1.1.95) [imported] - Yersinia pestis (strain CO92) gi\|16121219, gi\|... - gi\|218928087\|ref\|YP_002345962.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis CO92], gi\|16121... gi\|165937338, gi... - gi\|89104319\|ref\|ZP_01176865.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [Y... gi\|108778263, gi... - gi\|108806350\|ref\|YP_650266.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis Antiqua], gi\|10877... gi\|165925145, gi... - gi\|165925145\|ref\|ZP_02220977.1\| phosphoglycerate dehydrogenase [Yersinia pestis biovar Orientalis st... gi\|229679501, gi... - gi\|229903731\|ref\|ZP_04518844.1\| D-3-phosphoglycerate dehydrogenase [Yersinia pestis Nepal516], gi\|22...	0.0	[49..469]	[1..413]
gi\|15642477, gi\|... - gi\|9657060\|gb\|AAF95623.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae O1 biovar El Tor str. ... gi\|11354856 - pir\|\|C82072 D-3-phosphoglycerate dehydrogenase VC2481 [imported] - Vibrio cholerae (strain N16961 se... gi\|116188123, gi... - gi\|75829170\|ref\|ZP_00758483.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [V... gi\|146315088, gi... - gi\|75827743\|ref\|ZP_00757178.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [V... gi\|75814144, gi\|... - gi\|75814144\|ref\|ZP_00744778.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [V... gi\|229606966, gi... - gi\|229606966\|ref\|YP_002877614.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae MJ-1236], gi\|22... gi\|229344169, gi... - gi\|229519480\|ref\|ZP_04408923.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae RC9], gi\|2293441... gi\|121547398, gi... - gi\|121590757\|ref\|ZP_01678087.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae 2740-80], gi\|121... gi\|229507461, gi... - gi\|229507461\|ref\|ZP_04396966.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae BX 330286], gi\|2... gi\|124118869, gi... - gi\|153222432\|ref\|ZP_01953166.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae MAK 757], gi\|124... gi\|227082601, gi... - gi\|227082601\|ref\|YP_002811152.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae M66-2], gi\|2270... gi\|153819339, gi... - gi\|153819339\|ref\|ZP_01972006.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae NCTC 8457], gi\|1... gi\|153822868, gi... - gi\|229512344\|ref\|ZP_04401823.1\| D-3-phosphoglycerate dehydrogenase [Vibrio cholerae B33], gi\|2293523...	0.0	[49..469]	[1..409]
EG10944 - D-3-phosphoglycerate dehydrogenase / D-3-Phosphoglycerate dehydrogenase gi\|15803448, gi\|... - gi\|15803448\|ref\|NP_289481.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli O157:H7 EDL933], g... gi\|168753855, gi... - gi\|189358531\|gb\|EDU76950.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4401], g... gi\|254162824, gi... - gi\|254162824\|ref\|YP_003045932.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli B str. REL606]... gi\|188017939, gi... - gi\|188017939\|gb\|EDU56061.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4113], g... gi\|254594262, gi... - gi\|254794862\|ref\|YP_003079699.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. T... gi\|168766910, gi... - gi\|189363684\|gb\|EDU82103.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4486], g... gi\|168760045, gi... - gi\|189369216\|gb\|EDU87632.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4501], g... gi\|117625142, gi... - gi\|117625142\|ref\|YP_854130.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli APEC O1], gi\|1155... gi\|189000621, gi... - gi\|189000621\|gb\|EDU69607.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4076], g... gi\|124526182, gi... - gi\|124526182\|ref\|ZP_01698187.1\| D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Escheric... gi\|168773457, gi... - gi\|187770872\|gb\|EDU34716.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4196], g... gi\|189379849, gi... - gi\|189379849\|gb\|EDU98265.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC508], gi... gi\|189373809, gi... - gi\|189373809\|gb\|EDU92225.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC869], gi... gi\|209920366, gi... - gi\|209920366\|ref\|YP_002294450.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli SE11], gi\|2099... gi\|209159929, gi... - gi\|209398529\|ref\|YP_002272388.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC411... gi\|218555461, gi... - gi\|218555461\|ref\|YP_002388374.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli IAI1], gi\|2183... gi\|217326934, gi... - gi\|217326934\|ref\|ZP_03443017.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. TW1458... gi\|218691036, gi... - gi\|218691036\|ref\|YP_002399248.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli ED1a], gi\|2184... gi\|218559904, gi... - gi\|218559904\|ref\|YP_002392817.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli S88], gi\|21836... gi\|218433514, gi... - gi\|218706417\|ref\|YP_002413936.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli UMN026], gi\|21... gi\|218701620, gi... - gi\|218701620\|ref\|YP_002409249.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli IAI39], gi\|218... gi\|74313470, gi\|... - gi\|74313470\|ref\|YP_311889.1\| D-3-phosphoglycerate dehydrogenase [Shigella sonnei Ss046], gi\|73856947... gi\|170082472, gi... - gi\|170082472\|ref\|YP_001731792.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli str. K-12 subs... SERA_ECOL6 - D-3-phosphoglycerate dehydrogenase OS=Escherichia coli O6 GN=serA PE=3 SV=2 gi\|169753770, gi... - gi\|170018842\|ref\|YP_001723796.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli ATCC 8739], gi... gi\|75258512, gi\|... - gi\|75258512\|ref\|ZP_00729934.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [E... gi\|194431787, gi... - gi\|194431787\|ref\|ZP_03064078.1\| phosphoglycerate dehydrogenase [Shigella dysenteriae 1012], gi\|19442... gi\|188492574, gi... - gi\|75515304\|ref\|ZP_00737488.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [E... gi\|170683573, gi... - gi\|170683573\|ref\|YP_001745066.1\| phosphoglycerate dehydrogenase [Escherichia coli SMS-3-5], gi\|17052... gi\|208726279, gi... - gi\|208806478\|ref\|ZP_03248815.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4206... gi\|195936531 - gi\|195936531\|ref\|ZP_03081913.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC... gi\|81246877, gi\|... - gi\|82545466\|ref\|YP_409413.1\| D-3-phosphoglycerate dehydrogenase [Shigella boydii Sb227], gi\|81246877... gi\|208739477, gi... - gi\|208819354\|ref\|ZP_03259674.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4042... gi\|89109691, gi\|... - gi\|89109691\|ref\|AP_003471.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli str. K-12 substr. ... gi\|208733110, gi... - gi\|208811833\|ref\|ZP_03253162.1\| phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. EC4045... gi\|75187628, gi\|... - gi\|75187628\|ref\|ZP_00700895.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [E... gi\|191168219, gi... - gi\|75228580\|ref\|ZP_00715209.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [E... gi\|193067273, gi... - gi\|75239519\|ref\|ZP_00723490.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [E... gi\|157068052, gi... - gi\|75196864\|ref\|ZP_00706934.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [E... gi\|194426244, gi... - gi\|75212473\|ref\|ZP_00712497.1\| COG0111: Phosphoglycerate dehydrogenase and related dehydrogenases [E... gi\|91212292, gi\|... - gi\|91212292\|ref\|YP_542278.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli UTI89], gi\|9107386... gi\|13363256, gi\|... - gi\|15833038\|ref\|NP_311811.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli O157:H7 str. Sakai... gi\|110616362, gi... - gi\|110806814\|ref\|YP_690334.1\| D-3-phosphoglycerate dehydrogenase [Shigella flexneri 5 str. 8401], gi... gi\|227888462, gi... - gi\|227888462\|ref\|ZP_04006267.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli 83972], gi\|2278... gi\|237706440, gi... - gi\|237706440\|ref\|ZP_04536921.1\| D-3-phosphoglycerate dehydrogenase [Escherichia sp. 3_2_53FAA], gi\|2... gi\|238902037, gi... - gi\|238902037\|ref\|YP_002927833.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli BW2952], gi\|23... gi\|242378443, gi... - gi\|251786170\|ref\|YP_003000474.1\| hypothetical protein B21_02707 [Escherichia coli BL21], gi\|24237844... gi\|253978891, gi... - gi\|254289584\|ref\|YP_003055332.1\| D-3-phosphoglycerate dehydrogenase [Escherichia coli BL21(DE3)], gi... SERA_SHIFL - D-3-phosphoglycerate dehydrogenase OS=Shigella flexneri GN=serA PE=3 SV=2 SERA_ECOLI - D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (PGDH) - Escherichia coli gi\|24053306, gi\|... - gi\|24114165\|ref\|NP_708675.1\| D-3-phosphoglycerate dehydrogenase [Shigella flexneri 2a str. 301], gi\|... SERA_ECOL6 - D-3-phosphoglycerate dehydrogenase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN... gi\|30064223, gi\|... - gi\|30064223\|ref\|NP_838394.1\| D-3-phosphoglycerate dehydrogenase [Shigella flexneri 2a str. 2457T], g... SERA_ECO57 - D-3-phosphoglycerate dehydrogenase OS=Escherichia coli O157:H7 GN=serA PE=3 SV=2 EG10944 - D-3-phosphoglycerate dehydrogenase / D-3-Phosphoglycerate dehydrogenase	0.0	[49..469]	[1..410]
SERA_ECOLI - (P0A9T0) D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (PGDH) SERA_SHIFL - (P0A9T3) D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (PGDH) SERA_ECO57 - (P0A9T2) D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (PGDH) SERA_ECOL6 - (P0A9T1) D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (PGDH)	0.0	[50..469]	[1..409]
gi\|11360878 - pir\|\|B82587 D-3-phosphoglycerate dehydrogenase XF2206 [imported] - Xylella fastidiosa (strain 9a5c) gi\|15838797, gi\|... - gi\|9107351\|gb\|AAF85005.1\|AE004033_9 D-3-phosphoglycerate dehydrogenase [Xylella fastidiosa 9a5c], gi...	0.0	[48..469]	[2..413]

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Predicted Domain #1

Region A:
Residues: [1-152]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSYSAADNLQ DSFQRAMNFS GSPGAVSTSP TQSFMNTLPR RVSITKQPKA LKPFSTGDMN  60
   61 ILLLENVNAT AIKIFKDQGY QVEFHKSSLP EDELIEKIKD VHAIGIRSKT RLTEKILQHA 120
  121 RNLVCIGCFC IGTNQVDLKY AASKGIAVFN SP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [355-376]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AQSSIGIEVA TALSKYINEG NS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1164.0
Match:	1psdA_
Description:	Phosphoglycerate dehydrogenase; Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transferase activity, transferring aldehyde or ketonic groups	4.08159331332211	bayes_pls_golite062009
acetolactate synthase activity	3.48670706716817	bayes_pls_golite062009
catalytic activity	1.79741889688267	bayes_pls_golite062009
oxidoreductase activity	1.69771604880532	bayes_pls_golite062009
phosphoglycerate dehydrogenase activity	0.639509916626856	bayes_pls_golite062009
oxidoreductase activity, acting on CH-OH group of donors	0.418775403210681	bayes_pls_golite062009
binding	0.355184540089764	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.32207755075663	bayes_pls_golite062009
oxidoreductase activity, acting on NADH or NADPH	0.310712203379158	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [153-354]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FSNSRSVAEL VIGEIISLAR QLGDRSIELH TGTWNKVAAR CWEVRGKTLG IIGYGHIGSQ  60
   61 LSVLAEAMGL HVLYYDIVTI MALGTARQVS TLDELLNKSD FVTLHVPATP ETEKMLSAPQ 120
  121 FAAMKDGAYV INASRGTVVD IPSLIQAVKA NKIAGAALDV YPHEPAKNGE GSFNDELNSW 180
  181 TSELVSLPNI ILTPHIGGST EE

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [377-469]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VGSVNFPEVS LKSLDYDQEN TVRVLYIHRN VPGVLKTVND ILSDHNIEKQ FSDSHGEIAY  60
   61 LMADISSVNQ SEIKDIYEKL NQTSAKVSIR LLY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1164.0
Match:	1psdA_
Description:	Phosphoglycerate dehydrogenase; Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
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: