YRC Public Data Repository - Protein Structure Prediction

Protein:	PDH1
Organism:	Saccharomyces cerevisiae
Length:	516 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 PDH1.

Description	E-value	Query Range	Subject Range
gi\|190407946 - gi\|190407946\|gb\|EDV11211.1\| 2-methylcitrate dehydratase [Saccharomyces cerevisiae RM11-1a] gi\|207340433 - gi\|207340433\|gb\|EDZ68783.1\| YPR002Wp-like protein [Saccharomyces cerevisiae AWRI1631] PRPD_YEAST - Probable 2-methylcitrate dehydratase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PDH... PDH1 - Mitochondrial protein that participates in respiration, induced by diauxic shift; homologous to E. c... gi\|151942793 - gi\|151942793\|gb\|EDN61139.1\| prpd-like protein [Saccharomyces cerevisiae YJM789]	0.0	[1..516]	[1..516]
gi\|91209411, gi\|... - gi\|91209411\|ref\|YP_539397.1\| 2-methylcitrate dehydratase [Escherichia coli UTI89], gi\|91070985\|gb\|AB... gi\|117622616, gi... - gi\|117622616\|ref\|YP_851529.1\| 2-methylcitrate dehydratase [Escherichia coli APEC O1], gi\|115511740\|g... gi\|237707663, gi... - gi\|237707663\|ref\|ZP_04538144.1\| 2-methylcitrate dehydratase [Escherichia sp. 3_2_53FAA], gi\|22689887... gi\|26246349, gi\|... - gi\|26246349\|ref\|NP_752388.1\| 2-methylcitrate dehydratase [Escherichia coli CFT073], gi\|26106747\|gb\|A... gi\|227884648, gi... - gi\|227884648\|ref\|ZP_04002453.1\| 2-methylcitrate dehydratase [Escherichia coli 83972], gi\|227838383\|g... gi\|218557262, gi... - gi\|218557262\|ref\|YP_002390175.1\| 2-methylcitrate dehydratase [Escherichia coli S88], gi\|218364031\|em...	0.0	[27..514]	[2..482]
gi\|83586370, gi\|... - gi\|83586370\|ref\|ZP_00925005.1\| COG2079: Uncharacterized protein involved in propionate catabolism [E... gi\|218430718, gi... - gi\|218703621\|ref\|YP_002411140.1\| 2-methylcitrate dehydratase [Escherichia coli UMN026], gi\|218430718... PRPD_ECOLI - 2-methylcitrate dehydratase (EC 4.2.1.79) - Escherichia coli gi\|89107206, gi\|... - gi\|89107206\|ref\|AP_000986.1\| 2-methylcitrate dehydratase [Escherichia coli str. K-12 substr. W3110],... EG13603 - 2-methylcitrate dehydratase / 2-Methylcitrate dehydratase, 2-methylisocitrate hydratase; propionate ... EG13603 - 2-methylcitrate dehydratase / 2-Methylcitrate dehydratase, 2-methylisocitrate hydratase; propionate ...	0.0	[27..514]	[2..482]
gi\|33572717, gi\|... - gi\|33593361\|ref\|NP_881005.1\| 2-methylcitrate dehydratase [Bordetella pertussis Tohama I], gi\|3357271...	0.0	[24..514]	[1..484]
gi\|13359844, gi\|... - gi\|15829641\|ref\|NP_308414.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. Sakai], gi\|1... gi\|209159921, gi... - gi\|209398521\|ref\|YP_002268971.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4115],... gi\|217322854, gi... - gi\|217326633\|ref\|ZP_03442717.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. TW14588],... gi\|195937833 - gi\|195937833\|ref\|ZP_03083215.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4024] gi\|208728101, gi... - gi\|208808300\|ref\|ZP_03250637.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4206], ... gi\|208732387, gi... - gi\|208815739\|ref\|ZP_03256918.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4045], ... gi\|254791512, gi... - gi\|254791512\|ref\|YP_003076349.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. TW14359]... gi\|208823186, gi... - gi\|208823186\|ref\|ZP_03263504.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4042], ... gi\|187769073, gi... - gi\|187769073\|gb\|EDU32917.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4196], gi\|1... gi\|188999853, gi... - gi\|188999853\|gb\|EDU68839.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4076], gi\|1... gi\|189371708, gi... - gi\|189371708\|gb\|EDU90124.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC869], gi\|16... gi\|189377830, gi... - gi\|189377830\|gb\|EDU96246.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC508], gi\|16... gi\|188016477, gi... - gi\|188016477\|gb\|EDU54599.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4113], gi\|1... gi\|168755912, gi... - gi\|189356959\|gb\|EDU75378.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4401], gi\|1... gi\|168762004, gi... - gi\|189367672\|gb\|EDU86088.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4501], gi\|1... gi\|168769713, gi... - gi\|189361316\|gb\|EDU79735.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 str. EC4486], gi\|1... PRPD_ECO57 - 2-methylcitrate dehydratase OS=Escherichia coli O157:H7 GN=prpD PE=3 SV=3 gi\|209744756, gi... - pir\|\|F85527 hypothetical protein prpD [imported] - Escherichia coli (strain O157:H7, substrain EDL9... gi\|15800062, gi\|... - gi\|15800062\|ref\|NP_286074.1\| 2-methylcitrate dehydratase [Escherichia coli O157:H7 EDL933], gi\|12513...	0.0	[27..514]	[2..482]
gi\|33574191 - gi\|33574191\|emb\|CAE38522.1\| 2-methylcitrate dehydratase [Bordetella parapertussis] gi\|33597762 - gi\|33597762\|ref\|NP_885405.1\| 2-methylcitrate dehydratase [Bordetella parapertussis 12822] gi\|33602664, gi\|... - gi\|33602664\|ref\|NP_890224.1\| 2-methylcitrate dehydratase [Bordetella bronchiseptica RB50], gi\|335771...	0.0	[24..514]	[1..484]
PRPD_SALTY - 2-methylcitrate dehydratase OS=Salmonella typhimurium GN=prpD PE=3 SV=2 PRPD_SALTY - 2-methylcitrate dehydratase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=prpD ... PRPD_SALTY - 2-methylcitrate dehydratase OS=Salmonella typhimurium GN=prpD PE=3 SV=2 gi\|205329549, gi... - gi\|205329549\|gb\|EDZ16313.1\| 2-methylcitrate dehydratase [Salmonella enterica subsp. enterica serovar... gi\|168819032, gi... - gi\|205344121\|gb\|EDZ30885.1\| 2-methylcitrate dehydratase [Salmonella enterica subsp. enterica serovar... lcl\|NC_016856.1_... - [gene=prpD] [protein=2-methylcitrate dehydratase] [protein_id=YP_005236049.1] [location=420889..4223...	0.0	[27..514]	[2..482]
gi\|1648968 - gi\|1648968\|gb\|AAC44816.1\| PrpD [Salmonella typhimurium] gi\|1648968\|gb\|AA... - PrpD [Salmonella typhimurium]	0.0	[27..514]	[2..482]
gi\|213416961 - gi\|213416961\|ref\|ZP_03350105.1\| 2-methylcitrate dehydratase [Salmonella enterica subsp. enterica ser... gi\|29142880, gi\|... - gi\|29142880\|ref\|NP_806222.1\| 2-methylcitrate dehydratase [Salmonella enterica subsp. enterica serova... gi\|213425179 - gi\|213425179\|ref\|ZP_03357929.1\| 2-methylcitrate dehydratase [Salmonella enterica subsp. enterica ser... gi\|213854626 - gi\|213854626\|ref\|ZP_03382866.1\| 2-methylcitrate dehydratase [Salmonella enterica subsp. enterica ser...	0.0	[27..514]	[2..482]
PRPD_SALTI - 2-methylcitrate dehydratase OS=Salmonella typhi GN=prpD PE=3 SV=1 PRPD_SALTI - 2-methylcitrate dehydratase OS=Salmonella typhi GN=prpD PE=3 SV=1 gi\|16759348 - gi\|16759348\|ref\|NP_454965.1\| 2-methylcitrate dehydratase [Salmonella enterica subsp. enterica serova...	0.0	[27..514]	[2..482]

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Predicted Domain #1

Region A:
Residues: [1-516]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFLAKNLKNN KIKVCLPKKK FAALSTASIQ TNERPNPDKV LKDIAKYVHE TPLKSSLALD  60
   61 TARLCFLDTL GCGLAALKFK QAQNIIKPIV PGTIVPSGTK ILGTSYVMDP VKGAFAIGTL 120
  121 IRWLDYNDCW LAAEWGHPSD NLGGILAVAD HLSRLNKATH GKNGKQFLVK DVLEAMIKAH 180
  181 EIQGIIALEN SFNKVGLDHV VLVKVATAGV VSKMLGLSQE QTIEALSQAF VDGQSLRTYR 240
  241 HAPNTGSRKS WAAGDAVSRA VNLAYLVKNA NVGTIPSVLT ARTWGFYDVL FKGKPFSFQQ 300
  301 RSKYDSYVME NVLFKISFPA EFHAQTAVEA AVKAYRILAK QGKTFKDIKS IRIRTQEAAM 360
  361 RIIDKSGPLY NYADRDHCIQ YMIAVPLITG NLTATDYSDE VARNPEIDNL RSKMYCIEDT 420
  421 HLTQNYHDPD KRSIGNALLI ELNDGTQLDE IFVEYPVGHK FRREEGIPLL MNKFQRHLRE 480
  481 HFVESPDKVD LIMKVSSKTN FLNMQIDKYM DLFTEG

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	232.167491
Match:	PF03972
Description:	MmgE/PrpD family

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
catalytic activity	0.534516847146079	bayes_pls_golite062009

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: