YRC Public Data Repository - Protein Structure Prediction

Protein:	YDIB_ECOLI
Organism:	Escherichia coli
Length:	288 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 YDIB_ECOLI.

Description	E-value	Query Range	Subject Range
AROE_ALKMQ - Shikimate dehydrogenase (NADP(+)) OS=Alkaliphilus metalliredigens (strain QYMF) GN=aroE PE=3 SV=1	282.0	[0..3]	[284..5]
AROE_METKA - Shikimate dehydrogenase OS=Methanopyrus kandleri GN=aroE PE=3 SV=1 AROE_METKA - Shikimate dehydrogenase (NADP(+)) OS=Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC...	281.0	[0..2]	[286..6]
gi\|167037479, gi... - gi\|76797197\|ref\|ZP_00779533.1\| Quinate/Shikimate 5-dehydrogenase [Thermoanaerobacter ethanolicus ATC...	281.0	[0..1]	[286..1]
gi\|114845254, gi... - gi\|167040141\|ref\|YP_001663126.1\| shikimate 5-dehydrogenase [Thermoanaerobacter sp. X514], gi\|1668543...	281.0	[0..1]	[286..1]
AROE_THETN - Shikimate dehydrogenase OS=Thermoanaerobacter tengcongensis GN=aroE PE=3 SV=1 AROE_CALS4 - Shikimate dehydrogenase (NADP(+)) OS=Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM ... gi\|214034934, gi... - gi\|254479120\|ref\|ZP_05092471.1\| shikimate 5-dehydrogenase [Carboxydibrachium pacificum DSM 12653], g...	273.0	[0..1]	[285..1]
AROE_ALKOO - Shikimate dehydrogenase (NADP(+)) OS=Alkaliphilus oremlandii (strain OhILAs) GN=aroE PE=3 SV=1	270.0	[0..3]	[284..5]
gi\|170127636, gi... - gi\|170707392\|ref\|ZP_02897846.1\| shikimate 5-dehydrogenase [Bacillus anthracis str. A0389], gi\|170127... gi\|21402380, gi\|... - gi\|65321706\|ref\|ZP_00394665.1\| COG0169: Shikimate 5-dehydrogenase [Bacillus anthracis str. A2012], r... gi\|229268320, gi... - gi\|229603912\|ref\|YP_002868624.1\| shikimate dehydrogenase [Bacillus anthracis str. A0248], gi\|2292683... gi\|47529857, gi\|... - gi\|47529857\|ref\|YP_021206.1\| shikimate 5-dehydrogenase [Bacillus anthracis str. 'Ames Ancestor'], gi... gi\|30264406, gi\|... - gi\|30264406\|ref\|NP_846783.1\| shikimate 5-dehydrogenase [Bacillus anthracis str. Ames], gi\|30259064\|g...	266.0	[0..8]	[284..3]
AROE_BACSU - Shikimate dehydrogenase OS=Bacillus subtilis GN=aroD PE=3 SV=1 gi\|2635012, gi\|1... - gi\|2635012\|emb\|CAB14508.1\| shikimate 5-dehydrogenase [Bacillus subtilis subsp. subtilis str. 168], g...	266.0	[0..8]	[284..3]
AROE_BACCR - Shikimate dehydrogenase (NADP(+)) OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 1... gi\|228653732, gi... - gi\|229129615\|ref\|ZP_04258583.1\| Shikimate dehydrogenase [Bacillus cereus BDRD-Cer4], gi\|228653732\|gb... gi\|229111808, gi... - gi\|229111808\|ref\|ZP_04241354.1\| Shikimate dehydrogenase [Bacillus cereus Rock1-15], gi\|228671564\|gb\|... gi\|228723285, gi... - gi\|229048041\|ref\|ZP_04193616.1\| Shikimate dehydrogenase [Bacillus cereus AH676], gi\|228723285\|gb\|EEL... gi\|228799083, gi... - gi\|228960604\|ref\|ZP_04122251.1\| Shikimate dehydrogenase [Bacillus thuringiensis serovar pakistani st... gi\|229180612, gi... - gi\|229180612\|ref\|ZP_04307953.1\| Shikimate dehydrogenase [Bacillus cereus 172560W], gi\|228602855\|gb\|E... gi\|228630904, gi... - gi\|229152538\|ref\|ZP_04280728.1\| Shikimate dehydrogenase [Bacillus cereus m1550], gi\|228630904\|gb\|EEK... gi\|229146906, gi... - gi\|229146906\|ref\|ZP_04275270.1\| Shikimate dehydrogenase [Bacillus cereus BDRD-ST24], gi\|228636505\|gb... gi\|206735143, gi... - gi\|206969455\|ref\|ZP_03230409.1\| shikimate 5-dehydrogenase [Bacillus cereus AH1134], gi\|206735143\|gb\|... AROE_BACC4 - Shikimate dehydrogenase (NADP(+)) OS=Bacillus cereus (strain B4264) GN=aroE PE=3 SV=1	265.0	[0..8]	[286..3]
gi\|67849601, gi\|... - gi\|67916466\|ref\|ZP_00510176.1\| Shikimate/quinate 5-dehydrogenase [Clostridium thermocellum ATCC 2740...	265.0	[0..3]	[281..7]

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Predicted Domain #1

Region A:
Residues: [1-288]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDVTAKYELI GLMAYPIRHS LSPEMQNKAL EKAGLPFTYM AFEVDNDSFP GAIEGLKALK  60
   61 MRGTGVSMPN KQLACEYVDE LTPAAKLVGA INTIVNDDGY LRGYNTDGTG HIRAIKESGF 120
  121 DIKGKTMVLL GAGGASTAIG AQGAIEGLKE IKLFNRRDEF FDKALAFAQR VNENTDCVVT 180
  181 VTDLADQQAF AEALASADIL TNGTKVGMKP LENESLVNDI SLLHPGLLVT ECVYNPHMTK 240
  241 LLQQAQQAGC KTIDGYGMLL WQGAEQFTLW TGKDFPLEYV KQVMGFGA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	69.30103
Match:	1npdA
Description:	Putative shikimate dehydrogenase YdiB
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
shikimate 5-dehydrogenase activity	3.40568087442781	bayes_pls_golite062009
malate dehydrogenase activity	3.18316725684556	bayes_pls_golite062009
malic enzyme activity	2.5718745582089	bayes_pls_golite062009
oxidoreductase activity	2.15129810845685	bayes_pls_golite062009
catalytic activity	2.0643953589843	bayes_pls_golite062009
oxidoreductase activity, acting on CH-OH group of donors	1.43144163429682	bayes_pls_golite062009
malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity	0.858327241653065	bayes_pls_golite062009
fatty acid synthase activity	0.714637370305282	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.39426299750207	bayes_pls_golite062009
3-oxoacyl-[acyl-carrier-protein] reductase activity	0.192594057004213	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: