YRC Public Data Repository - Protein Structure Prediction

Protein:	TRUD_ECOLI
Organism:	Escherichia coli
Length:	349 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 TRUD_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|77976008 - gi\|77976008\|ref\|ZP_00831541.1\| COG0585: Uncharacterized conserved protein [Yersinia frederiksenii AT...	428.0	[0..1]	[349..1]
gi\|77962844 - gi\|77962844\|ref\|ZP_00826660.1\| COG0585: Uncharacterized conserved protein [Yersinia mollaretii ATCC ...	426.0	[0..2]	[349..1]
gi\|77956579 - gi\|77956579\|ref\|ZP_00820668.1\| COG0585: Uncharacterized conserved protein [Yersinia bercovieri ATCC ...	423.0	[0..2]	[349..1]
gi\|77979630, gi\|... - gi\|77979630\|ref\|ZP_00835047.1\| COG0585: Uncharacterized conserved protein [Yersinia intermedia ATCC ...	422.0	[0..2]	[349..1]
gi\|124499608, gi... - gi\|124529900\|ref\|ZP_01700744.1\| Pseudouridylate synthase [Escherichia coli B], gi\|124499608\|gb\|EAY47... gi\|254037787, gi... - gi\|254037787\|ref\|ZP_04871845.1\| tRNA pseudouridine synthase D TruD [Escherichia sp. 1_1_43], gi\|2268... TRUD_ECOLC - tRNA pseudouridine synthase D OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=truD PE=... TRUD_ECOHS - tRNA pseudouridine synthase D OS=Escherichia coli O9:H4 (strain HS) GN=truD PE=3 SV=1	418.0	[0..1]	[349..1]
TRUD_SHIF8 - tRNA pseudouridine synthase D OS=Shigella flexneri serotype 5b (strain 8401) GN=truD PE=3 SV=1	418.0	[0..1]	[349..1]
TRUD_ECOUT - tRNA pseudouridine synthase D OS=Escherichia coli (strain UTI89 / UPEC) GN=truD PE=3 SV=1 TRUD_ECO45 - tRNA pseudouridine synthase D OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=truD PE=3 SV=1 TRUD_ECOK1 - tRNA pseudouridine synthase D OS=Escherichia coli O1:K1 / APEC GN=truD PE=3 SV=1 gi\|226899666, gi... - gi\|237706626\|ref\|ZP_04537107.1\| tRNA pseudouridine synthase D [Escherichia sp. 3_2_53FAA], gi\|226899...	418.0	[0..1]	[349..1]
gi\|227888288, gi... - gi\|227888288\|ref\|ZP_04006093.1\| tRNA pseudouridine synthase D [Escherichia coli 83972], gi\|227834557... TRUD_ECOL6 - tRNA pseudouridine synthase D OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=truD... TRUD_ECOL6 - tRNA pseudouridine synthase D OS=Escherichia coli O6 GN=truD PE=3 SV=1	418.0	[0..1]	[349..1]
gi\|24114040, gi\|... - gi\|24114040\|ref\|NP_708550.1\| tRNA pseudouridine synthase D [Shigella flexneri 2a str. 301], gi\|24053... gi\|30042358, gi\|... - gi\|30064102\|ref\|NP_838273.1\| tRNA pseudouridine synthase D [Shigella flexneri 2a str. 2457T], gi\|300... TRUD_SHIFL - tRNA pseudouridine synthase D OS=Shigella flexneri GN=truD PE=3 SV=1	418.0	[0..1]	[349..1]
TRUD_SHIDS - tRNA pseudouridine synthase D OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=truD PE=3 SV=1	418.0	[0..1]	[349..1]

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Predicted Domain #1

Region A:
Residues: [1-349]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIEFDNLTYL HGKPQGTGLL KANPEDFVVV EDLGFEPDGE GEHILVRILK NGCNTRFVAD  60
   61 ALAKFLKIHA REVSFAGQKD KHAVTEQWLC ARVPGKEMPD LSAFQLEGCQ VLEYARHKRK 120
  121 LRLGALKGNA FTLVLREVSN RDDVEQRLID ICVKGVPNYF GAQRFGIGGS NLQGAQRWAQ 180
  181 TNTPVRDRNK RSFWLSAARS ALFNQIVAER LKKADVNQVV DGDALQLAGR GSWFVATTEE 240
  241 LAELQRRVND KELMITAALP GSGEWGTQRE ALAFEQAAVA AETELQALLV REKVEAARRA 300
  301 MLLYPQQLSW NWWDDVTVEI RFWLPAGSFA TSVVRELINT TGDYAHIAE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	117.0
Match:	1si7A
Description:	Structure of E. coli tRNA psi 13 pseudouridine synthase TruD
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
pseudouridine synthase activity	5.19957135839682	bayes_pls_golite062009
intramolecular transferase activity	3.78688422405974	bayes_pls_golite062009
isomerase activity	2.91720316078381	bayes_pls_golite062009
catalytic activity	2.02180970970004	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: