YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|187430711, gi...
Organism:	Shigella boydii CDC 3083-94
Length:	290 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 gi|187430711, gi....

Description	E-value	Query Range	Subject Range
gi\|194423727, gi... - gi\|83587116\|ref\|ZP_00925745.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... EG11921 - 23S rRNA pseudouridine(2604) synthase / 23S rRNA pseudouridine(2604) synthase gi\|89110743, gi\|... - gi\|89110743\|ref\|AP_004523.1\| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr. W31... EG11921 - 23S rRNA pseudouridine(2604) synthase / 23S rRNA pseudouridine(2604) synthase gi\|170083479, gi... - gi\|170083479\|ref\|YP_001732799.1\| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.... gi\|238859759, gi... - gi\|238903075\|ref\|YP_002928871.1\| 23S rRNA pseudouridine synthase [Escherichia coli BW2952], gi\|23885... gi\|251787279, gi... - gi\|251787279\|ref\|YP_003001583.1\| hypothetical protein B21_03854 [Escherichia coli BL21], gi\|24237955... gi\|253326398, gi... - gi\|254290708\|ref\|YP_003056456.1\| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)], gi\|25... gi\|226840120, gi... - gi\|254037014\|ref\|ZP_04871091.1\| ribosomal large subunit pseudouridine synthase F [Escherichia sp. 1_... RLUF_ECOLI - Ribosomal large subunit pseudouridine synthase F (EC 5.4.99.-) (rRNA-uridine isomerase F) (rRNA pseu... gi\|253975859, gi... - gi\|254163958\|ref\|YP_003047066.1\| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606], g...	249.0	[0..1]	[290..1]
gi\|75197880, gi\|... - gi\|75197880\|ref\|ZP_00707950.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps...	248.0	[0..1]	[290..1]
gi\|168750850, gi... - gi\|188015005\|gb\|EDU53127.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:... RLUF_ECO57 - 23S rRNA pseudouridine(2604) synthase OS=Escherichia coli O157:H7 GN=rluF PE=3 SV=1 gi\|168755170, gi... - gi\|189357499\|gb\|EDU75918.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:... gi\|168760865, gi... - gi\|189368503\|gb\|EDU86919.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:... gi\|13364481, gi\|... - gi\|15834259\|ref\|NP_313032.1\| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str. Sakai]... gi\|254796022, gi... - gi\|254796022\|ref\|YP_003080859.1\| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str. TW14... gi\|12518965, gi\|... - gi\|15804615\|ref\|NP_290656.1\| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 EDL933], gi... gi\|25324022, gi\|... - pir\|\|E91254 hypothetical protein ECs5005 [imported] - Escherichia coli (strain O157:H7, substrain R... gi\|208741255, gi... - gi\|208821132\|ref\|ZP_03261452.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O... gi\|209161790, gi... - gi\|209400390\|ref\|YP_002273541.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli ... gi\|209921498, gi... - gi\|209921498\|ref\|YP_002295582.1\| 23S rRNA pseudouridine synthase F [Escherichia coli SE11], gi\|20991... gi\|217321869, gi... - gi\|217325648\|ref\|ZP_03441732.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O... gi\|189379218, gi... - gi\|189379218\|gb\|EDU97634.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:... gi\|195935788 - gi\|195935788\|ref\|ZP_03081170.1\| 23S rRNA pseudouridine synthase F [Escherichia coli O157:H7 str. EC4... gi\|208728550, gi... - gi\|208808749\|ref\|ZP_03251086.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O... gi\|208733246, gi... - gi\|208811969\|ref\|ZP_03253298.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O... gi\|168766260, gi... - gi\|189364343\|gb\|EDU82762.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:... gi\|168774357, gi... - gi\|187769953\|gb\|EDU33797.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:... gi\|189001699, gi... - gi\|189001699\|gb\|EDU70685.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:... gi\|189374896, gi... - gi\|189374896\|gb\|EDU93312.1\| ribosomal large subunit pseudouridine synthase F [Escherichia coli O157:...	248.0	[0..1]	[290..1]
gi\|75229414, gi\|... - gi\|75229414\|ref\|ZP_00715966.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|218697724, gi... - gi\|218697724\|ref\|YP_002405391.1\| 23S rRNA pseudouridine synthase F [Escherichia coli 55989], gi\|2183... gi\|75188746, gi\|... - gi\|75188746\|ref\|ZP_00702013.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|169756908, gi... - gi\|170021980\|ref\|YP_001726934.1\| 23S rRNA pseudouridine synthase F [Escherichia coli ATCC 8739], gi\|... gi\|218363341, gi... - gi\|218556572\|ref\|YP_002389486.1\| 23S rRNA pseudouridine synthase F [Escherichia coli IAI1], gi\|21836... gi\|124531701, gi... - gi\|124531701\|ref\|ZP_01701869.1\| pseudouridine synthase [Escherichia coli B], gi\|124498414\|gb\|EAY4592... gi\|188487538, gi... - gi\|75514783\|ref\|ZP_00737012.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps...	248.0	[0..1]	[290..1]
gi\|110644361, gi... - gi\|110644361\|ref\|YP_672091.1\| 23S rRNA pseudouridine synthase F [Escherichia coli 536], gi\|110345953...	247.0	[0..1]	[290..1]
gi\|81243496, gi\|... - gi\|82779348\|ref\|YP_405697.1\| 23S rRNA pseudouridine synthase F [Shigella dysenteriae Sd197], gi\|8124...	246.0	[0..1]	[290..1]
gi\|218561092, gi... - gi\|218561092\|ref\|YP_002394005.1\| 23S rRNA pseudouridine synthase F [Escherichia coli S88], gi\|218367... RLUF_ECOL6 - Ribosomal large subunit pseudouridine synthase F OS=Escherichia coli O6 GN=rluF PE=3 SV=1 gi\|215489360, gi... - gi\|215489360\|ref\|YP_002331791.1\| 23S rRNA pseudouridine synthase F [Escherichia coli O127:H6 str. E2... gi\|218429871, gi... - gi\|218692307\|ref\|YP_002400519.1\| 23S rRNA pseudouridine synthase F [Escherichia coli ED1a], gi\|21842... RLUF_ECOL6 - 23S rRNA pseudouridine(2604) synthase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)... gi\|227836114, gi... - gi\|227886973\|ref\|ZP_04004778.1\| RluF protein [Escherichia coli 83972], gi\|227836114\|gb\|EEJ46580.1\| R... gi\|115515415, gi... - gi\|117626291\|ref\|YP_859614.1\| 23S rRNA pseudouridine synthase F [Escherichia coli APEC O1], gi\|11551... gi\|91213543, gi\|... - gi\|91213543\|ref\|YP_543529.1\| 23S rRNA pseudouridine synthase F [Escherichia coli UTI89], gi\|91075117... gi\|75241054, gi\|... - gi\|75241054\|ref\|ZP_00724928.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps...	245.0	[0..1]	[290..1]
gi\|75258940, gi\|... - gi\|75258940\|ref\|ZP_00730308.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|75238558, gi\|... - gi\|75238558\|ref\|ZP_00722547.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|194415237, gi... - gi\|75211903\|ref\|ZP_00711958.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps...	245.0	[0..1]	[290..1]
RLUF_SALTI - 23S rRNA pseudouridine(2604) synthase OS=Salmonella typhi GN=rluF PE=3 SV=1 gi\|213581144 - gi\|213581144\|ref\|ZP_03362970.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enteri... gi\|213420596 - gi\|213420596\|ref\|ZP_03353662.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enteri... gi\|29144382, gi\|... - gi\|29144382\|ref\|NP_807724.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enterica ... gi\|16762895 - gi\|16762895\|ref\|NP_458512.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enterica ... gi\|214001959 - gi\|214001959\|ref\|ZP_03412694.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enteri... gi\|213855503 - gi\|213855503\|ref\|ZP_03383743.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enteri... gi\|213647413 - gi\|213647413\|ref\|ZP_03377466.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enteri... RLUF_SALTI - Ribosomal large subunit pseudouridine synthase F OS=Salmonella typhi GN=rluF PE=3 SV=1	236.0	[0..1]	[290..1]
gi\|56130271, gi\|... - gi\|56416014\|ref\|YP_153089.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enterica ... gi\|197096418, gi... - gi\|197364941\|ref\|YP_002144578.1\| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp. enter...	233.0	[0..1]	[290..1]

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Predicted Domain #1

Region A:
Residues: [1-220]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLPDSSVRLN KYISESGICS RREADRYIEQ GNVFLNGKRA TIGDQVKPGD IVKVNGQLIE  60
   61 PREAEDLVLI ALNKPVGIVS TTEDGERDNI VDFVNHSKRV FPIGRLDKDS QGLIFLTNHG 120
  121 DLVNKILRAG NDHEKEYLVT VDKPITDEFI RGMGAGVPIL GTVTKKCKVK KEAPFVFRIT 180
  181 LVQGLNRQIR RMCEHFGYEV KKLERTRIMN VSLSGIPLGE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.522879
Match:	1vioA
Description:	Crystal structure of pseudouridylate synthase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
pseudouridine synthase activity	5.60483019625575	bayes_pls_golite062009
intramolecular transferase activity	4.62815459483632	bayes_pls_golite062009
isomerase activity	3.43067391737824	bayes_pls_golite062009
catalytic activity	2.39224964671205	bayes_pls_golite062009
structural constituent of ribosome	1.93805098366683	bayes_pls_golite062009
structural molecule activity	1.65902435754631	bayes_pls_golite062009
RNA binding	0.351909066993469	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [221-290]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WRDLTDDELI DLFKLIENSS SEAKPKAKAK PKTAGIKRPV VKMEKTAEKG GRPASNGKRF  60
   61 TSPGRKKKGR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.154902
Match:	2gmlA
Description:	No description for 2gmlA was found.

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: