YRC Public Data Repository - Protein Structure Prediction

Protein:	TRUA_SHIF8
Organism:	Shigella flexneri 5 str. 8401
Length:	270 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 TRUA_SHIF8.

Description	E-value	Query Range	Subject Range
TRUA_SHIBS - tRNA pseudouridine synthase A OS=Shigella boydii serotype 4 (strain Sb227) GN=truA PE=3 SV=1	384.0	[0..1]	[270..1]
gi\|293415611\|ref... - tRNA pseudouridine synthase A [Escherichia coli B185] TRUA_ECOL6 - tRNA pseudouridine synthase A OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=truA... gi\|209764792, gi... - pir\|\|C85873 pseudouridylate synthase I [imported] - Escherichia coli (strain O157:H7, substrain EDL... gi\|291283559\|ref... - tRNA pseudouridine synthase A [Escherichia coli O55:H7 str. CB9615] gi\|12516677, gi\|... - gi\|15802865\|ref\|NP_288892.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 EDL933], gi\|125... gi\|189362830, gi... - gi\|189362830\|gb\|EDU81249.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4486], gi... TRUA_ECO57 - tRNA pseudouridine synthase A OS=Escherichia coli O157:H7 GN=truA PE=3 SV=1 gi\|168761239, gi... - gi\|189368293\|gb\|EDU86709.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4501], gi... TRUA_ECOL6 - tRNA pseudouridine synthase A OS=Escherichia coli O6 GN=truA PE=3 SV=1 gi\|189357607, gi... - gi\|189357607\|gb\|EDU76026.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4401], gi... gi\|293410675\|ref... - tRNA pseudouridine synthase A [Escherichia coli B354] gi\|261223227\|ref... - tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. FRIK2000] gi\|188017261, gi... - gi\|188017261\|gb\|EDU55383.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4113], gi... gi\|168798493, gi... - gi\|189378874\|gb\|EDU97290.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC508], gi\|... gi\|168787230, gi... - gi\|189372810\|gb\|EDU91226.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC869], gi\|... gi\|168780178, gi... - gi\|189001906\|gb\|EDU70892.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4076], gi... gi\|187771144, gi... - gi\|187771144\|gb\|EDU34988.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4196], gi... gi\|293405784\|ref... - tRNA pseudouridine synthase A [Escherichia coli FVEC1412] gi\|13362672, gi\|... - gi\|15832456\|ref\|NP_311229.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. Sakai], gi... gi\|261259223\|ref... - tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. FRIK966] TRUA_ECOLU - tRNA pseudouridine synthase A OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=truA PE=3 S... TRUA_ECO7I - tRNA pseudouridine synthase A OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=truA PE=3 SV=1 gi\|208811862, gi... - gi\|208811862\|ref\|ZP_03253191.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4045]... gi\|208727696, gi... - gi\|208807895\|ref\|ZP_03250232.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4206]... gi\|195935697 - gi\|195935697\|ref\|ZP_03081079.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4024] TRUA_ECOSM - tRNA pseudouridine synthase A OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=truA PE=3 SV=1 TRUA_ECO55 - tRNA pseudouridine synthase A OS=Escherichia coli (strain 55989 / EAEC) GN=truA PE=3 SV=1 gi\|217319539, gi... - gi\|217327172\|ref\|ZP_03443255.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. TW14588... TRUA_ECO5E - tRNA pseudouridine synthase A OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=truA PE=3 SV=1 gi\|208741667, gi... - gi\|208821544\|ref\|ZP_03261864.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. EC4042]... gi\|293446655\|ref... - tRNA pseudouridine synthase A [Escherichia coli B088] gi\|254794211, gi... - gi\|254794211\|ref\|YP_003079048.1\| tRNA pseudouridine synthase A [Escherichia coli O157:H7 str. TW1435... gi\|227887378, gi... - gi\|227887378\|ref\|ZP_04005183.1\| tRNA pseudouridine synthase A [Escherichia coli 83972], gi\|227835728... TRUA_SHIDS - tRNA pseudouridine synthase A OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=truA PE=3 SV=1	384.0	[0..1]	[270..1]
TRUA_ECO27 - tRNA pseudouridine synthase A OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=truA PE=3 SV=1 gi\|226901163, gi... - gi\|237704797\|ref\|ZP_04535278.1\| tRNA pseudouridylate synthase I [Escherichia sp. 3_2_53FAA], gi\|2269... gi\|191170294, gi... - gi\|75243129\|ref\|ZP_00726835.1\| COG0101: Pseudouridylate synthase [Escherichia coli F11], gi\|19117029... TRUA_ECO45 - tRNA pseudouridine synthase A OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=truA PE=3 SV=1 TRUA_ECO24 - tRNA pseudouridine synthase A OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=truA PE=3 SV=1 sp\|B7UFX6\|TRUA_ECO27 - tRNA pseudouridine synthase A OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=truA PE=3 SV=1 TRUA_ECO81 - tRNA pseudouridine synthase A OS=Escherichia coli O81 (strain ED1a) GN=truA PE=3 SV=1 TRUA_ECOK1 - tRNA pseudouridine synthase A OS=Escherichia coli O1:K1 / APEC GN=truA PE=3 SV=1 TRUA_ECOL5 - tRNA pseudouridine synthase A OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=truA PE=3 SV=1 TRUA_ECOUT - tRNA pseudouridine synthase A OS=Escherichia coli (strain UTI89 / UPEC) GN=truA PE=3 SV=1	384.0	[0..1]	[270..1]
gi\|193068139, gi... - gi\|75238101\|ref\|ZP_00722106.1\| COG0101: Pseudouridylate synthase [Escherichia coli E110019], gi\|1930...	384.0	[0..1]	[270..1]
gi\|194424745, gi... - gi\|83588301\|ref\|ZP_00926926.1\| COG0101: Pseudouridylate synthase [Escherichia coli 101-1], gi\|194436... gi\|256021997\|ref... - tRNA pseudouridine synthase A [Escherichia sp. 4_1_40B] TRUA_ECOLC - tRNA pseudouridine synthase A OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=truA PE=... gi\|253772758, gi... - gi\|254289088\|ref\|YP_003054836.1\| tRNA pseudouridine synthase A [Escherichia coli BL21(DE3)], gi\|2539... gi\|251785678, gi... - gi\|251785678\|ref\|YP_002999982.1\| hypothetical protein B21_02203 [Escherichia coli BL21], gi\|24237795... gi\|254162327, gi... - gi\|254162327\|ref\|YP_003045435.1\| tRNA pseudouridine synthase A [Escherichia coli B str. REL606], gi\|... gi\|124526483, gi... - gi\|124526483\|ref\|ZP_01698436.1\| tRNA pseudouridine synthase A [Escherichia coli B], gi\|124501954\|gb\|... gi\|75515683, gi\|... - gi\|75515683\|ref\|ZP_00737818.1\| COG0101: Pseudouridylate synthase [Escherichia coli 53638], gi\|188492... TRUA_ECOHS - tRNA pseudouridine synthase A OS=Escherichia coli O9:H4 (strain HS) GN=truA PE=3 SV=1	383.0	[0..1]	[270..1]
EG10454 - tRNA pseudouridine(38-40) synthase / tRNA pseudouridine(38-40) synthase; mutations derepress the his... TRUA_ECOLI - tRNA pseudouridine synthase A (EC 5.4.99.12) (tRNA-uridine isomerase I) (tRNA pseudouridylate syntha... TRUA_ECOBW - tRNA pseudouridine synthase A OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=truA PE=3 SV=1 EG10454 - tRNA pseudouridine(38-40) synthase / tRNA pseudouridine(38-40) synthase; mutations derepress the his... gi\|89109138, gi\|... - gi\|89109138\|ref\|AP_002918.1\| pseudouridylate synthase I [Escherichia coli str. K-12 substr. W3110], ... TRUA_ECODH - tRNA pseudouridine synthase A OS=Escherichia coli (strain K12 / DH10B) GN=truA PE=3 SV=1	383.0	[0..1]	[270..1]
gi\|195183057 - gi\|195183057\|dbj\|BAG66617.1\| pseudouridylate synthase I [Escherichia coli O111:H-] gi\|75209305, gi\|... - gi\|75209305\|ref\|ZP_00709545.1\| COG0101: Pseudouridylate synthase [Escherichia coli B171], gi\|1944294...	383.0	[0..1]	[270..1]
TRUA_SHISS - tRNA pseudouridine synthase A OS=Shigella sonnei (strain Ss046) GN=truA PE=3 SV=1	382.0	[0..1]	[270..1]
TRUA_SALCH - tRNA pseudouridine synthase A OS=Salmonella choleraesuis GN=truA PE=3 SV=1 TRUA_SALTI - tRNA pseudouridine synthase A OS=Salmonella typhi GN=truA PE=3 SV=1 TRUA_SALA4 - tRNA pseudouridine synthase A OS=Salmonella agona (strain SL483) GN=truA PE=3 SV=1 TRUA_SALPK - tRNA pseudouridine synthase A OS=Salmonella paratyphi A (strain AKU_12601) GN=truA PE=3 SV=1 TRUA_SALDC - tRNA pseudouridine synthase A OS=Salmonella dublin (strain CT_02021853) GN=truA PE=3 SV=1 gi\|200388490, gi... - gi\|200388490\|ref\|ZP_03215102.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... TRUA_SALNS - tRNA pseudouridine synthase A OS=Salmonella newport (strain SL254) GN=truA PE=3 SV=1 TRUA_SALHS - tRNA pseudouridine synthase A OS=Salmonella heidelberg (strain SL476) GN=truA PE=3 SV=1 TRUA_SALPA - tRNA pseudouridine synthase A OS=Salmonella paratyphi A GN=truA PE=3 SV=1 gi\|194471784, gi... - gi\|194471784\|ref\|ZP_03077768.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... TRUA_SALPB - tRNA pseudouridine synthase A OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=truA PE=3 S... TRUA_SALSV - tRNA pseudouridine synthase A OS=Salmonella schwarzengrund (strain CVM19633) GN=truA PE=3 SV=1 gi\|238912353 - gi\|238912353\|ref\|ZP_04656190.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... gi\|29136636, gi\|... - gi\|29141011\|ref\|NP_804353.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica sero... gi\|197289616, gi... - gi\|197289616\|gb\|EDY28979.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov... gi\|16761293 - gi\|16761293\|ref\|NP_456910.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica sero... gi\|168242494, gi... - gi\|205338670\|gb\|EDZ25434.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov... gi\|168465920, gi... - gi\|195631471\|gb\|EDX50031.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov... TRUA_SALTI - tRNA pseudouridine synthase A OS=Salmonella typhi GN=truA PE=3 SV=1 gi\|205344778, gi... - gi\|205344778\|gb\|EDZ31542.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov... gi\|205325206, gi... - gi\|205325206\|gb\|EDZ13045.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov... gi\|205335762, gi... - gi\|205335762\|gb\|EDZ22526.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov... gi\|214002040 - gi\|214002040\|ref\|ZP_03412775.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... TRUA_SALPC - tRNA pseudouridine synthase A OS=Salmonella paratyphi C (strain RKS4594) GN=truA PE=3 SV=1 gi\|213161334 - gi\|213161334\|ref\|ZP_03347044.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... gi\|213426977 - gi\|213426977\|ref\|ZP_03359727.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... TRUA_SALCH - tRNA pseudouridine synthase A OS=Salmonella choleraesuis GN=truA PE=3 SV=1 gi\|213646800 - gi\|213646800\|ref\|ZP_03376853.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... TRUA_SALPB - tRNA pseudouridine synthase A OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=truA PE=3 S... gi\|213852689 - gi\|213852689\|ref\|ZP_03382221.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... gi\|204929209, gi... - gi\|204929209\|ref\|ZP_03220352.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... TRUA_SALG2 - tRNA pseudouridine synthase A OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=truA PE=3 SV=... TRUA_SALCH - tRNA pseudouridine synthase A OS=Salmonella choleraesuis (strain SC-B67) GN=truA PE=3 SV=1 TRUA_SALEP - tRNA pseudouridine synthase A OS=Salmonella enteritidis PT4 (strain P125109) GN=truA PE=3 SV=1 TRUA_SALPA - tRNA pseudouridine synthase A OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=truA PE=3 SV=... gi\|213022210 - gi\|213022210\|ref\|ZP_03336657.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s...	380.0	[0..1]	[270..1]
lcl\|NC_016856.1_... - [gene=truA] [protein=tRNA pseudouridine synthase A] [protein_id=YP_005238451.1] [location=complement... TRUA_SALTY - tRNA pseudouridine synthase A OS=Salmonella typhimurium GN=truA PE=3 SV=1 TRUA_SALTY - tRNA pseudouridine synthase A OS=Salmonella typhimurium GN=truA PE=3 SV=1 TRUA_SALTY - tRNA pseudouridine synthase A OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=tru... gi\|197263425, gi... - gi\|197263425\|ref\|ZP_03163499.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica s... gi\|168261608, gi... - gi\|205349584\|gb\|EDZ36215.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov... gi\|205328800, gi... - gi\|205328800\|gb\|EDZ15564.1\| tRNA pseudouridine synthase A [Salmonella enterica subsp. enterica serov...	376.0	[0..1]	[270..1]

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Predicted Domain #1

Region A:
Residues: [1-270]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDQQQLPVY KIALGIEYDG SKYYGWQRQN EVRSVQEKLE KALSQVANEP ITVFCAGRTD  60
   61 AGVHGTGQVV HFETTAQRKD AAWTLGVNAN LPGDIAVRWV KAVPDDFHAR FSATARRYRY 120
  121 IIYNHRLRPA VLSKGVTHFY EPLDAERMHR AAQCLLGEND FTSFRAVQCQ SRTPWRNVMH 180
  181 INVTRHGPYV VVDIKANAFV HHMVRNIVGS LMEVGAHNQP ESWIAELLAA KDRTLAAATA 240
  241 KAEGLYLVAV DYPDRYDLPK PPMGPLFLAD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	107.0
Match:	2nqpA
Description:	No description for 2nqpA was found.

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

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: