YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|194403161, gi...
Organism:	Salmonella enterica subsp. enterica serovar Newport str. SL254
Length:	291 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|194403161, gi....

Description	E-value	Query Range	Subject Range
gi\|89108115, gi\|... - gi\|89108115\|ref\|AP_001895.1\| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12 substr. W... gi\|254161349, gi... - gi\|254161349\|ref\|YP_003044457.1\| 23S rRNA pseudouridylate synthase [Escherichia coli B str. REL606],... gi\|169755295, gi... - gi\|170020367\|ref\|YP_001725321.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli ATCC 8739], g... gi\|170682451, gi... - gi\|170682451\|ref\|YP_001743918.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli ... gi\|170080946, gi... - gi\|170080946\|ref\|YP_001730266.1\| 23S rRNA pseudouridylate synthase [Escherichia coli str. K-12 subst... gi\|218699976, gi... - gi\|218699976\|ref\|YP_002407605.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli IAI39], gi\|21... gi\|194435058, gi... - gi\|194435058\|ref\|ZP_03067297.1\| ribosomal large subunit pseudouridine synthase B [Shigella dysenteri... RLUB_ECOLI - Ribosomal large subunit pseudouridine synthase B (EC 5.4.99.-) (rRNA-uridine isomerase B) (rRNA pseu... gi\|188487400, gi... - gi\|75515119\|ref\|ZP_00737323.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|157160774, gi... - gi\|75195417\|ref\|ZP_00705487.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... EG12433 - 23S rRNA pseudouridine(2605) synthase / 23S rRNA pseudouridine(2605) synthase EG12433 - 23S rRNA pseudouridine(2605) synthase / 23S rRNA pseudouridine(2605) synthase gi\|124528352, gi... - gi\|124528352\|ref\|ZP_01699662.1\| pseudouridine synthase [Escherichia coli B], gi\|124500584\|gb\|EAY4805... gi\|238900502, gi... - gi\|238900502\|ref\|YP_002926298.1\| 23S rRNA pseudouridylate synthase [Escherichia coli BW2952], gi\|238... gi\|242377048, gi... - gi\|251784775\|ref\|YP_002999079.1\| hypothetical protein B21_01255 [Escherichia coli BL21], gi\|24237704... gi\|254288157, gi... - gi\|254288157\|ref\|YP_003053905.1\| 23S rRNA pseudouridylate synthase [Escherichia coli BL21(DE3)], gi\|...	1.0E-65	[1..291]	[1..291]
gi\|62180286, gi\|... - gi\|62180286\|ref\|YP_216703.1\| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp. enteric...	1.0E-65	[1..291]	[1..291]
gi\|16760161 - gi\|16760161\|ref\|NP_455778.1\| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp. enteric... RLUB_SALTI - Ribosomal large subunit pseudouridine synthase B OS=Salmonella typhi GN=rluB PE=3 SV=1 RLUB_SALTI - Ribosomal large subunit pseudouridine synthase B OS=Salmonella typhi GN=rluB PE=3 SV=1	1.0E-65	[1..291]	[1..291]
gi\|194436993, gi... - gi\|83587406\|ref\|ZP_00926034.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps...	2.0E-65	[1..291]	[1..291]
gi\|215486564, gi... - gi\|215486564\|ref\|YP_002328995.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli O127:H6 str. ... gi\|226900049, gi... - gi\|237705292\|ref\|ZP_04535773.1\| ribosomal large subunit pseudouridine synthase B [Escherichia sp. 3_... gi\|218356581, gi... - gi\|218549040\|ref\|YP_002382831.1\| 23S rRNA pseudouridylate synthase B [Escherichia fergusonii ATCC 35... gi\|227886303, gi... - gi\|227886303\|ref\|ZP_04004108.1\| 23S rRNA pseudouridylate synthase [Escherichia coli 83972], gi\|22783... RLUB_ECOL6 - Ribosomal large subunit pseudouridine synthase B OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700... gi\|218365023, gi... - gi\|218558254\|ref\|YP_002391167.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli S88], gi\|2183... gi\|91210560, gi\|... - gi\|91210560\|ref\|YP_540546.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli UTI89], gi\|910721... gi\|218704792, gi... - gi\|218704792\|ref\|YP_002412311.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli UMN026], gi\|2... gi\|110641498, gi... - gi\|110641498\|ref\|YP_669228.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli 536], gi\|1103430... RLUB_ECOL6 - Ribosomal large subunit pseudouridine synthase B OS=Escherichia coli O6 GN=rluB PE=3 SV=1 gi\|75242068, gi\|... - gi\|75242068\|ref\|ZP_00725862.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps...	3.0E-65	[1..291]	[1..291]
gi\|117623529, gi... - gi\|117623529\|ref\|YP_852442.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli APEC O1], gi\|115...	3.0E-65	[1..291]	[1..291]
gi\|189366282, gi... - gi\|189366282\|gb\|EDU84698.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|13361306, gi\|... - gi\|15831095\|ref\|NP_309868.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str. Saka... gi\|189359963, gi... - gi\|189359963\|gb\|EDU78382.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|187769333, gi... - gi\|187769333\|gb\|EDU33177.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|188998981, gi... - gi\|188998981\|gb\|EDU67967.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|189370413, gi... - gi\|189370413\|gb\|EDU88829.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|168801615, gi... - gi\|189376287\|gb\|EDU94703.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|195939202 - gi\|195939202\|ref\|ZP_03084584.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str. E... gi\|208724418, gi... - gi\|208810912\|ref\|ZP_03252745.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O... gi\|194426137, gi... - gi\|75212706\|ref\|ZP_00712704.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|191166646, gi... - gi\|75230175\|ref\|ZP_00716676.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|157076759, gi... - gi\|75190353\|ref\|ZP_00703620.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|15801910, gi\|... - gi\|15801910\|ref\|NP_287930.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 EDL933], ... gi\|73855839, gi\|... - gi\|74312362\|ref\|YP_310781.1\| 23S rRNA pseudouridylate synthase B [Shigella sonnei Ss046], gi\|7385583... gi\|25323994, gi\|... - pir\|\|F85760 hypothetical protein yciL [imported] - Escherichia coli (strain O157:H7, substrain EDL9... gi\|81245688, gi\|... - gi\|82544277\|ref\|YP_408224.1\| 23S rRNA pseudouridylate synthase B [Shigella boydii Sb227], gi\|8124568... gi\|193069992, gi... - gi\|75235225\|ref\|ZP_00719462.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|168751157, gi... - gi\|188014796\|gb\|EDU52918.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|193062722, gi... - gi\|75259379\|ref\|ZP_00730698.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps... gi\|189354811, gi... - gi\|189354811\|gb\|EDU73230.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O157:... gi\|208815453, gi... - gi\|208815453\|ref\|ZP_03256632.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O... gi\|208740929, gi... - gi\|208820806\|ref\|ZP_03261126.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O... gi\|209158122, gi... - gi\|209396722\|ref\|YP_002270323.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli ... gi\|209911767, gi... - gi\|209918508\|ref\|YP_002292592.1\| 23S rRNA pseudouridylate synthase B [Escherichia coli SE11], gi\|209... gi\|217329090, gi... - gi\|217329090\|ref\|ZP_03445170.1\| ribosomal large subunit pseudouridine synthase B [Escherichia coli O... RLUB_ECO57 - Ribosomal large subunit pseudouridine synthase B OS=Escherichia coli O157:H7 GN=rluB PE=3 SV=1 gi\|254592257, gi... - gi\|254792857\|ref\|YP_003077694.1\| 23S rRNA pseudouridylate synthase [Escherichia coli O157:H7 str. TW...	2.0E-64	[1..289]	[1..289]
gi\|187428458, gi... - gi\|75179087\|ref\|ZP_00699105.1\| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related ps...	2.0E-64	[1..289]	[1..289]
gi\|30062791, gi\|... - gi\|30062791\|ref\|NP_836962.1\| 23S rRNA pseudouridylate synthase B [Shigella flexneri 2a str. 2457T], ... RLUB_SHIFL - Ribosomal large subunit pseudouridine synthase B OS=Shigella flexneri GN=rluB PE=3 SV=1 gi\|110805271, gi... - gi\|110805271\|ref\|YP_688791.1\| 23S rRNA pseudouridylate synthase B [Shigella flexneri 5 str. 8401], g...	8.0E-64	[1..289]	[1..289]
gi\|82776628, gi\|... - gi\|82776628\|ref\|YP_402977.1\| 23S rRNA pseudouridylate synthase B [Shigella dysenteriae Sd197], gi\|81...	1.0E-63	[1..289]	[1..289]

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Predicted Domain #1

Region A:
Residues: [1-291]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEKLQKVLA RAGHGSRREI ESIIEAGRVS VDGKIATLGD RVEVTPGLKI RIDGHLISVK  60
   61 ESAEQICRVL AYYKPEGELC TRNDPEGRPT VFDRLPKLRG ARWIAVGRLD VNTCGLLLFT 120
  121 TDGELANRLM HPSREVEREY AVRVFGQVDE SKLRDLSRGV QLEDGPAAFK TIKFSGGEGI 180
  181 NQWYNVTLTE GRNREVRRLW EAVGVQVSRL IRVRYGDIPL PKGLPRGGWT ELDLAQTNYL 240
  241 RGLVELPPET SSKVAVEKDR RRMKANQIRR AVKRHSQIAG GRRSGGRNNN G

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.522879
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

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: