YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229899460, gi...
Organism:	Yersinia pestis biovar Orientalis str. India 195
Length:	325 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|229899460, gi....

Description	E-value	Query Range	Subject Range
gi\|126208592, gi... - gi\|126208592\|ref\|YP_001053817.1\| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae ... gi\|190150449, gi... - gi\|190150449\|ref\|YP_001968974.1\| ribosomal large subunit pseudouridine synthase D [Actinobacillus pl... gi\|53728774 - gi\|53728774\|ref\|ZP_00135229.2\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Actinobacillus ... gi\|165976548, gi... - gi\|165976548\|ref\|YP_001652141.1\| 23S rRNA pseudouridine synthase D [Actinobacillus pleuropneumoniae ...	7.0E-82	[1..325]	[1..325]
gi\|170025566, gi... - gi\|170025566\|ref\|YP_001722071.1\| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis YPII... gi\|145600172, gi... - gi\|145600172\|ref\|YP_001164248.1\| 23S rRNA pseudouridine synthase D [Yersinia pestis Pestoides F], gi... gi\|186894214, gi... - gi\|186894214\|ref\|YP_001871326.1\| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis PB1/... Q66E47\|Q66E47_YERPS - Pseudouridine synthase - Yersinia pseudotuberculosis gi\|51595196, gi\|... - gi\|51595196\|ref\|YP_069387.1\| 23S rRNA pseudouridine synthase D [Yersinia pseudotuberculosis IP 32953... gi\|45435362, gi\|... - gi\|45440505\|ref\|NP_992044.1\| 23S rRNA pseudouridine synthase D [Yersinia pestis biovar Microtus str.... gi\|162353585, gi... - gi\|77633068\|ref\|ZP_00795222.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Yersinia pestis... gi\|229896561, gi... - gi\|229896561\|ref\|ZP_04511728.1\| 23S rRNA pseudouridine synthase [Yersinia pestis Pestoides A], gi\|22...	8.0E-82	[1..325]	[1..325]
gi\|81246458, gi\|... - gi\|82545047\|ref\|YP_408994.1\| 23S rRNA pseudouridine synthase D [Shigella boydii Sb227], gi\|81246458\|... gi\|187429681, gi... - gi\|75178203\|ref\|ZP_00698262.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Shigella boydii...	1.0E-81	[1..325]	[1..325]
gi\|30063991, gi\|... - gi\|30063991\|ref\|NP_838162.1\| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 2457T], gi... gi\|73856630, gi\|... - gi\|74313153\|ref\|YP_311572.1\| 23S rRNA pseudouridine synthase D [Shigella sonnei Ss046], gi\|73856630\|... RLUD_SHIFL - Ribosomal large subunit pseudouridine synthase D OS=Shigella flexneri GN=rluD PE=3 SV=2 RLUD_ECOL6 - Ribosomal large subunit pseudouridine synthase D OS=Escherichia coli O6 GN=rluD PE=3 SV=2 gi\|24053038, gi\|... - gi\|24113932\|ref\|NP_708442.1\| 23S rRNA pseudouridine synthase D [Shigella flexneri 2a str. 301], gi\|2... RLUD_ECOL6 - Ribosomal large subunit pseudouridine synthase D OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700... gi\|218555174, gi... - gi\|218555174\|ref\|YP_002388087.1\| 23S rRNA pseudouridine synthase D [Escherichia coli IAI1], gi\|21836... gi\|218352951, gi... - gi\|218696219\|ref\|YP_002403886.1\| 23S rRNA pseudouridine synthase D [Escherichia coli 55989], gi\|2183... gi\|75236018, gi\|... - gi\|75236018\|ref\|ZP_00720152.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|110344349, gi... - gi\|110642757\|ref\|YP_670487.1\| 23S rRNA pseudouridine synthase D [Escherichia coli 536], gi\|110344349... gi\|110806535, gi... - gi\|110806535\|ref\|YP_690055.1\| 23S rRNA pseudouridine synthase D [Shigella flexneri 5 str. 8401], gi\|...	1.0E-81	[1..325]	[1..325]
EG12098 - 23S rRNA pseudouridine(1911,1915,1917) synthase / 23S rRNA pseudouridine(1911,1915,1917) synthase; m... gi\|238901755, gi... - gi\|238901755\|ref\|YP_002927551.1\| 23S rRNA pseudouridine synthase [Escherichia coli BW2952], gi\|23885... RLUD_ECOLI - Ribosomal large subunit pseudouridine synthase D (EC 5.4.99.-) (rRNA-uridine isomerase D) (rRNA pseu... gi\|251785917, gi... - gi\|251785917\|ref\|YP_003000221.1\| hypothetical protein B21_02448 [Escherichia coli BL21], gi\|24237819... gi\|124500887, gi... - gi\|124527995\|ref\|ZP_01699348.1\| pseudouridine synthase, RluA family [Escherichia coli B], gi\|1245008... gi\|254289326, gi... - gi\|254289326\|ref\|YP_003055074.1\| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)], gi\|25... EG12098 - 23S rRNA pseudouridine(1911,1915,1917) synthase / 23S rRNA pseudouridine(1911,1915,1917) synthase; m... gi\|226839295, gi... - gi\|254037671\|ref\|ZP_04871729.1\| 23S rRNA pseudouridine synthase D [Escherichia sp. 1_1_43], gi\|22683... gi\|253974466, gi... - gi\|254162565\|ref\|YP_003045673.1\| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606], g... gi\|194439337, gi... - gi\|83585274\|ref\|ZP_00923923.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|157162070, gi... - gi\|75196609\|ref\|ZP_00706679.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|188493998, gi... - gi\|75513200\|ref\|ZP_00735642.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|89109396, gi\|... - gi\|89109396\|ref\|AP_003176.1\| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr. W31... gi\|169890034, gi... - gi\|170082199\|ref\|YP_001731519.1\| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.... gi\|169754055, gi... - gi\|170019127\|ref\|YP_001724081.1\| 23S rRNA pseudouridine synthase D [Escherichia coli ATCC 8739], gi\|...	1.0E-81	[1..325]	[1..325]
gi\|193064062, gi... - gi\|75258015\|ref\|ZP_00729489.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|75227673, gi\|... - gi\|75227673\|ref\|ZP_00714414.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|193071695, gi... - gi\|75214714\|ref\|ZP_00713222.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|75208570, gi\|... - gi\|75208570\|ref\|ZP_00708883.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|209913330, gi... - gi\|209920071\|ref\|YP_002294155.1\| 23S rRNA pseudouridine synthase D [Escherichia coli SE11], gi\|20991... gi\|157078638, gi... - gi\|75187343\|ref\|ZP_00700610.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col...	1.0E-81	[1..325]	[1..325]
gi\|226899857, gi... - gi\|237706817\|ref\|ZP_04537298.1\| 23S rRNA pseudouridine synthase D [Escherichia sp. 3_2_53FAA], gi\|22... gi\|117624818, gi... - gi\|117624818\|ref\|YP_853731.1\| 23S rRNA pseudouridine synthase D [Escherichia coli APEC O1], gi\|11551... gi\|218559515, gi... - gi\|218559515\|ref\|YP_002392428.1\| 23S rRNA pseudouridine synthase D [Escherichia coli S88], gi\|218366...	2.0E-81	[1..325]	[1..325]
gi\|91211928, gi\|... - gi\|91211928\|ref\|YP_541914.1\| 23S rRNA pseudouridine synthase D [Escherichia coli UTI89], gi\|91073502...	3.0E-81	[1..325]	[1..325]
gi\|209762680, gi... - pir\|\|A91061 suppressor of ftsH mutation [imported] - Escherichia coli (strain O157:H7, substrain RI... gi\|13362928, gi\|... - gi\|15832711\|ref\|NP_311484.1\| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. Sakai]... gi\|168801712, gi... - gi\|189376176\|gb\|EDU94592.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... RLUD_ECO57 - Ribosomal large subunit pseudouridine synthase D OS=Escherichia coli O157:H7 GN=rluD PE=3 SV=3 gi\|168789497, gi... - gi\|189370886\|gb\|EDU89302.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|189003176, gi... - gi\|189003176\|gb\|EDU72162.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|187770638, gi... - gi\|187770638\|gb\|EDU34482.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|208821085, gi... - gi\|208821085\|ref\|ZP_03261405.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|208734055, gi... - gi\|208812778\|ref\|ZP_03254107.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|208728533, gi... - gi\|208808732\|ref\|ZP_03251069.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|195940189 - gi\|195940189\|ref\|ZP_03085571.1\| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. EC4... gi\|254794542, gi... - gi\|254794542\|ref\|YP_003079379.1\| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str. TW14... gi\|168771700, gi... - gi\|189359603\|gb\|EDU78022.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|168762387, gi... - gi\|189367297\|gb\|EDU85713.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|189354550, gi... - gi\|189354550\|gb\|EDU72969.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|188014009, gi... - gi\|188014009\|gb\|EDU52131.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|217326855, gi... - gi\|217326855\|ref\|ZP_03442938.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|209158035, gi... - gi\|209396635\|ref\|YP_002272067.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli ...	3.0E-81	[1..325]	[1..325]
gi\|238791395, gi... - gi\|77976239\|ref\|ZP_00831748.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Yersinia interm...	5.0E-81	[1..325]	[1..325]

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Predicted Domain #1

Region A:
Residues: [1-325]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAQQVQLSAT VAESQLGQRL DQALAELFPD YSRSRIKEWI LDSRVTVNGK KINKPKEKVL  60
   61 GGELVAIDAQ IEEDARWAPQ EIPLDIVYED NDILVINKPR GLVVHPGAGN PDGTVLNALL 120
  121 HYYPEIMDVP RAGIVHRLDK DTTGLMVVAK TVPAQTRLVE ALQAREITRE YEAVAIGNMT 180
  181 AGGRVDEPIS RHSTKRTHMA VHPMGKPATT HYRIMEHFRA HTRLRLRLET GRTHQIRVHM 240
  241 SHINHPLVGD QLYGGRPRPP KGASDSFIAI LRGFDRQALH ATMLRLYHPI RGIQMEWHAA 300
  301 LPEDMVELIN ALKADTEEFK DQMDW

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	83.69897
Match:	1qyuA
Description:	Structure of the catalytic domain of 23S rRNA pseudouridine synthase RluD
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

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: