YRC Public Data Repository - Protein Structure Prediction

Protein:	PUS6
Organism:	Saccharomyces cerevisiae
Length:	404 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 PUS6.

Description	E-value	Query Range	Subject Range
PUS6_YEAST - tRNA pseudouridine(31) synthase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PUS6 PE=... PUS6 - tRNA:pseudouridine synthase, catalyzes the conversion of uridine to pseudouridine at position 31 in ...	6.0E-98	[1..404]	[1..404]
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\|...	5.0E-70	[24..390]	[6..322]
gi\|108774632, gi... - gi\|229901200\|ref\|ZP_04516323.1\| 23S rRNA pseudouridine synthase [Yersinia pestis Nepal516], gi\|22968... gi\|166010204, gi... - gi\|166010204\|ref\|ZP_02231102.1\| ribosomal large subunit pseudouridine synthase D [Yersinia pestis bi... gi\|166205832, gi... - gi\|166213045\|ref\|ZP_02239080.1\| ribosomal large subunit pseudouridine synthase D [Yersinia pestis bi... gi\|167398582, gi... - gi\|167398582\|ref\|ZP_02304106.1\| ribosomal large subunit pseudouridine synthase D [Yersinia pestis bi... gi\|167421637, gi... - gi\|167421637\|ref\|ZP_02313390.1\| ribosomal large subunit pseudouridine synthase D [Yersinia pestis bi... gi\|167057483, gi... - gi\|167423313\|ref\|ZP_02315066.1\| ribosomal large subunit pseudouridine synthase D [Yersinia pestis bi... gi\|167470273 - gi\|167470273\|ref\|ZP_02334977.1\| 23S rRNA pseudouridine synthase D [Yersinia pestis FV-1] gi\|165915384, gi... - gi\|89103056\|ref\|ZP_01175652.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Yersinia pestis... gi\|108808759, gi... - gi\|108808759\|ref\|YP_652675.1\| 23S rRNA pseudouridine synthase D [Yersinia pestis Antiqua], gi\|108780... gi\|15981211, gi\|... - gi\|218930302\|ref\|YP_002348177.1\| 23S rRNA pseudouridine synthase D [Yersinia pestis CO92], gi\|161234... gi\|21957646, gi\|... - gi\|22124820\|ref\|NP_668243.1\| 23S rRNA pseudouridine synthase D [Yersinia pestis KIM], gi\|21957646\|gb... gi\|229899460, gi... - gi\|229899460\|ref\|ZP_04514603.1\| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis s... gi\|165926534, gi... - gi\|165926534\|ref\|ZP_02222366.1\| ribosomal large subunit pseudouridine synthase D [Yersinia pestis bi... gi\|229695259, gi... - gi\|229838893\|ref\|ZP_04459052.1\| 23S rRNA pseudouridine synthase [Yersinia pestis biovar Orientalis s... RLUD_YERPE - Ribosomal large subunit pseudouridine synthase D OS=Yersinia pestis GN=rluD PE=3 SV=1 gi\|153997673, gi... - gi\|153997673\|ref\|ZP_02022773.1\| ribosomal large subunit pseudouridine synthase D [Yersinia pestis CA...	7.0E-70	[24..398]	[6..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 ...	1.0E-69	[24..390]	[6..322]
gi\|25322380 - gi\|25322380\|pir\|\|G85905 suppressor of ftsH mutation [imported] - Escherichia coli (strain O157:H7, ... gi\|12517018, gi\|... - gi\|15803118\|ref\|NP_289149.1\| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 EDL933], gi...	4.0E-69	[24..390]	[6..322]
gi\|15615105, gi\|... - gi\|15615105\|ref\|NP_243408.1\| hypothetical protein BH2542 [Bacillus halodurans C-125], gi\|10175162\|db... gi\|25322336 - pir\|\|F83967 hypothetical protein BH2542 [imported] - Bacillus halodurans (strain C-125)	3.0E-68	[24..349]	[4..304]
gi\|213999722 - gi\|213999722\|ref\|ZP_03410457.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... gi\|224469042, gi... - gi\|224584515\|ref\|YP_002638313.1\| ftsH suppressor protein SfhB [Salmonella enterica subsp. enterica s... gi\|213585773 - gi\|213585773\|ref\|ZP_03367599.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... gi\|213619387 - gi\|213619387\|ref\|ZP_03373213.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... gi\|213646598 - gi\|213646598\|ref\|ZP_03376651.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... gi\|213850144 - gi\|213850144\|ref\|ZP_03381042.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... gi\|204929503, gi... - gi\|204929503\|ref\|ZP_03220577.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteric... gi\|206709815, gi... - gi\|207858012\|ref\|YP_002244663.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enter... gi\|213051815 - gi\|213051815\|ref\|ZP_03344693.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... gi\|213424875 - gi\|213424875\|ref\|ZP_03357625.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... RLUD_SALTY - Ribosomal large subunit pseudouridine synthase D OS=Salmonella typhimurium GN=rluD PE=1 SV=2 gi\|167553892, gi... - gi\|205321769\|gb\|EDZ09608.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su... gi\|62128868, gi\|... - gi\|62181235\|ref\|YP_217652.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica ... gi\|197240719, gi... - gi\|197262464\|ref\|ZP_03162538.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteric... RLUD_SALTI - Ribosomal large subunit pseudouridine synthase D OS=Salmonella typhi GN=rluD PE=3 SV=2 gi\|197095033, gi... - gi\|197363556\|ref\|YP_002143193.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enter... gi\|198242257, gi... - gi\|198242257\|ref\|YP_002216673.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteri... gi\|199606291, gi... - gi\|200389193\|ref\|ZP_03215805.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteric... RLUD_SALTY - Ribosomal large subunit pseudouridine synthase D OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ... gi\|194447791, gi... - gi\|194447791\|ref\|YP_002046668.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enter... gi\|29142987, gi\|... - gi\|29142987\|ref\|NP_806329.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica ... gi\|194471474, gi... - gi\|194471474\|ref\|ZP_03077458.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteric... RLUD_SALTY - Ribosomal large subunit pseudouridine synthase D OS=Salmonella typhimurium GN=rluD PE=3 SV=2 gi\|194737121, gi... - gi\|194737121\|ref\|YP_002115673.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteri... RLUD_SALTI - Ribosomal large subunit pseudouridine synthase D OS=Salmonella typhi GN=rluD PE=3 SV=2 gi\|197211109, gi... - gi\|197247406\|ref\|YP_002147565.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteri... gi\|238909508 - gi\|238909508\|ref\|ZP_04653345.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enteri... gi\|205349079, gi... - gi\|205349079\|gb\|EDZ35710.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su... gi\|168464166, gi... - gi\|195633435\|gb\|EDX51849.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su... gi\|16761516 - gi\|16761516\|ref\|NP_457133.1\| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp. enterica ... gi\|168822474, gi... - gi\|205341144\|gb\|EDZ27908.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su... gi\|194446496, gi... - gi\|194446496\|ref\|YP_002041926.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enteri... gi\|205329256, gi... - gi\|205329256\|gb\|EDZ16020.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su... lcl\|NC_016856.1_... - [gene=rluD] [protein=23S rRNA pseudouridine synthase D] [protein_id=YP_005238784.1] [location=comple... gi\|205331842, gi... - gi\|205331842\|gb\|EDZ18606.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su... gi\|197287851, gi... - gi\|197287851\|gb\|EDY27239.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su... gi\|168244683, gi... - gi\|205336483\|gb\|EDZ23247.1\| ribosomal large subunit pseudouridine synthase D [Salmonella enterica su...	4.0E-68	[24..389]	[6..321]
gi\|32468746, gi\|... - gi\|50812225\|ref\|NP_389429.2\| hypothetical protein BSU15460 [Bacillus subtilis subsp. subtilis str. 1... YLYB_BACSU - Uncharacterized RNA pseudouridine synthase ylyB OS=Bacillus subtilis GN=ylyB PE=3 SV=2	2.0E-67	[28..350]	[7..303]
gi\|14023962, gi\|... - gi\|14023962\|dbj\|BAB50567.1\| pseudouridine synthase [Mesorhizobium loti MAFF303099], gi\|13473214\|ref\|...	9.0E-67	[26..381]	[1..327]

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Predicted Domain #1

Region A:
Residues: [1-112]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSTIKVIEVY TQNGLRKVRP YYNRRSAFVK GRWLGKLLID VLVSEFKLRP RAYYLDQIRK  60
   61 GTYRLIRDGV PLVPDHLMTT IIKNHDVLET TTHKHEPPVK QWCSQEVEAE DL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.0
Match:	1kskA_
Description:	Ribosomal small subunit pseudouridine 516 synthase RsuA; Pseudouridine synthase RsuA N-terminal domain
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
transcription regulator activity	1.21173188039059	bayes_pls_golite062009
DNA binding	0.950713703876672	bayes_pls_golite062009
nucleic acid binding	0.909704702595901	bayes_pls_golite062009
binding	0.730744558777463	bayes_pls_golite062009
RNA binding	0.706879359688019	bayes_pls_golite062009
transferase activity	0.237728328252954	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [113-404]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGRIAGFNIV FEDESILVID KPSGIPVHPT GQFYQNTITE LLKLHGVDAL PCYRLDKITS  60
   61 GLLILAKNSQ SAGEIQKSIR SRDMIKIYLA RVKGRFPHSE LILDNENAAE TTFEDTSKVT 120
  121 VEMTPIYSID PKRQFPVGLS TSKDAITKFY PIRYFSHADE TVVACKPITG RTHQIRIHLA 180
  181 RLGHPIVNDS VYCSHITKYP ERLKFITQFP RWENQQDLDA EELKVRFQKF VDETKNNCRT 240
  241 METFCPECHT VDLKDPVLSD LELWLHAWKY EEINGKFKFK TDLPKWAQLD NS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.0
Match:	1kskA_
Description:	Ribosomal small subunit pseudouridine 516 synthase RsuA; Pseudouridine synthase RsuA N-terminal domain
Matching Structure (courtesy of the PDB):

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: