YRC Public Data Repository - Protein Structure Prediction

Protein:	RIB2
Organism:	Saccharomyces cerevisiae
Length:	591 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 RIB2.

Description	E-value	Query Range	Subject Range
RIB2 - Bifunctional enzyme with DRAP deaminase and tRNA:pseudouridine synthase activity; the deaminase cata... RIB2_YEAST - Bifunctional protein RIB2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RIB2 PE=1 SV=1	0.0	[1..591]	[1..591]
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-79	[91..394]	[8..302]
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\|...	2.0E-77	[89..417]	[8..324]
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-77	[91..397]	[7..303]
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 ...	4.0E-77	[89..417]	[8..324]
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...	1.0E-76	[89..417]	[8..324]
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...	6.0E-76	[89..417]	[8..324]
PUS7_ARATH - RNA pseudouridine synthase 7 OS=Arabidopsis thaliana GN=At5g51140 PE=2 SV=1	7.0E-76	[26..422]	[1..393]
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...	1.0E-75	[91..417]	[10..324]

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Predicted Domain #1

Region A:
Residues: [1-100]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEDSNNEASD DFNNLLNKEI ESAKEVKLRK FANRNNNRNE NSSKVKDASG FRLRVIQTDG  60
   61 HKTKKTDPDY EVTIDGPLRK IEPYFFTYKT FCKERWRDRK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	3.221849
Match:	1fjgD_
Description:	Ribosomal protein S4
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [101-166]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LVDVFVSEFR DREPSYYSKT IAEGKVYLND EPANLDTIIR DGDLITHKVH RHEPPVTSKP  60
   61 IDIVFE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.154902
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 #3

Region A:
Residues: [167-368]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DEDILVIDKP SSIPVHPTGR YRFNTITKML ERQLGYSVHP CNRLDKPTSG LMFLAKTPLG  60
   61 ADRMGDQMKA REVTKEYVAR VKGEFPIGIV EVDKPVRSVN PKVALNAVCE MSDENAKHAK 120
  121 TVFQRVSYDG QTSIVKCKPL TGRTHQIRVH LQYLGFPIAN DPIYSNPDIW GPDLGRGGLQ 180
  181 NYDDIVLKLD AIGKTNPAES WI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.154902
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
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	3.83901378721842	bayes_pls_golite062009
deaminase activity	2.68802865527462	bayes_pls_golite062009
catalytic activity	1.70756445127105	bayes_pls_golite062009
cyclohydrolase activity	1.34791174229508	bayes_pls_golite062009
methyltransferase activity	1.24697538679504	bayes_pls_golite062009
transferase activity, transferring one-carbon groups	1.16679252289538	bayes_pls_golite062009
binding	1.05190374148481	bayes_pls_golite062009
transferase activity	0.771056210634777	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [369-426]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HPHSEGEYLL GRQCEECEAE MYTDPGTNDL DLWLHAFRYE SLERNSDTQK PLWSYRTK

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #5

Region A:
Residues: [427-591]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YPEWALEPHR RYMEMAVKEA GKCGPTKTAF SVGAVLVHGT QVLATGYSRE LPGNTHAEQC  60
   61 ALIKYSQLHP NCPTIVPMGT VLYTTMEPCS FRLSGNEPCC DRILATQGAI GTVFVGVMEP 120
  121 DTFVKNNTSL NKLESHGVNY IQIPGYEEEC TIIAFKGHDN SDDKA

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	11.14
Match:	1jtkA
Description:	mono-domain cytidine deaminase
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:

Predicted functions: