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 are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.297	a.4.1	Homeodomain-like
View	Download	0.218	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.205	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.210	a.4.12	TrpR-like
View	Download	0.252	a.4.7	Ribosomal protein L11, C-terminal domain
View	Download	0.204	d.52.5	Probable GTPase Der, C-terminal 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: