YRC Public Data Repository - Protein Structure Prediction

Protein:	DUS4
Organism:	Saccharomyces cerevisiae
Length:	367 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

[What does the above image mean?]

[Show Ginzu Version Information]

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 DUS4.

Description	E-value	Query Range	Subject Range
DUS4 - Dihydrouridine synthase, member of a widespread family of conserved proteins including Smm1p, Dus1p,... DUS4_YEAST - tRNA-dihydrouridine(20a/20b) synthase [NAD(P)+] OS=Saccharomyces cerevisiae (strain ATCC 204508 / S2...	4.0E-86	[1..367]	[1..367]
gi\|12721426, gi\|... - gi\|15602952\|ref\|NP_246024.1\| hypothetical protein PM1087 [Pasteurella multocida subsp. multocida str...	5.0E-71	[28..338]	[1..325]
gi\|168786153, gi... - gi\|189373964\|gb\|EDU92380.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC869], gi... gi\|168783829, gi... - gi\|188998885\|gb\|EDU67871.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4076], g... gi\|187767124, gi... - gi\|187767124\|gb\|EDU30968.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4196], g... gi\|189361809, gi... - gi\|189361809\|gb\|EDU80228.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4486], g... gi\|170680881, gi... - gi\|170680881\|ref\|YP_001745531.1\| tRNA-dihydrouridine synthase B [Escherichia coli SMS-3-5], gi\|17051... gi\|169890623, gi... - gi\|170082788\|ref\|YP_001732108.1\| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr. ... gi\|169753425, gi... - gi\|170018497\|ref\|YP_001723451.1\| tRNA-dihydrouridine synthase B [Escherichia coli ATCC 8739], gi\|169... gi\|227887986, gi... - gi\|227887986\|ref\|ZP_04005791.1\| tRNA-dihydrouridine synthase B [Escherichia coli 83972], gi\|22783538... gi\|168802602, gi... - gi\|189375438\|gb\|EDU93854.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC508], gi... gi\|238863714, gi... - gi\|238902359\|ref\|YP_002928155.1\| tRNA-dihydrouridine synthase B [Escherichia coli BW2952], gi\|238863... gi\|237705982, gi... - gi\|237705982\|ref\|ZP_04536463.1\| tRNA-dihydrouridine synthase B [Escherichia sp. 3_2_53FAA], gi\|22689... gi\|253771910, gi... - gi\|254289945\|ref\|YP_003055693.1\| tRNA-dihydrouridine synthase B [Escherichia coli BL21(DE3)], gi\|253... gi\|242378794, gi... - gi\|251786521\|ref\|YP_003000825.1\| hypothetical protein B21_03069 [Escherichia coli BL21], gi\|24237879... gi\|253975096, gi... - gi\|254163195\|ref\|YP_003046303.1\| tRNA-dihydrouridine synthase B [Escherichia coli B str. REL606], gi... gi\|168764879, gi... - gi\|189365202\|gb\|EDU83618.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4501], g... DUSB_ECOLI - tRNA-dihydrouridine synthase B (EC 1.-.-.-) - Escherichia coli gi\|254038424, gi... - gi\|254038424\|ref\|ZP_04872482.1\| tRNA-dihydrouridine synthase B [Escherichia sp. 1_1_43], gi\|22684004... gi\|168758937, gi... - gi\|189354344\|gb\|EDU72763.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4401], g... gi\|168752560, gi... - gi\|188013631\|gb\|EDU51753.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4113], g... gi\|254594603, gi... - gi\|254795203\|ref\|YP_003080040.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. TW143... DUSB_ECOL6 - tRNA-dihydrouridine synthase B OS=Escherichia coli O6 GN=dusB PE=3 SV=1 gi\|81247042, gi\|... - gi\|82545631\|ref\|YP_409578.1\| tRNA-dihydrouridine synthase B [Shigella boydii Sb227], gi\|81247042\|gb\|... gi\|85676051, gi\|... - gi\|89110020\|ref\|AP_003800.1\| tRNA-dihydrouridine synthase B [Escherichia coli str. K-12 substr. W311... gi\|74313789, gi\|... - gi\|74313789\|ref\|YP_312208.1\| tRNA-dihydrouridine synthase B [Shigella sonnei Ss046], gi\|73857266\|gb\|... gi\|81242717, gi\|... - gi\|82778569\|ref\|YP_404918.1\| tRNA-dihydrouridine synthase B [Shigella dysenteriae Sd197], gi\|8124271... gi\|91074265, gi\|... - gi\|91212691\|ref\|YP_542677.1\| tRNA-dihydrouridine synthase B [Escherichia coli UTI89], gi\|91074265\|gb... gi\|15833386, gi\|... - gi\|15833386\|ref\|NP_312159.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. Sakai], g... gi\|110643504, gi... - gi\|110643504\|ref\|YP_671234.1\| tRNA-dihydrouridine synthase B [Escherichia coli 536], gi\|110345096\|gb... gi\|208814013, gi... - gi\|208814013\|ref\|ZP_03255342.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4045... gi\|208806407, gi... - gi\|208806407\|ref\|ZP_03248744.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4206... gi\|195940004 - gi\|195940004\|ref\|ZP_03085386.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4024... gi\|194421031, gi... - gi\|194440027\|ref\|ZP_03072084.1\| tRNA-dihydrouridine synthase B [Escherichia coli 101-1], gi\|19442103... gi\|124500557, gi... - gi\|124528534\|ref\|ZP_01699823.1\| putative TIM-barrel protein, nifR3 family [Escherichia coli B], gi\|1... gi\|157162741, gi... - gi\|157162741\|ref\|YP_001460059.1\| tRNA-dihydrouridine synthase B [Escherichia coli HS], gi\|157068421\|... gi\|215488567, gi... - gi\|215488567\|ref\|YP_002330998.1\| tRNA-dihydrouridine synthase B [Escherichia coli O127:H6 str. E2348... gi\|157078205, gi... - gi\|157156175\|ref\|YP_001464734.1\| tRNA-dihydrouridine synthase B [Escherichia coli E24377A], gi\|15707... gi\|115514675, gi... - gi\|117625551\|ref\|YP_858874.1\| tRNA-dihydrouridine synthase B [Escherichia coli APEC O1], gi\|11551467... gi\|209913991, gi... - gi\|209920732\|ref\|YP_002294816.1\| tRNA-dihydrouridine synthase B [Escherichia coli SE11], gi\|20991399... gi\|209396246, gi... - gi\|209396246\|ref\|YP_002272722.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC411... gi\|208821905, gi... - gi\|208821905\|ref\|ZP_03262225.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. EC4042... gi\|191169157, gi... - gi\|191169157\|ref\|ZP_03030915.1\| tRNA-dihydrouridine synthase B [Escherichia coli B7A], gi\|190900799\|... gi\|188486958, gi... - gi\|188491759\|ref\|ZP_02999029.1\| tRNA-dihydrouridine synthase B [Escherichia coli 53638], gi\|18848695... gi\|187431038, gi... - gi\|187734046\|ref\|YP_001881952.1\| tRNA-dihydrouridine synthase B [Shigella boydii CDC 3083-94], gi\|18... gi\|170124811, gi... - gi\|170765665\|ref\|ZP_02900476.1\| tRNA-dihydrouridine synthase B [Escherichia albertii TW07627], gi\|17... EG11311 - tRNA-dihydrouridine synthase B / tRNA-dihydrouridine synthase B gi\|194435099, gi... - gi\|194435099\|ref\|ZP_03067336.1\| tRNA-dihydrouridine synthase B [Shigella dysenteriae 1012], gi\|19441... gi\|193071520, gi... - gi\|193071520\|ref\|ZP_03052430.1\| tRNA-dihydrouridine synthase B [Escherichia coli E110019], gi\|192955... gi\|193066463, gi... - gi\|193066463\|ref\|ZP_03047508.1\| tRNA-dihydrouridine synthase B [Escherichia coli E22], gi\|192925892\|... gi\|190905864, gi... - gi\|191173814\|ref\|ZP_03035335.1\| tRNA-dihydrouridine synthase B [Escherichia coli F11], gi\|190905864\|... DUSB_ECOL6 - tRNA-dihydrouridine synthase B OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=dus... DUSB_ECO57 - tRNA-dihydrouridine synthase B OS=Escherichia coli O157:H7 GN=dusB PE=3 SV=1 EG11311 - tRNA-dihydrouridine synthase B / tRNA-dihydrouridine synthase B gi\|12517887, gi\|... - gi\|15803794\|ref\|NP_289828.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 EDL933], gi\|12... gi\|218560329, gi... - gi\|218560329\|ref\|YP_002393242.1\| tRNA-dihydrouridine synthase B [Escherichia coli S88], gi\|218367098... gi\|218555824, gi... - gi\|218555824\|ref\|YP_002388737.1\| tRNA-dihydrouridine synthase B [Escherichia coli IAI1], gi\|21836259... gi\|218550544, gi... - gi\|218550544\|ref\|YP_002384335.1\| tRNA-dihydrouridine synthase B [Escherichia fergusonii ATCC 35469],... gi\|217327776, gi... - gi\|217327776\|ref\|ZP_03443859.1\| tRNA-dihydrouridine synthase B [Escherichia coli O157:H7 str. TW1458... gi\|218706874, gi... - gi\|218706874\|ref\|YP_002414393.1\| tRNA-dihydrouridine synthase B [Escherichia coli UMN026], gi\|218433... gi\|218702033, gi... - gi\|218702033\|ref\|YP_002409662.1\| tRNA-dihydrouridine synthase B [Escherichia coli IAI39], gi\|2183720... gi\|218696959, gi... - gi\|218696959\|ref\|YP_002404626.1\| tRNA-dihydrouridine synthase B [Escherichia coli 55989], gi\|2183536... gi\|218429115, gi... - gi\|218691551\|ref\|YP_002399763.1\| tRNA-dihydrouridine synthase B [Escherichia coli ED1a], gi\|21842911...	1.0E-69	[32..333]	[3..318]
gi\|205322522, gi... - gi\|205322522\|gb\|EDZ10361.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica sero... gi\|205336039, gi... - gi\|205336039\|gb\|EDZ22803.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica sero... gi\|197287911, gi... - gi\|197287911\|gb\|EDY27299.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica sero... gi\|168233971, gi... - gi\|205332030\|gb\|EDZ18794.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica sero... gi\|205328090, gi... - gi\|205328090\|gb\|EDZ14854.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica sero... gi\|205274066, gi... - gi\|205354285\|ref\|YP_002228086.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica... gi\|204931223, gi... - gi\|204931223\|ref\|ZP_03222017.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... gi\|199604562, gi... - gi\|200387464\|ref\|ZP_03214076.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... gi\|198242306, gi... - gi\|198242306\|ref\|YP_002217354.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica... gi\|213580280 - gi\|213580280\|ref\|ZP_03362106.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... gi\|213428299 - gi\|213428299\|ref\|ZP_03361049.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... DUSB_SALTY - tRNA-dihydrouridine synthase B OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=du... gi\|213051972 - gi\|213051972\|ref\|ZP_03344850.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... DUSB_SALTI - tRNA-dihydrouridine synthase B OS=Salmonella typhi GN=dusB PE=3 SV=1 gi\|207858632, gi... - gi\|207858632\|ref\|YP_002245283.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica... gi\|194450924, gi... - gi\|194450924\|ref\|YP_002047412.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica... gi\|194443531, gi... - gi\|194443531\|ref\|YP_002042640.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica... gi\|205340899, gi... - gi\|205340899\|gb\|EDZ27663.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica sero... gi\|168463378, gi... - gi\|195633240\|gb\|EDX51654.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica sero... gi\|197240605, gi... - gi\|197262350\|ref\|ZP_03162424.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... gi\|197211526, gi... - gi\|197247823\|ref\|YP_002148308.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica... gi\|194712862, gi... - gi\|194737360\|ref\|YP_002116332.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica... gi\|194455308, gi... - gi\|194468944\|ref\|ZP_03074928.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... gi\|213853023 - gi\|213853023\|ref\|ZP_03382555.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... DUSB_SALTY - tRNA-dihydrouridine synthase B OS=Salmonella typhimurium GN=dusB PE=3 SV=1 gi\|213619017 - gi\|213619017\|ref\|ZP_03372843.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... gi\|62181892, gi\|... - gi\|62181892\|ref\|YP_218309.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ser... lcl\|NC_016856.1_... - [gene=yhdG] [protein=tRNA-dihydrouridine synthase B] [protein_id=YP_005239574.1] [location=3569170..... gi\|238913536 - gi\|238913536\|ref\|ZP_04657373.1\| tRNA-dihydrouridine synthase B [Salmonella enterica subsp. enterica ... DUSB_SALTI - tRNA-dihydrouridine synthase B OS=Salmonella typhi GN=dusB PE=3 SV=1 DUSB_SALTY - tRNA-dihydrouridine synthase B OS=Salmonella typhimurium GN=dusB PE=3 SV=1	2.0E-69	[32..333]	[3..318]
DUSB_PROVU - tRNA-dihydrouridine synthase B OS=Proteus vulgaris GN=dusB PE=3 SV=2	2.0E-69	[32..333]	[3..318]
DUSB_YERPE - tRNA-dihydrouridine synthase B OS=Yersinia pestis GN=dusB PE=3 SV=1 gi\|153997407, gi... - gi\|153997407\|ref\|ZP_02022507.1\| tRNA-dihydrouridine synthase B [Yersinia pestis CA88-4125], gi\|14928... Q665E2\|Q665E2_YERPS - Putative uncharacterized protein - Yersinia pseudotuberculosis gi\|115349276, gi... - gi\|218930665\|ref\|YP_002348540.1\| tRNA-dihydrouridine synthase B [Yersinia pestis CO92], gi\|16123797\|... gi\|145209273, gi... - gi\|145597577\|ref\|YP_001161653.1\| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides F], gi\|14... gi\|51597867, gi\|... - gi\|51597867\|ref\|YP_072058.1\| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis IP 32953], ... gi\|77630577, gi\|... - gi\|77630577\|ref\|ZP_00793163.1\| COG0042: tRNA-dihydrouridine synthase [Yersinia pseudotuberculosis IP... gi\|108809658, gi... - gi\|108809658\|ref\|YP_653574.1\| tRNA-dihydrouridine synthase B [Yersinia pestis Antiqua], gi\|108781571... gi\|229904177, gi... - gi\|229904177\|ref\|ZP_04519288.1\| tRNA-dihydrouridine synthase B [Yersinia pestis Nepal516], gi\|229678... gi\|229836798, gi... - gi\|229836798\|ref\|ZP_04456963.1\| tRNA-dihydrouridine synthase B [Yersinia pestis Pestoides A], gi\|229... gi\|229695668, gi... - gi\|229839302\|ref\|ZP_04459461.1\| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis st... gi\|165914498, gi... - gi\|89105374\|ref\|ZP_01177894.1\| COG0042: tRNA-dihydrouridine synthase [Yersinia pestis biovar Orienta... gi\|229687358, gi... - gi\|229899866\|ref\|ZP_04515007.1\| tRNA-dihydrouridine synthase B [Yersinia pestis biovar Orientalis st... gi\|186700088, gi... - gi\|186897062\|ref\|YP_001874174.1\| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis PB1/+],... gi\|77634311 - gi\|77634311\|ref\|ZP_00796414.1\| COG0042: tRNA-dihydrouridine synthase [Yersinia pestis Angola] gi\|166011363, gi... - gi\|166011363\|ref\|ZP_02232261.1\| dihydrouridine synthase [Yersinia pestis biovar Antiqua str. E197900... gi\|167420730, gi... - gi\|167420730\|ref\|ZP_02312483.1\| dihydrouridine synthase [Yersinia pestis biovar Orientalis str. MG05... gi\|166214187, gi... - gi\|166214187\|ref\|ZP_02240222.1\| dihydrouridine synthase [Yersinia pestis biovar Antiqua str. B420030... gi\|169749238, gi... - gi\|170022704\|ref\|YP_001719209.1\| tRNA-dihydrouridine synthase B [Yersinia pseudotuberculosis YPIII],... gi\|167055558, gi... - gi\|167425544\|ref\|ZP_02317297.1\| dihydrouridine synthase [Yersinia pestis biovar Mediaevalis str. K19...	2.0E-69	[32..333]	[3..318]
DUSB_PECCA - tRNA-dihydrouridine synthase B OS=Pectobacterium carotovorum GN=dusB PE=3 SV=2	4.0E-69	[32..333]	[3..318]
DUSB_KLEPN - tRNA-dihydrouridine synthase B OS=Klebsiella pneumoniae GN=dusB PE=3 SV=1	4.0E-69	[32..333]	[3..318]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	4.0E-69	[32..333]	[3..318]

Back

Predicted Domain #1

Region A:
Residues: [1-279]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MHTMHIPSGD VLIPKPKLIT EETDPLHIIK TRQKTHGRPV TIAGPMVRYS KLPFRQLCRE  60
   61 YNVDIVYSPM ILAREYVRNE HARISDLSTN NEDTPLIVQV GVNNVADLLK FVEMVAPYCD 120
  121 GIGINCGCPI KEQIREGIGC ALIYNSDLLC SMVHAVKDKY GDKLRIETKI RIHEALDETV 180
  181 ELCRKLCDAG VDWITIHGRT RRTRSSQPAN LDAIKYIIEN ISDKNVPVIA NGDCFKLSDL 240
  241 ERITKYTGAH GVMAVRGLLS NPALFAGYTT CPWGCIEKF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	29.39794
Match:	1ep1A_
Description:	Dihydroorotate dehydrogenase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	1.94749091175302	bayes_pls_golite062009
tRNA dihydrouridine synthase activity	1.94490879164338	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-CH group of donors	0.876786102965635	bayes_pls_golite062009
oxidoreductase activity	0.80115790656025	bayes_pls_golite062009
nucleic acid binding	0.453918901387506	bayes_pls_golite062009
binding	0.256396206082349	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [280-367]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 CYWALEFGGL PFQLAQHHLY CMLENMELKK SLLKKMMNLK NYISLIDWFN KTFEFKRYGE  60
   61 DGFGMGVEIP YKANSCVQRS ASVVERQE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.0
Match:	1h5yA_
Description:	Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF
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: