YRC Public Data Repository - Protein Structure Prediction

Protein:	SMM1
Organism:	Saccharomyces cerevisiae
Length:	384 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 SMM1.

Description	E-value	Query Range	Subject Range
DUS2_YEAST - tRNA-dihydrouridine(20) synthase [NAD(P)+] OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ... gi\|151944543 - gi\|151944543\|gb\|EDN62821.1\| tRNA dihydrouridine synthase [Saccharomyces cerevisiae YJM789] gi\|207341587 - gi\|207341587\|gb\|EDZ69599.1\| YNR015Wp-like protein [Saccharomyces cerevisiae AWRI1631] gi\|190408986 - gi\|190408986\|gb\|EDV12251.1\| tRNA-dihydrouridine synthase 2 [Saccharomyces cerevisiae RM11-1a] SMM1 - Dihydrouridine synthase, member of a family of dihydrouridine synthases including Dus1p, Smm1p, Dus3...	6.0E-74	[1..384]	[1..384]
gi\|10172709, gi\|... - gi\|15612660\|ref\|NP_240963.1\| nitrogen regulation transcriptional regulator [Bacillus halodurans C-12... gi\|25332164 - pir\|\|A83662 transcription regulator involved in nitrogen regulation (NifR3/Smm1 family) BH0097 [imp...	9.0E-62	[2..352]	[7..333]
gi\|12721426, gi\|... - gi\|15602952\|ref\|NP_246024.1\| hypothetical protein PM1087 [Pasteurella multocida subsp. multocida str...	2.0E-61	[4..329]	[10..320]
gi\|168211211, gi... - gi\|170710780\|gb\|EDT22962.1\| putative dihydrouridine synthase [Clostridium perfringens B str. ATCC 36... gi\|110803269, gi... - gi\|110803269\|ref\|YP_699723.1\| putative dihydrouridine synthase [Clostridium perfringens SM101], gi\|1... gi\|170661755, gi... - gi\|170661755\|gb\|EDT14438.1\| putative dihydrouridine synthase [Clostridium perfringens E str. JGS1987... gi\|110673779, gi... - gi\|110799132\|ref\|YP_697155.1\| putative dihydrouridine synthase [Clostridium perfringens ATCC 13124],... gi\|182626021, gi... - gi\|182626021\|ref\|ZP_02953784.1\| putative dihydrouridine synthase [Clostridium perfringens D str. JGS... gi\|182379765, gi... - gi\|182379765\|gb\|EDT77244.1\| putative dihydrouridine synthase [Clostridium perfringens NCTC 8239], gi... gi\|168215145, gi... - gi\|170713442\|gb\|EDT25624.1\| putative dihydrouridine synthase [Clostridium perfringens CPE str. F4969... gi\|18311449, gi\|... - gi\|18311449\|ref\|NP_563383.1\| putative dihydrouridine synthase [Clostridium perfringens str. 13], gi\|...	4.0E-61	[2..342]	[6..322]
DUSB_KLEPN - tRNA-dihydrouridine synthase B OS=Klebsiella pneumoniae GN=dusB PE=3 SV=1	5.0E-61	[4..330]	[8..319]
DUSB_PROVU - tRNA-dihydrouridine synthase B OS=Proteus vulgaris GN=dusB PE=3 SV=2	5.0E-61	[4..330]	[8..319]
gi\|5834292 - gi\|5834292\|gb\|AAD53896.1\|AF176314_6 NifR3-like protein [Zymomonas mobilis] gi\|5834292\|gb\|AA... - NifR3-like protein [Zymomonas mobilis]	6.0E-61	[2..351]	[21..342]
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	3.0E-60	[4..330]	[8..319]
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...	4.0E-60	[4..330]	[8..319]
gi\|7447008 - pir\|\|S76519 hypothetical protein - Synechocystis sp. (strain PCC 6803) DUS1_SYNY3 - Probable tRNA-dihydrouridine synthase 1 OS=Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1) GN... DUS1_SYNY3 - Probable tRNA-dihydrouridine synthase 1 OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=dus1 PE=3...	6.0E-60	[2..330]	[38..340]

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Predicted Domain #1

Region A:
Residues: [1-273]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVTYAGKLVL APMVRAGELP TRLMALAHGA DLVWSPEIID KKLIQCVRKE NTALQTVDYV  60
   61 VPSKVQTRPE TLVFRTYPKL ESSKLIFQIG SASPALATQA ALKVINDVSG IDINAGCPKH 120
  121 FSIHSGMGSA LLRTPDTLCL ILKELVKNVG NPHSKPISVK IRLLDTKQDT LQLVKRLCAT 180
  181 GITNLTVHCR KTEMRNREQP ITDYIAEIYE ICQANNVSLI VNGAIRDRSH FHDLQANHWK 240
  241 NTNIGGMIAE CAERDPTVFD HTSKPSEDGP SWV

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [353-384]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NANAIAKQKR KQTDHIGSDT KKQKVVPLPT DI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	45.69897
Match:	1gt8A_
Description:	Dihydropyrimidine dehydrogenase, N-terminal domain; Dihydropyrimidine dehydrogenase, domain 4; Dihydropyrimidine dehydrogenase, domain 3; Dihydropyrimidine dehydrogenase, domain 2; Dihydropyrimidine dehydrogenase, C-terminal domain
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
nucleic acid binding	1.03692680161964	bayes_pls_golite062009
binding	0.68572942532795	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [274-352]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VACREFIQWA TKFDNHIGNT KYMLSRIVPG KSVFFQYFAR CKSPEEVSFV LKQLNDDGSA  60
   61 QTDPSEYLEN CRAQEKALK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	45.69897
Match:	1gt8A_
Description:	Dihydropyrimidine dehydrogenase, N-terminal domain; Dihydropyrimidine dehydrogenase, domain 4; Dihydropyrimidine dehydrogenase, domain 3; Dihydropyrimidine dehydrogenase, domain 2; Dihydropyrimidine dehydrogenase, C-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: