YRC Public Data Repository - Protein Structure Prediction

Protein:	DUS1
Organism:	Saccharomyces cerevisiae
Length:	423 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 DUS1.

Description	E-value	Query Range	Subject Range
DUS1_YEAST - tRNA-dihydrouridine(16/17) synthase [NAD(P)(+)] OS=Saccharomyces cerevisiae (strain ATCC 204508 / S2... DUS1 - Dihydrouridine synthase, member of a widespread family of conserved proteins including Smm1p, Dus3p,...	0.0	[1..423]	[1..423]
CE09942 - Yeast protein 8248 like status:Partially_confirmed UniProt:Q9XVN8 protein_id:CAB03067.1	2.0E-81	[10..419]	[52..458]
gi\|220955978 - gi\|220955978\|gb\|ACL90532.1\| CG3645-PA [synthetic construct] FBpp0307923, CG3... - This gene is referred to in FlyBase by the symbol Dmel\CG3645 (CG3645, FBgn0031238). It is a protein...	2.0E-79	[16..407]	[14..383]
DUS1_SCHPO - tRNA-dihydrouridine(16/17) synthase [NAD(P)(+)] OS=Schizosaccharomyces pombe (strain 972 / ATCC 2484... SPBC36B7.04 - tRNA dihydrouridine synthase Dus1	4.0E-79	[16..406]	[5..393]
DUSB_PROVU - tRNA-dihydrouridine synthase B OS=Proteus vulgaris GN=dusB PE=3 SV=2	1.0E-71	[22..341]	[3..323]
gi\|5834292 - gi\|5834292\|gb\|AAD53896.1\|AF176314_6 NifR3-like protein [Zymomonas mobilis] gi\|5834292\|gb\|AA... - NifR3-like protein [Zymomonas mobilis]	2.0E-71	[17..328]	[13..325]
DUSB_PECCA - tRNA-dihydrouridine synthase B OS=Pectobacterium carotovorum GN=dusB PE=3 SV=2	1.0E-70	[22..338]	[3..320]
gi\|12721426, gi\|... - gi\|15602952\|ref\|NP_246024.1\| hypothetical protein PM1087 [Pasteurella multocida subsp. multocida str...	2.0E-70	[19..336]	[2..320]
gi\|15603891 - gi\|15603891\|ref\|NP_220406.1\| NIFR3-like protein (nifR3) [Rickettsia prowazekii str. Madrid E] DUS_RICPR - (Q9ZED2) Probable tRNA-dihydrouridine synthase (EC 1.-.-.-)	2.0E-70	[9..334]	[2..332]
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-70	[22..338]	[3..320]

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Predicted Domain #1

Region A:
Residues: [1-365]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTEPALSSAN NALMQKLTGR QLFDKIGRPT RIVAPMVDQS ELAWRILSRR YGATLAYTPM  60
   61 LHAKLFATSK KYREDNWSSL DGSSVDRPLV VQFCANDPEY LLAAAKLVED KCDAVDLNLG 120
  121 CPQGIAKKGH YGSFLMEEWD LIHNLINTLH KNLKVPVTAK IRIFDDCEKS LNYAKMVLDA 180
  181 GAQFLTVHGR VREQKGQKTG LANWETIKYL RDNLPKETVF FANGNILYPE DISRCMEHIG 240
  241 ADAVMSAEGN LYNPGVFNVG QTKNKEKIFP RVDKIIREYF QIVKECQESK ASKTAMKSHF 300
  301 FKILRPFLPH HTDIRSTLAT MNAKATWEEW EEQVVKPVEK VVQEIFEQPD IAIKDEITIG 360
  361 EKQSW

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	35.154902
Match:	1gox__
Description:	Glycolate oxidase
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
oxidoreductase activity, acting on the CH-CH group of donors	0.876786102965635	bayes_pls_golite062009
oxidoreductase activity	0.80115790656025	bayes_pls_golite062009
binding	0.68572942532795	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [366-423]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GGSYRTVPYW RCQPYFRPVN GITGDKRVMQ GLIDESVNKK RKADVPLESA DKKKDVKA

[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	0.527	a.4.1	Homeodomain-like
View	Download	0.372	a.5.2	UBA-like
View	Download	0.442	a.65.1	Annexin
View	Download	0.374	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View	Download	0.406	a.5.1	DNA helicase RuvA subunit, C-terminal domain
View	Download	0.527	a.4.1	Homeodomain-like
View	Download	0.442	a.65.1	Annexin
View	Download	0.406	a.5.1	DNA helicase RuvA subunit, C-terminal domain
View	Download	0.374	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View	Download	0.372	a.5.2	UBA-like
View	Download	0.371	a.164.1	C-terminal domain of DFF45/ICAD (DFF-C domain)
View	Download	0.371	a.140.1	LEM domain
View	Download	0.344	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.338	a.5.1	DNA helicase RuvA subunit, C-terminal domain
View	Download	0.303	a.180.1	N-terminal, cytoplasmic domain of anti-sigmaE factor RseA
View	Download	0.301	a.144.1	PABC (PABP) domain
View	Download	0.290	d.47.1	Ribosomal protein L11, N-terminal domain
View	Download	0.275	a.43.1	Met repressor-like
View	Download	0.274	a.4.1	Homeodomain-like
View	Download	0.273	a.60.4	DNA repair protein Rad51, N-terminal domain
View	Download	0.271	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.249	a.36.1	Signal peptide-binding domain
View	Download	0.244	a.64.1	Saposin
View	Download	0.242	a.28.3	Retrovirus capsid protein C-terminal domain
View	Download	0.235	a.39.1	EF-hand
View	Download	0.233	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.225	a.58.1	Chemotaxis receptor methyltransferase CheR, N-terminal domain
View	Download	0.212	a.4.1	Homeodomain-like
View	Download	0.211	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.205	a.22.1	Histone-fold

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: