YRC Public Data Repository - Protein Structure Prediction

Protein:	DSS1
Organism:	Saccharomyces cerevisiae
Length:	969 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 DSS1.

Description	E-value	Query Range	Subject Range
gi\|557724 - gi\|557724\|gb\|AAC49144.1\| DSS-1	0.0	[1..969]	[1..969]
gi\|238903286, gi... - gi\|238903286\|ref\|YP_002929082.1\| exoribonuclease R, RNase R [Escherichia coli BW2952], gi\|238861060\|... gi\|194439533, gi... - gi\|83585083\|ref\|ZP_00923736.1\| COG0557: Exoribonuclease R [Escherichia coli 101-1], gi\|194439533\|ref... EG11259 - exoribonuclease R, RNase R / Exoribonuclease R, RNase R gi\|85676930, gi\|... - gi\|89110899\|ref\|AP_004679.1\| exoribonuclease R, RNase R [Escherichia coli str. K-12 substr. W3110], ... RNR_ECOLI - Ribonuclease R (EC 3.1.-.-) (RNase R) (Protein vacB) - Escherichia coli EG11259 - exoribonuclease R, RNase R / Exoribonuclease R, RNase R gi\|169891460, gi... - gi\|170083625\|ref\|YP_001732945.1\| exoribonuclease R, RNase R [Escherichia coli str. K-12 substr. DH10... gi\|253976009, gi... - gi\|254164108\|ref\|YP_003047216.1\| exoribonuclease R, RNase R [Escherichia coli B str. REL606], gi\|253... gi\|253775196, gi... - gi\|254290858\|ref\|YP_003056606.1\| exoribonuclease R, RNase R [Escherichia coli BL21(DE3)], gi\|2539801... gi\|251787428, gi... - gi\|251787428\|ref\|YP_003001732.1\| hypothetical protein B21_04008 [Escherichia coli BL21], gi\|24237970...	0.0	[354..940]	[105..677]
gi\|15804768, gi\|... - gi\|15804768\|ref\|NP_290809.1\| putative enzyme [Escherichia coli O157:H7 EDL933], gi\|12519167\|gb\|AAG59... gi\|13364632 - gi\|13364632\|dbj\|BAB38578.1\| putative enzyme [Escherichia coli O157:H7 str. Sakai] gi\|13364632 - gi\|13364632\|dbj\|BAB38578.1\| putative enzyme [Escherichia coli O157:H7] gi\|25298860, gi\|... - pir\|\|C86114 probable enzyme vacB [imported] - Escherichia coli (strain O157:H7, substrain EDL933), ...	0.0	[354..940]	[119..691]
RNR_SHIFL - Ribonuclease R OS=Shigella flexneri GN=rnr PE=3 SV=4 gi\|161485844 - gi\|161485844\|ref\|NP_710044.2\| exoribonuclease R [Shigella flexneri 2a str. 301] gi\|161486368 - gi\|161486368\|ref\|NP_839722.2\| exoribonuclease R [Shigella flexneri 2a str. 2457T]	0.0	[354..940]	[105..677]
RNR_HAEIN - Ribonuclease R OS=Haemophilus influenzae GN=rnr PE=3 SV=1 RNR_HAEIN - Ribonuclease R OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=rnr PE=3 SV=...	0.0	[353..935]	[112..681]
gi\|12722391, gi\|... - gi\|15603819\|ref\|NP_246893.1\| hypothetical protein PM1954 [Pasteurella multocida subsp. multocida str...	0.0	[356..935]	[115..682]
gi\|213582912 - gi\|213582912\|ref\|ZP_03364738.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Typhi... gi\|213648976 - gi\|213648976\|ref\|ZP_03379029.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Typhi... gi\|213852965 - gi\|213852965\|ref\|ZP_03382497.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Typhi... gi\|214003353 - gi\|214003353\|ref\|ZP_03414088.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Typhi... gi\|197096561, gi... - gi\|197365084\|ref\|YP_002144721.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Para... gi\|205274906, gi... - gi\|205355125\|ref\|YP_002228926.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Gall... gi\|207859513, gi... - gi\|207859513\|ref\|YP_002246164.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Ente... gi\|213052275 - gi\|213052275\|ref\|ZP_03345153.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Typhi... gi\|168822506, gi... - gi\|205341075\|gb\|EDZ27839.1\| ribonuclease R [Salmonella enterica subsp. enterica serovar Weltevreden ... gi\|194409041, gi... - gi\|194450737\|ref\|YP_002048411.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Heid... gi\|238910526 - gi\|238910526\|ref\|ZP_04654363.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Tenne... gi\|194457010, gi... - gi\|194470646\|ref\|ZP_03076630.1\| ribonuclease R [Salmonella enterica subsp. enterica serovar Kentucky... lcl\|NC_016856.1_... - [gene=vacB] [protein=exoribonuclease R] [protein_id=YP_005240681.1] [location=4623894..4626332] gi\|197247664, gi... - gi\|197247664\|ref\|YP_002149282.1\| ribonuclease R [Salmonella enterica subsp. enterica serovar Agona s... gi\|161617638, gi... - gi\|161617638\|ref\|YP_001591603.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Para... gi\|205327245, gi... - gi\|205327245\|gb\|EDZ14009.1\| ribonuclease R [Salmonella enterica subsp. enterica serovar 4,[5],12:i:-... gi\|205334286, gi... - gi\|205334286\|gb\|EDZ21050.1\| ribonuclease R [Salmonella enterica subsp. enterica serovar Kentucky str... gi\|205336060, gi... - gi\|205336060\|gb\|EDZ22824.1\| ribonuclease R [Salmonella enterica subsp. enterica serovar Heidelberg s... gi\|16505495, gi\|... - gi\|25298865\|pir\|\|AH1049 ribonuclease R (RNase R) (EC 3.1.-.-) [imported] - Salmonella enterica subsp... gi\|29140305, gi\|... - gi\|29144666\|ref\|NP_808008.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Typhi st... gi\|56416159, gi\|... - gi\|56416159\|ref\|YP_153234.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Paratyph... gi\|16767614, gi\|... - gi\|16767614\|ref\|NP_463229.1\| exoribonuclease R [Salmonella typhimurium LT2], gi\|16422929\|gb\|AAL23188... gi\|16763187 - gi\|16763187\|ref\|NP_458804.1\| exoribonuclease R [Salmonella enterica subsp. enterica serovar Typhi st...	0.0	[354..940]	[105..677]
RNR_BACSU - Ribonuclease R OS=Bacillus subtilis (strain 168) GN=rnr PE=2 SV=1 gi\|221324838 - gi\|221324838\|ref\|ZP_03606132.1\| ribonuclease R [Bacillus subtilis subsp. subtilis str. SMY] gi\|221320554 - gi\|221320554\|ref\|ZP_03601848.1\| ribonuclease R [Bacillus subtilis subsp. subtilis str. JH642] gi\|221315638 - gi\|221315638\|ref\|ZP_03597443.1\| ribonuclease R [Bacillus subtilis subsp. subtilis str. NCIB 3610] RNR_BACSU - Ribonuclease R OS=Bacillus subtilis GN=rnr PE=3 SV=1	0.0	[356..951]	[95..681]
gi\|89102912, gi\|... - gi\|89102912\|ref\|ZP_01175514.1\| COG0557: Exoribonuclease R [Yersinia pestis biovar Orientalis str. IP... gi\|108781807, gi... - gi\|108809894\|ref\|YP_653810.1\| exoribonuclease R [Yersinia pestis Antiqua], gi\|108781807\|gb\|ABG15865.... gi\|170026006, gi... - gi\|170026006\|ref\|YP_001722511.1\| exoribonuclease R [Yersinia pseudotuberculosis YPIII], gi\|169752540... gi\|229679701, gi... - gi\|229903931\|ref\|ZP_04519044.1\| exoribonuclease R, RNase R [Yersinia pestis Nepal516], gi\|229679701\|... gi\|150260576, gi... - gi\|150260576\|ref\|ZP_01917304.1\| ribonuclease R [Yersinia pestis CA88-4125], gi\|149289984\|gb\|EDM40061... Q66FA8\|Q66FA8_YERPS - Ribonuclease R - Yersinia pseudotuberculosis gi\|162419638, gi... - gi\|162419638\|ref\|YP_001605272.1\| exoribonuclease R [Yersinia pestis Angola], gi\|162352453\|gb\|ABX8640... gi\|165989243, gi... - gi\|166011884\|ref\|ZP_02232782.1\| ribonuclease R [Yersinia pestis biovar Antiqua str. E1979001], gi\|16... gi\|165926755, gi... - gi\|165926755\|ref\|ZP_02222587.1\| ribonuclease R [Yersinia pestis biovar Orientalis str. F1991016], gi... gi\|167400711, gi... - gi\|167400711\|ref\|ZP_02306220.1\| ribonuclease R [Yersinia pestis biovar Antiqua str. UG05-0454], gi\|1... gi\|166204825, gi... - gi\|166214030\|ref\|ZP_02240065.1\| ribonuclease R [Yersinia pestis biovar Antiqua str. B42003004], gi\|1... gi\|167423328, gi... - gi\|167423328\|ref\|ZP_02315081.1\| ribonuclease R [Yersinia pestis biovar Mediaevalis str. K1973002], g... gi\|167419145, gi... - gi\|167419145\|ref\|ZP_02310898.1\| ribonuclease R [Yersinia pestis biovar Orientalis str. MG05-1020], g... gi\|25298864 - pir\|\|AD0047 ribonuclease R (EC 3.1.-.-) [imported] - Yersinia pestis (strain CO92) gi\|45440390, gi\|... - gi\|45440390\|ref\|NP_991929.1\| exoribonuclease R [Yersinia pestis biovar Microtus str. 91001], gi\|4543... gi\|21957350, gi\|... - gi\|22124551\|ref\|NP_667974.1\| exoribonuclease R [Yersinia pestis KIM], gi\|21957350\|gb\|AAM84225.1\|AE01... gi\|115346194, gi... - gi\|218927583\|ref\|YP_002345458.1\| exoribonuclease R [Yersinia pestis CO92], gi\|16120715\|ref\|NP_404028... gi\|51588066, gi\|... - gi\|51594784\|ref\|YP_068975.1\| exoribonuclease R [Yersinia pseudotuberculosis IP 32953], gi\|51588066\|e... gi\|153947076, gi... - gi\|77631431\|ref\|ZP_00794017.1\| COG0557: Exoribonuclease R [Yersinia pseudotuberculosis IP 31758], gi... gi\|229836640, gi... - gi\|229836640\|ref\|ZP_04456806.1\| exoribonuclease R, RNase R [Yersinia pestis Pestoides A], gi\|2297063... gi\|229840252, gi... - gi\|229840252\|ref\|ZP_04460411.1\| exoribonuclease R, RNase R [Yersinia pestis biovar Orientalis str. P... gi\|229690640, gi... - gi\|229842330\|ref\|ZP_04462485.1\| exoribonuclease R, RNase R [Yersinia pestis biovar Orientalis str. I...	0.0	[354..940]	[105..678]

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Predicted Domain #1

Region A:
Residues: [1-434]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVVRRKVHVL LIARSFHSYT PCFRVTTRGK RQRSKSKQQA KVELDHTREL DNDQATETVV  60
   61 DRSVGPEKDI ESINKDFLQR TKGLEPDIEL KQLPQIKQEF NQRYKDRYVK PSEDWYVNSW 120
  121 RSLTKPKIPL YKLINSDFQL ITKLKAPNPM EFQPVQLMES PLNVGDFVLL KMRPNELAMC 180
  181 VSLPSSTMDP RYTFVTIDGT MCFATKNRVL LRIPHKLPAG IHSLIQPESH HKHLPIGTVK 240
  241 NFSNQTNILP IVARQLITSR YPAQISKLAW KDLPITTKKL QLLHRSLQNY MGPWQIPFFT 300
  301 LVGLVQKLDL NKALDDKNGI NYLTSLVNNY HTVNDIPINS PTFVSTYWAI MQQQESNLWG 360
  361 EIHLNTALLS PISVTIIPLK SQHLYYAQVI EKLEANSYRE VNKFVKLVNE RKYRDISALY 420
  421 PSVIQLLKDF AAGN

[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 #2

Region A:
Residues: [435-852]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FHNNGIIVAL ISKIFRKIER YKDCDITRDI CQDLINEITP NSIPNPLLLN MDLALPASSK  60
   61 LVKWQQKLYD LTNIEELQWK KSGTDDDRYD FGDLRVFCID SETAHEIDDG VSVKNYGRDG 120
  121 LYTLYIHIAD PTSMFPESTN VDIEGISTDI LNVALKRSFT TYLPDTVVPM LPQSICHLSD 180
  181 LGKQGQRTKT ISFSVDVKIT SKCSGKSIEI MYDSFKIRKG IVSNFPKATY EDVDRILGTP 240
  241 NSEASPVKKD LESLSMISKL LREQRIKNSN AVIFGEGFNK GLVMLNADSE GELTEVTFSD 300
  301 QEETLSTILV SEMMILANTL TGRYFAENKI GGVFRCYKQL PLGEVAQQQY DSMITSTKKG 360
  361 IFPKLKDIVK LSSLLNSSFY TGRPFRHEMI GAKQYLTVTS PLRRFPDLIN HLQIHRHL

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	115.236572
Match:	PF00773
Description:	RNB-like protein

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [853-969]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QKKPLCFNQT QIDSLIWPIQ SRADILKRAS RNSSTYWTLN YLKKLTKLEP ERTFDVMVTS  60
   61 VPQNGFTGCV FPDLSFARGT LKLHPSSMHY PMIGDIVKNC KISKIDCLEG MLELEKL

[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 functions:

Term	Confidence	Notes
ribonuclease activity	3.55580959453362	bayes_pls_golite062009
nucleic acid binding	2.8041095803798	bayes_pls_golite062009
DNA binding	2.12131488750007	bayes_pls_golite062009
binding	1.81248034004657	bayes_pls_golite062009
exoribonuclease activity	1.69948951519417	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	1.66992550564008	bayes_pls_golite062009
3'-5'-exoribonuclease activity	1.15063310147711	bayes_pls_golite062009
structure-specific DNA binding	1.10289736160471	bayes_pls_golite062009
single-stranded DNA binding	0.96886436248958	bayes_pls_golite062009
structural constituent of ribosome	0.71554089842467	bayes_pls_golite062009
structural molecule activity	0.4798318776164	bayes_pls_golite062009
transcription regulator activity	0.398606646713208	bayes_pls_golite062009
hydrolase activity	0.357828165699872	bayes_pls_golite062009
nuclease activity	0.192509675054684	bayes_pls_golite062009

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: