YRC Public Data Repository - Protein Structure Prediction

Protein:	RIM1
Organism:	Saccharomyces cerevisiae
Length:	135 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 RIM1.

Description	E-value	Query Range	Subject Range
gi\|194684063, gi... - gi\|197286576\|ref\|YP_002152448.1\| single-strand binding protein [Proteus mirabilis HI4320], gi\|194684... SSB_PROMI - Single-stranded DNA-binding protein OS=Proteus mirabilis GN=ssb PE=1 SV=2	3.0E-38	[17..125]	[4..122]
SSB3_LISIN - Single-stranded DNA-binding protein 3 OS=Listeria innocua GN=ssb3 PE=3 SV=1 SSB3_LISIN - Single-stranded DNA-binding protein 3 OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=ssb3 PE=...	5.0E-37	[19..134]	[2..121]
SSB_SHEHA - Single-stranded DNA-binding protein OS=Shewanella hanedai GN=ssb PE=3 SV=1	5.0E-37	[17..119]	[4..113]
gi\|3851548 - gi\|3851548\|gb\|AAC72352.1\| single strand DNA-binding protein; SSB [Vibrio cholerae]	6.0E-37	[17..135]	[19..150]
gi\|116188064, gi... - gi\|75829062\|ref\|ZP_00758381.1\| COG0629: Single-stranded DNA-binding protein [Vibrio cholerae MO10], ... gi\|227012252, gi... - gi\|75828375\|ref\|ZP_00757810.1\| COG0629: Single-stranded DNA-binding protein [Vibrio cholerae O395], ... SSB_VIBCH - Single-stranded DNA-binding protein OS=Vibrio cholerae GN=ssb PE=3 SV=1 gi\|121630381, gi... - gi\|75816801\|ref\|ZP_00747261.1\| COG0629: Single-stranded DNA-binding protein [Vibrio cholerae V52], g... gi\|121548170, gi... - gi\|121587597\|ref\|ZP_01677362.1\| single-strand binding protein [Vibrio cholerae 2740-80], gi\|12154817... gi\|124118341, gi... - gi\|153223244\|ref\|ZP_01953741.1\| single-strand binding protein [Vibrio cholerae MAK 757], gi\|12411834... gi\|153818249, gi... - gi\|153818249\|ref\|ZP_01970916.1\| single-strand binding protein [Vibrio cholerae NCTC 8457], gi\|126511... gi\|126520207, gi... - gi\|153822251\|ref\|ZP_01974918.1\| single-strand binding protein [Vibrio cholerae B33], gi\|126520207\|gb... SSB_VIBCH - Single-stranded DNA-binding protein OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba... gi\|227008496, gi... - gi\|227080608\|ref\|YP_002809159.1\| single-strand binding protein [Vibrio cholerae M66-2], gi\|227008496...	6.0E-37	[17..135]	[4..135]
gi\|213646761 - gi\|213646761\|ref\|ZP_03376814.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enteri... SSB2_SALTI - Single-stranded DNA-binding protein 2 OS=Salmonella typhi GN=ssb2 PE=3 SV=1 gi\|213609821 - gi\|213609821\|ref\|ZP_03369647.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enteri... gi\|213428139 - gi\|213428139\|ref\|ZP_03360889.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enteri... gi\|213161420 - gi\|213161420\|ref\|ZP_03347130.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enteri... gi\|32454454 - gi\|32454454\|gb\|AAP83026.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enterica se... SSB2_SALTI - Single-stranded DNA-binding protein 2 OS=Salmonella typhi GN=ssb2 PE=3 SV=1 gi\|224586099, gi... - gi\|224586099\|ref\|YP_002639898.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enter... gi\|29140135, gi\|... - gi\|29144497\|ref\|NP_807839.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enterica ... gi\|16763010 - gi\|16763010\|ref\|NP_458627.1\| single-strand DNA-binding protein [Salmonella enterica subsp. enterica ...	8.0E-37	[17..122]	[4..119]
SSB_NEIMA - Single-stranded DNA-binding protein OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z249... SSB_NEIMB - Single-stranded DNA-binding protein OS=Neisseria meningitidis serogroup B (strain MC58) GN=ssb PE=3 ... SSB_NEIMA - Single-stranded DNA-binding protein OS=Neisseria meningitidis serogroup A GN=ssb PE=3 SV=1 SSB_NEIMB - Single-stranded DNA-binding protein OS=Neisseria meningitidis serogroup B GN=ssb PE=3 SV=1 gi\|254669859 - gi\|254669859\|emb\|CBA04297.1\| single-strand binding protein [Neisseria meningitidis alpha153] gi\|254805239, gi... - gi\|254805239\|ref\|YP_003083460.1\| single-strand binding protein [Neisseria meningitidis], gi\|25466878... gi\|120866852, gi... - gi\|121635146\|ref\|YP_975391.1\| single-stranded binding protein [Neisseria meningitidis FAM18], gi\|120... gi\|11275250 - pir\|\|A81080 single-strand binding protein NMB1460 [imported] - Neisseria meningitidis (strain MC58 s... gi\|254672122 - gi\|254672122\|emb\|CBA04860.1\| single-strand binding protein [Neisseria meningitidis serogroup W135]	1.0E-36	[17..132]	[1..128]
gi\|116052269, gi... - gi\|116052269\|ref\|YP_788887.1\| single-stranded DNA-binding protein [Pseudomonas aeruginosa UCBPP-PA14... gi\|218769662, gi... - gi\|218889439\|ref\|YP_002438303.1\| single-stranded DNA-binding protein [Pseudomonas aeruginosa LESB58]... gi\|126196282, gi... - gi\|254242904\|ref\|ZP_04936226.1\| single-stranded DNA-binding protein [Pseudomonas aeruginosa 2192], g... gi\|194548082, gi... - gi\|254237097\|ref\|ZP_04930420.1\| single-stranded DNA-binding protein [Pseudomonas aeruginosa C3719], ... gi\|152984573, gi... - gi\|152984573\|ref\|YP_001346254.1\| single-stranded DNA-binding protein [Pseudomonas aeruginosa PA7], g... SSB_PSEAE - Single-stranded DNA-binding protein OS=Pseudomonas aeruginosa GN=ssb PE=1 SV=3 SSB_PSEAE - Single-stranded DNA-binding protein OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 1...	1.0E-36	[15..126]	[1..122]
gi\|218697768, gi... - gi\|218697768\|ref\|YP_002405435.1\| single-stranded DNA-binding protein [Escherichia coli 55989], gi\|21... gi\|218372710, gi... - gi\|218702724\|ref\|YP_002410353.1\| single-stranded DNA-binding protein [Escherichia coli IAI39], gi\|21... gi\|218434778, gi... - gi\|218707681\|ref\|YP_002415200.1\| single-stranded DNA-binding protein [Escherichia coli UMN026], gi\|2... gi\|15834295, gi\|... - gi\|15834295\|ref\|NP_313068.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. Saka... gi\|110644406, gi... - gi\|110644406\|ref\|YP_672136.1\| single-stranded DNA-binding protein [Escherichia coli 536], gi\|1103459... gi\|110617472, gi... - gi\|110807924\|ref\|YP_691444.1\| single-strand DNA-binding protein [Shigella flexneri 5 str. 8401], gi\|... SSB_SHIFL - Single-stranded DNA-binding protein OS=Shigella flexneri GN=ssb PE=3 SV=2 gi\|168748095, gi... - gi\|188017416\|gb\|EDU55538.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC411... SSB_ECOLI - Single-stranded DNA-binding protein (SSB) (Helix-destabilizing protein) - Escherichia coli gi\|168755227, gi... - gi\|189357468\|gb\|EDU75887.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC440... SSB_ECOL6 - Single-stranded DNA-binding protein OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) G... gi\|168760906, gi... - gi\|189368538\|gb\|EDU86954.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC450... gi\|30042907, gi\|... - gi\|30064648\|ref\|NP_838819.1\| single-strand DNA-binding protein [Shigella flexneri 2a str. 2457T], gi... gi\|189364141, gi... - gi\|189364141\|gb\|EDU82560.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC448... SSB_ECO57 - Single-stranded DNA-binding protein OS=Escherichia coli O157:H7 GN=ssb PE=3 SV=2 gi\|168774415, gi... - gi\|187769924\|gb\|EDU33768.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC419... EG10976 - single-stranded DNA-binding protein / Single-stranded DNA-binding protein; alkali-inducible; homotet... gi\|168780470, gi... - gi\|189001691\|gb\|EDU70677.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC407... gi\|189374931, gi... - gi\|189374931\|gb\|EDU93347.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC869... gi\|189379074, gi... - gi\|189379074\|gb\|EDU97490.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. EC508... gi\|82546402, gi\|... - gi\|82546402\|ref\|YP_410349.1\| single-strand DNA-binding protein [Shigella boydii Sb227], gi\|81247813\|... gi\|85676811, gi\|... - gi\|89110780\|ref\|AP_004560.1\| Single-stranded DNA-binding protein [Escherichia coli str. K-12 substr.... gi\|73858030, gi\|... - gi\|74314553\|ref\|YP_312972.1\| single-strand DNA-binding protein [Shigella sonnei Ss046], gi\|73858030\|... SSB_ECOL6 - Single-stranded DNA-binding protein OS=Escherichia coli O6 GN=ssb PE=3 SV=2 gi\|56384074, gi\|... - gi\|56480523\|ref\|NP_709860.2\| single-strand DNA-binding protein [Shigella flexneri 2a str. 301], gi\|5... gi\|162138311 - gi\|162138311\|ref\|YP_543584.2\| single-strand DNA-binding protein [Escherichia coli UTI89] gi\|162317560 - gi\|162317560\|ref\|YP_859663.2\| single-strand DNA-binding protein [Escherichia coli APEC O1] gi\|75211987, gi\|... - gi\|75211987\|ref\|ZP_00712042.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli B171],... gi\|209397137, gi... - gi\|209397137\|ref\|YP_002273599.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. ... gi\|190901176, gi... - gi\|75227985\|ref\|ZP_00714676.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli B7A], ... gi\|209921544, gi... - gi\|209921544\|ref\|YP_002295628.1\| single-stranded DNA-binding protein [Escherichia coli SE11], gi\|209... gi\|157158944, gi... - gi\|75188783\|ref\|ZP_00702050.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli E24377... gi\|215489405, gi... - gi\|215489405\|ref\|YP_002331836.1\| single-stranded DNA-binding protein [Escherichia coli O127:H6 str. ... gi\|227836060, gi... - gi\|227886919\|ref\|ZP_04004724.1\| single-stranded DNA-binding protein [Escherichia coli 83972], gi\|227... gi\|157163528, gi... - gi\|75197918\|ref\|ZP_00707988.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli HS], g... gi\|217320876, gi... - gi\|217324655\|ref\|ZP_03440739.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. T... gi\|238903169, gi... - gi\|238903169\|ref\|YP_002928965.1\| single-stranded DNA-binding protein [Escherichia coli BW2952], gi\|2... gi\|75258977, gi\|... - gi\|75258977\|ref\|ZP_00730345.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli E22], ... gi\|218358922, gi... - gi\|218551380\|ref\|YP_002385172.1\| single-stranded DNA-binding protein [Escherichia fergusonii ATCC 35... gi\|242379587, gi... - gi\|251787314\|ref\|YP_003001618.1\| hypothetical protein B21_03891 [Escherichia coli BL21], gi\|24237958... gi\|75514818, gi\|... - gi\|75514818\|ref\|ZP_00737047.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli 53638]... gi\|218363386, gi... - gi\|218556617\|ref\|YP_002389531.1\| single-stranded DNA-binding protein [Escherichia coli IAI1], gi\|218... gi\|253980052, gi... - gi\|254290745\|ref\|YP_003056493.1\| single-strand DNA-binding protein [Escherichia coli BL21(DE3)], gi\|... gi\|192958856, gi... - gi\|75238595\|ref\|ZP_00722584.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli E11001... gi\|218561142, gi... - gi\|218561142\|ref\|YP_002394055.1\| single-stranded DNA-binding protein [Escherichia coli S88], gi\|2183... gi\|253975896, gi... - gi\|254163995\|ref\|YP_003047103.1\| single-strand DNA-binding protein [Escherichia coli B str. REL606],... gi\|75241099, gi\|... - gi\|75241099\|ref\|ZP_00724973.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli F11], ... gi\|218692349, gi... - gi\|218692349\|ref\|YP_002400561.1\| single-stranded DNA-binding protein [Escherichia coli ED1a], gi\|218... gi\|254796079, gi... - gi\|254796079\|ref\|YP_003080916.1\| Single-stranded DNA-binding protein [Escherichia coli O157:H7 str. ... gi\|170021942, gi... - gi\|170021942\|ref\|YP_001726896.1\| single-stranded DNA-binding protein [Escherichia coli ATCC 8739], g... gi\|169891350, gi... - gi\|170083515\|ref\|YP_001732835.1\| single-stranded DNA-binding protein [Escherichia coli str. K-12 sub... gi\|170520013, gi... - gi\|170682295\|ref\|YP_001746449.1\| single-stranded DNA-binding protein [Escherichia coli SMS-3-5], gi\|... gi\|194432319, gi... - gi\|194432319\|ref\|ZP_03064607.1\| single-stranded DNA-binding protein [Shigella dysenteriae 1012], gi\|... gi\|195935843 - gi\|195935843\|ref\|ZP_03081225.1\| single-strand DNA-binding protein [Escherichia coli O157:H7 str. EC4... gi\|83587182, gi\|... - gi\|83587182\|ref\|ZP_00925811.1\| COG0629: Single-stranded DNA-binding protein [Escherichia coli 101-1]... gi\|208726257, gi... - gi\|208806456\|ref\|ZP_03248793.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. E... gi\|208735285, gi... - gi\|208814008\|ref\|ZP_03255337.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. E... gi\|208738557, gi... - gi\|208818434\|ref\|ZP_03258754.1\| single-stranded DNA-binding protein [Escherichia coli O157:H7 str. E... EG10976 - single-stranded DNA-binding protein / Single-stranded DNA-binding protein; alkali-inducible; homotet... gi\|124527698, gi... - gi\|124527698\|ref\|ZP_01699133.1\| single-strand binding protein [Escherichia coli B], gi\|124501141\|gb\|...	1.0E-36	[17..122]	[4..119]
SSB_SERMA - Single-stranded DNA-binding protein OS=Serratia marcescens GN=ssb PE=1 SV=2	1.0E-36	[17..122]	[4..119]

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Predicted Domain #1

Region A:
Residues: [1-135]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFLRTQARFF HATTKKMDFS KMSIVGRIGS EFTEHTSANN NRYLKYSIAS QPRRDGQTNW  60
   61 YNITVFNEPQ INFLTEYVRK GALVYVEADA ANYVFERDDG SKGTTLSLVQ KDINLLKNGK 120
  121 KLEDAEGQEN AASSE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	33.154902
Match:	3ullA_
Description:	ssDNA-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	2.69275272183315	bayes_pls_golite062009
single-stranded DNA binding	2.3572495084765	bayes_pls_golite062009
structure-specific DNA binding	2.34831682853439	bayes_pls_golite062009
binding	2.25744085310968	bayes_pls_golite062009
DNA binding	1.97161900822354	bayes_pls_golite062009
structural constituent of ribosome	1.39029069959347	bayes_pls_golite062009
structural molecule activity	1.10843643894126	bayes_pls_golite062009
nucleotidyltransferase activity	0.377540062296145	bayes_pls_golite062009
protein binding	0.360033745054291	bayes_pls_golite062009
ribonuclease activity	0.35415853560434	bayes_pls_golite062009
translation regulator activity	0.31332179848255	bayes_pls_golite062009
translation factor activity, nucleic acid binding	0.263197317040851	bayes_pls_golite062009
nuclease activity	0.192509675054684	bayes_pls_golite062009
transcription regulator activity	0.157816897728538	bayes_pls_golite062009
DNA-directed RNA polymerase activity	0.1542034177713	bayes_pls_golite062009
RNA polymerase activity	0.1542034177713	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: