YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229836640, gi...
Organism:	Yersinia pestis Pestoides A
Length:	844 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 gi|229836640, gi....

Description	E-value	Query Range	Subject Range
gi\|81243587, gi\|... - gi\|82779439\|ref\|YP_405788.1\| putative enzyme [Shigella dysenteriae Sd197], gi\|81243587\|gb\|ABB64297.1...	0.0	[1..768]	[15..781]
gi\|24054862, gi\|... - gi\|24115534\|ref\|NP_710044.1\| putative enzyme [Shigella flexneri 2a str. 301], gi\|24054862\|gb\|AAN4575... gi\|30065551, gi\|... - gi\|30065551\|ref\|NP_839722.1\| putative enzyme [Shigella flexneri 2a str. 2457T], gi\|30043815\|gb\|AAP19...	0.0	[1..740]	[15..753]
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	[1..740]	[1..739]
gi\|49176467, gi\|... - gi\|49176467\|ref\|NP_418600.3\| RNase R [Escherichia coli K12], gb\|AAC77136.1\| ribonuclease R; RNase R ... gi\|1361201, gi\|5... - gi\|537020\|gb\|AAA97075.1\| vacB [Escherichia coli], pir\|\|S56404 virulence-associated protein vacB homo... gi\|537020\|gb\|AAA... - vacB [Escherichia coli]	0.0	[1..768]	[15..785]
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	[1..768]	[1..771]
gi\|193066029, gi... - gi\|75255906\|ref\|ZP_00727638.1\| COG0557: Exoribonuclease R [Escherichia coli E22], gi\|193066029\|ref\|Z... gi\|75212272, gi\|... - gi\|75212272\|ref\|ZP_00712312.1\| COG0557: Exoribonuclease R [Escherichia coli B171], gi\|194426579\|ref\|...	0.0	[1..768]	[1..771]
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	[1..768]	[15..785]
gi\|217325473, gi... - gi\|217325473\|ref\|ZP_03441557.1\| ribonuclease R [Escherichia coli O157:H7 str. TW14588], gi\|217321694... gi\|209398640, gi... - gi\|209398640\|ref\|YP_002273721.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4115], gi\|209160040... gi\|208738865, gi... - gi\|208818742\|ref\|ZP_03259062.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4042], gi\|208738865\|... gi\|208814409, gi... - gi\|208814409\|ref\|ZP_03255738.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4045], gi\|208735686\|... gi\|254796198, gi... - gi\|254796198\|ref\|YP_003081035.1\| exoribonuclease R, RNase R [Escherichia coli O157:H7 str. TW14359],... gi\|208806677, gi... - gi\|208806677\|ref\|ZP_03249014.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4206], gi\|208726478\|... gi\|195935969 - gi\|195935969\|ref\|ZP_03081351.1\| exoribonuclease R [Escherichia coli O157:H7 str. EC4024] gi\|38704239 - gi\|38704239\|ref\|NP_313182.2\| hypothetical protein ECs5155 [Escherichia coli O157:H7] gi\|38704239 - gi\|38704239\|ref\|NP_313182.2\| exoribonuclease R [Escherichia coli O157:H7 str. Sakai] gi\|168801833, gi... - gi\|189376071\|gb\|EDU94487.1\| ribonuclease R [Escherichia coli O157:H7 str. EC508], gi\|168801833\|ref\|Z... gi\|189375137, gi... - gi\|189375137\|gb\|EDU93553.1\| ribonuclease R [Escherichia coli O157:H7 str. EC869], gi\|168784815\|ref\|Z... gi\|168780610, gi... - gi\|189001856\|gb\|EDU70842.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4076], gi\|168780610\|ref\|... gi\|187770293, gi... - gi\|187770293\|gb\|EDU34137.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4196], gi\|168774109\|ref\|... gi\|168766457, gi... - gi\|189364335\|gb\|EDU82754.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4486], gi\|168766457\|ref\|... gi\|168760420, gi... - gi\|189368979\|gb\|EDU87395.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4501], gi\|168760420\|ref\|... gi\|189357916, gi... - gi\|189357916\|gb\|EDU76335.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4401], gi\|168754749\|ref\|... gi\|168751470, gi... - gi\|188014490\|gb\|EDU52612.1\| ribonuclease R [Escherichia coli O157:H7 str. EC4113], gi\|168751470\|ref\|... gi\|161367456 - gi\|161367456\|ref\|NP_290809.2\| exoribonuclease R [Escherichia coli O157:H7 EDL933]	0.0	[1..768]	[1..771]
gi\|75188890, gi\|... - gi\|75188890\|ref\|ZP_00702157.1\| COG0557: Exoribonuclease R [Escherichia coli E24377A], gi\|157156656\|r... gi\|110808097, gi... - gi\|110808097\|ref\|YP_691617.1\| exoribonuclease R [Shigella flexneri 5 str. 8401], gi\|110617645\|gb\|ABF... gi\|170021811, gi... - gi\|170021811\|ref\|YP_001726765.1\| exoribonuclease R [Escherichia coli ATCC 8739], gi\|169756739\|gb\|ACA... gi\|218363500, gi... - gi\|218556731\|ref\|YP_002389645.1\| exoribonuclease R [Escherichia coli IAI1], gi\|218363500\|emb\|CAR0115... gi\|218354660, gi... - gi\|218697928\|ref\|YP_002405595.1\| exoribonuclease R [Escherichia coli 55989], gi\|218354660\|emb\|CAV016... gi\|170681596, gi... - gi\|170681596\|ref\|YP_001746574.1\| ribonuclease R [Escherichia coli SMS-3-5], gi\|170519314\|gb\|ACB17492... gi\|194417183, gi... - gi\|194434598\|ref\|ZP_03066855.1\| ribonuclease R [Shigella dysenteriae 1012], gi\|194417183\|gb\|EDX33295... gi\|75515418, gi\|... - gi\|75515418\|ref\|ZP_00737575.1\| COG0557: Exoribonuclease R [Escherichia coli 53638], gi\|188492518\|ref... gi\|124528238, gi... - gi\|124528238\|ref\|ZP_01699562.1\| VacB and RNase II family 3'-5' exoribonucleases [Escherichia coli B]... gi\|192955794, gi... - gi\|75234272\|ref\|ZP_00718660.1\| COG0557: Exoribonuclease R [Escherichia coli E110019], gi\|193070848\|r... gi\|190904342, gi... - gi\|75231228\|ref\|ZP_00717635.1\| COG0557: Exoribonuclease R [Escherichia coli B7A], gi\|191165647\|ref\|Z... gi\|75198025, gi\|... - gi\|75198025\|ref\|ZP_00708095.1\| COG0557: Exoribonuclease R [Escherichia coli HS], gi\|157163643\|ref\|YP...	0.0	[1..768]	[1..771]
tr\|I7B0F4\|I7B0F4... - Ribonuclease R OS=Pseudomonas putida (strain DOT-T1E) GN=vacB PE=3 SV=1 gi\|82740154, gi\|... - gi\|82740154\|ref\|ZP_00902909.1\| 3'-5' exoribonuclease, VacB and RNase II:Ribonuclease R [Pseudomonas ... tr\|E4R7M6\|E4R7M6... - Ribonuclease R OS=Pseudomonas putida (strain BIRD-1) GN=rnr PE=3 SV=1	0.0	[2..827]	[6..857]

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Predicted Domain #1

Region A:
Residues: [1-735]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSQDPFLERE AEKYESPIPS REFILAHLAK RETPASREEL ANELNLTGEE PLEALRRRLR  60
   61 AMERDGQLVF TRRQCYALPE RLDLLRGTVI GHRDGYGFLR VEGSKDDLYL SAEQMKMAIH 120
  121 GDVVLAQVVG ADRKGRREAR IVRVLVPKTS QIVGRYFTDA GTGFVVPDDS RLSFDILIPA 180
  181 EATCGARMGF VVVVELTQRP TRRTKAVGKI VEVLGENMGT SMAVDIALRT HEIPHTWPPQ 240
  241 VEKQVADLKE QVPEEAKKGR VDLRDLPLVT IDGEDARDFD DAVYCEKKRG GGWRLWVAIA 300
  301 DVSYYVRPQT ALDDEARSRG NSVYFPSQVI PMLPEVLSNG LCSLNPQVDR LCMVCEMTIS 360
  361 SQGKLSSYKF YEAVMSSHAR LTYTKVWRII DGEESLREQY KPLVPHLEEL HAMYKVLDQA 420
  421 RAERGGIAFE TEEAKFIFNA ERRIERIEPT VRNDAHKLIE ECMILANIAA ARFVEKHEEP 480
  481 ALFRVHDRPS DDHIVALRSV LNELGLTLGG GLKPQPKDYS VLMDEISDRP DHEMLQTMLL 540
  541 RSMKQAVYDP ENRGHFGLAL ASYGHFTSPI RRYPDLAMHR AIKYQLAKEH GNLKDRWTPT 600
  601 GGWHSDFEDM LQLGQHCSMT ERRADEATRD VADWLKCDFM LDQVGNVFTG IIASVTGFGF 660
  661 FVRLDDLFID GLVHVSSLDN DYYRYDNIGQ RLIGESSGVV YRLGDTVEIR VDAVHMDERK 720
  721 IDFALVSSTR KPRGE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	138.0
Match:	2id0A
Description:	No description for 2id0A was found.

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	2.50222432647158	bayes_pls_golite062009
binding	2.45645422079711	bayes_pls_golite062009
ribonuclease activity	2.29464134578835	bayes_pls_golite062009
DNA binding	2.01509187496805	bayes_pls_golite062009
RNA binding	0.764074810825563	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	0.645338044440112	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	0.645324285187609	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	0.645324285187609	bayes_pls_golite062009
exoribonuclease activity	0.625278911312822	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.593594938681299	bayes_pls_golite062009
transcription regulator activity	0.579049615800331	bayes_pls_golite062009
hydrolase activity	0.184672913742179	bayes_pls_golite062009
structure-specific DNA binding	0.00505175337890207	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [736-844]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKTARDKAKN NGQRTLRSNS AGRGSSSGSS RRDGAPTAGG QKRPRRAKKP VNFEPDSAFR  60
   61 PDAAAAKPDD KALAEKKAKA KAKRASAKTK KIAAATKAKR AKKKTTSDQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.522879
Match:	1yz6A
Description:	Crystal structure of intact alpha subunit of aIF2 from Pyrococcus abyssi
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: