YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|1361201, gi\|5...
Organism:	Escherichia coli
Length:	827 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|1361201, gi|5....

Description	E-value	Query Range	Subject Range
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), ...	871.0	[0..1]	[809..1]
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...	871.0	[0..1]	[809..1]
gi\|73858141, gi\|... - gi\|74314664\|ref\|YP_313083.1\| putative enzyme [Shigella sonnei Ss046], gi\|73858141\|gb\|AAZ90848.1\| put...	869.0	[0..1]	[809..1]
gi\|82546580, gi\|... - gi\|82546580\|ref\|YP_410527.1\| putative enzyme [Shigella boydii Sb227], gi\|81247991\|gb\|ABB68699.1\| put...	868.0	[0..1]	[809..1]
gi\|117626525, gi... - gi\|117626525\|ref\|YP_859848.1\| exoribonuclease R [Escherichia coli APEC O1], gi\|115515649\|gb\|ABJ03724... gi\|237703846, gi... - gi\|237703846\|ref\|ZP_04534327.1\| exoribonuclease R [Escherichia sp. 3_2_53FAA], gi\|226901758\|gb\|EEH88... gi\|91213728, gi\|... - gi\|91213728\|ref\|YP_543714.1\| putative enzyme [Escherichia coli UTI89], gi\|91075302\|gb\|ABE10183.1\| pu...	868.0	[0..1]	[786..1]
gi\|75179450 - gi\|75179450\|ref\|ZP_00699454.1\| COG0557: Exoribonuclease R [Shigella boydii BS512]	867.0	[0..1]	[809..1]
gi\|81243587, gi\|... - gi\|82779439\|ref\|YP_405788.1\| putative enzyme [Shigella dysenteriae Sd197], gi\|81243587\|gb\|ABB64297.1...	866.0	[0..1]	[809..1]
gi\|227836351, gi... - gi\|227886778\|ref\|ZP_04004583.1\| exoribonuclease R [Escherichia coli 83972], gi\|227836351\|gb\|EEJ46817... gi\|26251071, gi\|... - gi\|26251071\|ref\|NP_757111.1\| Ribonuclease R [Escherichia coli CFT073], gi\|26111503\|gb\|AAN83685.1\|AE0...	866.0	[0..1]	[786..1]
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...	858.0	[0..15]	[809..1]
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]	858.0	[0..15]	[809..1]

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Predicted Domain #1

Region A:
Residues: [1-748]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTKIFIRDDN GGTEMSQDPF QEREAEKYAN PIPSREFILE HLTKREKPAS RDELAVELHI  60
   61 EGEEQLEGLR RRLRAMERDG QLVFTRRQCY ALPERLDLVK GTVIGHRDGY GFLRVEGRKD 120
  121 DLYLSSEQMK TCIHGDQVLA QPLGADRKGR REARIVRVLV PKTSQIVGRY FTEAGVGFVV 180
  181 PDDSRLSFDI LIPPDQIMGA RMGFVVVVEL TQRPTRRTKA VGKIVEVLGD NMGTGMAVDI 240
  241 ALRTHEIPYI WPQAVEQQVA GLKEEVPEEA KAGRVDLRDL PLVTIDGEDA RDFDDAVYCE 300
  301 KKRGGGWRLW VAIADVSYYV RPSTPLDREA RNRGTSVYFP SQVIPMLPEV LSNGLCSLNP 360
  361 QVDRLCMVCE MTVSSKGRLT GYKFYEAVMS SHARLTYTKV WHILQGDQDL REQYAPLVKH 420
  421 LEELHNLYKV LDKAREERGG ISFESEEAKF IFNAERRIER IEQTQRNDAH KLIEECMILA 480
  481 NISAARFVEK AKEPALFRIH DKPSTEAITS FRSVLAELGL ELPGGNKPEP RDYAELLESV 540
  541 ADRPDAEMLQ TMLLRSMKQA IYDPENRGHF GLALQSYAHF TSPIRRYPDL TLHRAIKYLL 600
  601 AKEQGHQGNT TETGGYHYSM EEMLQLGQHC SMAERRADEA TRDVADWLKC DFMLDQVGNV 660
  661 FKGVISSVTG FGFFVRLDDL FIDGLVHVSS LDNDYYRFDQ VGQRLMGESS GQTYRLGDRV 720
  721 EVRVEAVNMD ERKIDFSLIS SERAPRNV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	137.0
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: [749-827]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKTAREKAKK GDAGKKGGKR RQVGKKVNFE PDSAFRGEKK TKPKAAKKDA RKAKKPSAKT  60
   61 QKIAAATKAK RAAKKKVAE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	24.522879
Match:	2oceA
Description:	No description for 2oceA was found.

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: