YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24375423, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	808 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|24375423, gi|....

Description	E-value	Query Range	Subject Range
gi\|82494752, gi\|... - gi\|82494752\|ref\|ZP_00880331.1\| 3'-5' exoribonuclease, VacB and RNase II:Ribonuclease R [Shewanella s...	840.0	[0..1]	[808..1]
gi\|113887634, gi... - gi\|78692299\|ref\|ZP_00856848.1\| 3'-5' exoribonuclease, VacB and RNase II:Ribonuclease R [Shewanella s...	839.0	[0..1]	[808..1]
gi\|117919149, gi... - gi\|78688342\|ref\|ZP_00853044.1\| 3'-5' exoribonuclease, VacB and RNase II:Ribonuclease R [Shewanella s...	829.0	[0..1]	[808..1]
gi\|229354854, gi... - gi\|229507349\|ref\|ZP_04396854.1\| ribonuclease R [Vibrio cholerae BX 330286], gi\|229354854\|gb\|EEO19775... gi\|227082716, gi... - gi\|227082716\|ref\|YP_002811267.1\| ribonuclease R [Vibrio cholerae M66-2], gi\|227010604\|gb\|ACP06816.1\|... gi\|229606855, gi... - gi\|229606855\|ref\|YP_002877503.1\| ribonuclease R [Vibrio cholerae MJ-1236], gi\|229369510\|gb\|ACQ59933.... gi\|229516852, gi... - gi\|229516852\|ref\|ZP_04406298.1\| ribonuclease R [Vibrio cholerae RC9], gi\|229345915\|gb\|EEO10887.1\| ri... RNR_VIBCH - Ribonuclease R OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=rnr PE=3 ... gi\|153225383, gi... - gi\|153225383\|ref\|ZP_01954739.1\| ribonuclease R [Vibrio cholerae MAK 757], gi\|124117330\|gb\|EAY36073.1... gi\|153824007, gi... - gi\|229509728\|ref\|ZP_04399209.1\| ribonuclease R [Vibrio cholerae B33], gi\|229353202\|gb\|EEO18141.1\| ri... RNR_VIBCH - Ribonuclease R OS=Vibrio cholerae GN=rnr PE=3 SV=1	809.0	[0..4]	[808..8]
gi\|23467938, gi\|... - gi\|23467938\|ref\|ZP_00123514.1\| COG0557: Exoribonuclease R [Haemophilus somnus 129PT], gi\|113460297\|r...	809.0	[0..1]	[795..17]
gi\|121728988, gi... - gi\|75814697\|ref\|ZP_00745255.1\| COG0557: Exoribonuclease R [Vibrio cholerae V52], gi\|121728988\|ref\|ZP... gi\|147675348, gi... - gi\|75827850\|ref\|ZP_00757285.1\| COG0557: Exoribonuclease R [Vibrio cholerae O395], gi\|227119038\|ref\|Y... gi\|229527471, gi... - gi\|229527471\|ref\|ZP_04416863.1\| ribonuclease R [Vibrio cholerae 12129(1)], gi\|229335103\|gb\|EEO00588.... gi\|153214904, gi... - gi\|153214904\|ref\|ZP_01949702.1\| ribonuclease R [Vibrio cholerae 1587], gi\|124115063\|gb\|EAY33883.1\| r... gi\|148873499, gi... - gi\|153831021\|ref\|ZP_01983688.1\| ribonuclease R [Vibrio cholerae 623-39], gi\|148873499\|gb\|EDL71634.1\|... gi\|153827410, gi... - gi\|153827410\|ref\|ZP_01980077.1\| ribonuclease R [Vibrio cholerae MZO-2], gi\|149738683\|gb\|EDM53025.1\| ... gi\|229341259, gi... - gi\|229521665\|ref\|ZP_04411083.1\| ribonuclease R [Vibrio cholerae TM 11079-80], gi\|229341259\|gb\|EEO062... gi\|229349399, gi... - gi\|229513522\|ref\|ZP_04402986.1\| ribonuclease R [Vibrio cholerae TMA 21], gi\|229349399\|gb\|EEO14355.1\|...	809.0	[0..4]	[808..8]
gi\|254851139, gi... - gi\|254851139\|ref\|ZP_05240489.1\| ribonuclease R [Vibrio cholerae MO10], gi\|254846844\|gb\|EET25258.1\| r... tr\|C6YKQ8\|C6YKQ8... - Ribonuclease R OS=Vibrio cholerae MO10 GN=rnr PE=3 SV=1	808.0	[0..4]	[808..8]
gi\|59712921, gi\|... - gi\|59712921\|ref\|YP_205697.1\| exoribonuclease R, RNase R [Vibrio fischeri ES114], gi\|59481022\|gb\|AAW8...	808.0	[0..1]	[762..5]
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]	807.0	[0..1]	[772..15]
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...	807.0	[0..1]	[772..1]

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Predicted Domain #1

Region A:
Residues: [1-726]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIKDPHFERE QDKYENPIPS REYIIEYLRS QKSPITRDSI AAALQIHDEE QLEALRRRLR  60
   61 AMERDGELVF TRGQSYGLPE KMDLISGTVL GHKEGYGFFK PDEGGDDLFI SNRDMLMYFH 120
  121 GDKVLAQKVG MDRKGRREAR IVRLIQPRSA AIVGRFHVDS GMAFVIADDK RITQEILIAS 180
  181 EDRNGARQGD VVVVELTRRP GRFVKAAGKV TEVLGKQMAP GMEIEIALRN YDLPHTWSAA 240
  241 IEKKLRRIPD EVTESDKVGR VDLRSLPLVT IDGEDARDFD DAVYAEVKPS GGWRLWVAIA 300
  301 DVSYYVRTDS ALDTEARARG NSVYFPSQVI PMLPEKISNG LCSLNPHVDR LCMVAEMTIS 360
  361 ARGKLSGYKF YPAVMHSHAR FTYTQVAAML EGGPIAPEHE ALFVHLQCLQ SLYLALDEQR 420
  421 AERGAIAFET IETQFIFNDQ RKIDKIVPRA RNQAHKIIEE CMILANVSAA KFVKKHKGEI 480
  481 LYRVHESPSE QKLANFKEFL AERGLSMGGG LEPTPADYQN VMLQIADRPD AELIQVMLLR 540
  541 SMRQAIYTPD NEGHFGLALE EYAHFTSPIR RYPDLVLHRV IRYLLAKEKG EANEKWTPDG 600
  601 GYHYQLDELD QLGEECSTTE RRADEATRDV SDWLKCEFMQ DHVGDTFEAV IASVTNFGLF 660
  661 VRLNDLFIDG LVHISSLGSD YYQFDPMRQR LIGEHTGQVY QVGDPVTVKV AAVNLDDRQI 720
  721 DLMMLG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	134.0
Match:	2ix0A
Description:	No description for 2ix0A was found.

Predicted functions:

Term	Confidence	Notes
ribonuclease activity	2.44085181318323	bayes_pls_golite062009
nucleic acid binding	2.26271782657431	bayes_pls_golite062009
binding	2.01819468874386	bayes_pls_golite062009
DNA binding	1.81052012500635	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	0.66506775853341	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	0.66506775853341	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	0.66324605171607	bayes_pls_golite062009
transcription regulator activity	0.537716356194117	bayes_pls_golite062009
RNA binding	0.32835157709956	bayes_pls_golite062009
hydrolase activity	0.24776517765284	bayes_pls_golite062009
exoribonuclease activity	0.18451322024956	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.131695664491341	bayes_pls_golite062009
structural constituent of ribosome	0.0989196136046104	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [727-808]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DSGKGGRRKA APSRDKPMTA RERVNREGAK MAKTAKSSGA KSKAGSGKAA SKSKSKAGTK  60
   61 PKKSVKDTAK KPKAAKRSTR KK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	34.09691
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: