YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229841012, gi...
Organism:	Yersinia pestis biovar Orientalis str. PEXU2
Length:	154 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|229841012, gi....

Description	E-value	Query Range	Subject Range
gi\|26246158, gi\|... - gi\|26246158\|ref\|NP_752197.1\| ribonuclease H [Escherichia coli CFT073], gi\|26106555\|gb\|AAN78741.1\|AE0...	8.0E-49	[1..154]	[38..191]
gi\|24111645, gi\|... - gi\|24111645\|ref\|NP_706155.1\| ribonuclease H [Shigella flexneri 2a str. 301], gi\|24050418\|gb\|AAN41862...	2.0E-48	[1..154]	[38..191]
gi\|91070856, gi\|... - gi\|91209282\|ref\|YP_539268.1\| ribonuclease H [Escherichia coli UTI89], gi\|91070856\|gb\|ABE05737.1\| RNa... gi\|117622496, gi... - gi\|117622496\|ref\|YP_851409.1\| ribonuclease H [Escherichia coli APEC O1], gi\|115511620\|gb\|ABI99694.1\|... gi\|226899001, gi... - gi\|237707791\|ref\|ZP_04538272.1\| ribonuclease H [Escherichia sp. 3_2_53FAA], gi\|226899001\|gb\|EEH85260... gi\|194419057, gi... - gi\|194432795\|ref\|ZP_03065080.1\| ribonuclease H [Shigella dysenteriae 1012], gi\|194419057\|gb\|EDX35141...	2.0E-48	[1..154]	[38..191]
gi\|110613810, gi... - gi\|110804262\|ref\|YP_687781.1\| ribonuclease H [Shigella flexneri 5 str. 8401], gi\|110613810\|gb\|ABF024...	3.0E-48	[1..154]	[38..191]
gi\|238721803, gi... - gi\|77973125\|ref\|ZP_00828677.1\| COG0328: Ribonuclease HI [Yersinia frederiksenii ATCC 33641], gi\|2387...	5.0E-48	[1..154]	[6..159]
gi\|229341106, gi... - gi\|229522181\|ref\|ZP_04411598.1\| ribonuclease HI [Vibrio cholerae TM 11079-80], gi\|229341106\|gb\|EEO06... tr\|D7HE19\|D7HE19... - Ribonuclease H OS=Vibrio cholerae GN=rnhA PE=3 SV=1, Ribonuclease H OS=Vibrio cholerae MZO-3 GN=rnhA... gi\|229513877, gi... - gi\|229513877\|ref\|ZP_04403339.1\| ribonuclease HI [Vibrio cholerae TMA 21], gi\|229349058\|gb\|EEO14015.1... gi\|229528762, gi... - gi\|229528762\|ref\|ZP_04418152.1\| ribonuclease HI [Vibrio cholerae 12129(1)], gi\|229332536\|gb\|EEN98022... gi\|229524237, gi... - gi\|229524237\|ref\|ZP_04413642.1\| ribonuclease HI [Vibrio cholerae bv. albensis VL426], gi\|229337818\|g... gi\|183179466, gi... - gi\|183179466\|ref\|ZP_02957677.1\| ribonuclease HI [Vibrio cholerae MZO-3], gi\|183012877\|gb\|EDT88177.1\|... gi\|125621681, gi... - gi\|75820873\|ref\|ZP_00750911.1\| COG0328: Ribonuclease HI [Vibrio cholerae V51], gi\|254225775\|ref\|ZP_0... gi\|254286457, gi... - gi\|254286457\|ref\|ZP_04961414.1\| ribonuclease HI [Vibrio cholerae AM-19226], gi\|197751981\|ref\|YP_0021... gi\|116218205, gi... - gi\|75824347\|ref\|ZP_00753804.1\| COG0328: Ribonuclease HI [Vibrio cholerae RC385], gi\|116218205\|ref\|ZP... gi\|153829943, gi... - gi\|153829943\|ref\|ZP_01982610.1\| ribonuclease HI [Vibrio cholerae 623-39], gi\|148874578\|gb\|EDL72713.1... gi\|153825359, gi... - gi\|153825359\|ref\|ZP_01978026.1\| ribonuclease HI [Vibrio cholerae MZO-2], gi\|149741043\|gb\|EDM55112.1\|...	6.0E-48	[1..154]	[1..154]
gi\|157833638, gi... - gi\|494540\|pdb\|1RBR\| Chain , Ribonuclease H (E.C.3.1.26.4) Mutant With His 62 Replaced By Pro (H62p...	7.0E-48	[1..154]	[1..154]
gi\|116190167, gi... - gi\|75831266\|ref\|ZP_00760531.1\| COG0328: Ribonuclease HI [Vibrio cholerae MO10], gi\|254849365\|ref\|ZP_... RNH_VIBC3 - Ribonuclease H OS=Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) GN=rn... gi\|121726567, gi... - gi\|75817017\|ref\|ZP_00747473.1\| COG0328: Ribonuclease HI [Vibrio cholerae V52], gi\|121726567\|ref\|ZP_0... RNH_VIBCM - Ribonuclease H OS=Vibrio cholerae serotype O1 (strain M66-2) GN=rnhA PE=3 SV=1 gi\|229507691, gi... - gi\|229507691\|ref\|ZP_04397196.1\| ribonuclease HI [Vibrio cholerae BX 330286], gi\|229355196\|gb\|EEO2011... gi\|229519249, gi... - gi\|229519249\|ref\|ZP_04408692.1\| ribonuclease HI [Vibrio cholerae RC9], gi\|229343938\|gb\|EEO08913.1\| r... gi\|229607195, gi... - gi\|229607195\|ref\|YP_002877843.1\| ribonuclease HI [Vibrio cholerae MJ-1236], gi\|229369850\|gb\|ACQ60273... gi\|121549502, gi... - gi\|121586236\|ref\|ZP_01676026.1\| ribonuclease HI [Vibrio cholerae 2740-80], gi\|121549502\|gb\|EAX59528.... gi\|153213821, gi... - gi\|153213821\|ref\|ZP_01949029.1\| ribonuclease HI [Vibrio cholerae 1587], gi\|124115745\|gb\|EAY34565.1\| ... gi\|153221241, gi... - gi\|153221241\|ref\|ZP_01952256.1\| ribonuclease HI [Vibrio cholerae MAK 757], gi\|124119770\|gb\|EAY38513.... gi\|153817118, gi... - gi\|153817118\|ref\|ZP_01969785.1\| ribonuclease HI [Vibrio cholerae NCTC 8457], gi\|126512386\|gb\|EAZ7498... gi\|126521594, gi... - gi\|229512114\|ref\|ZP_04401593.1\| ribonuclease HI [Vibrio cholerae B33], gi\|229352079\|gb\|EEO17020.1\| r... RNH_VIBCH - Ribonuclease HI OS=Vibrio cholerae GN=rnhA PE=3 SV=1 RNH_VIBCH - Ribonuclease HI OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=rnhA PE=...	7.0E-48	[1..154]	[1..154]
RNH_ECO8A - Ribonuclease H OS=Escherichia coli O8 (strain IAI1) GN=rnhA PE=3 SV=1 RNH_ECO45 - Ribonuclease H OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=rnhA PE=3 SV=1 RNH_ECO81 - Ribonuclease H OS=Escherichia coli O81 (strain ED1a) GN=rnhA PE=3 SV=1 RNH_ECO7I - Ribonuclease H OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=rnhA PE=3 SV=1 RNH_ECOLU - Ribonuclease H OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=rnhA PE=3 SV=1 gi\|195938586 - gi\|195938586\|ref\|ZP_03083968.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4024] gi\|208808292, gi... - gi\|208808292\|ref\|ZP_03250629.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4206], gi\|208728093\|... gi\|208733274, gi... - gi\|208811997\|ref\|ZP_03253326.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4045], gi\|208733274\|... gi\|208820698, gi... - gi\|208820698\|ref\|ZP_03261018.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4042], gi\|208740821\|... RNH_ECO5E - Ribonuclease H OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=rnhA PE=3 SV=1 RNH_ECOSE - Ribonuclease H OS=Escherichia coli (strain SE11) GN=rnhA PE=3 SV=1 gi\|217324249, gi... - gi\|217324249\|ref\|ZP_03440333.1\| ribonuclease H [Escherichia coli O157:H7 str. TW14588], gi\|217320470... RNH_ESCF3 - Ribonuclease H OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73) GN=rnhA PE=3 ... gi\|124500997, gi... - gi\|124527833\|ref\|ZP_01699222.1\| ribonuclease H [Escherichia coli B], gi\|124500997\|gb\|EAY48464.1\| rib... RNH_SHIDS - Ribonuclease H OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rnhA PE=3 SV=1 RNH_SHIBS - Ribonuclease H OS=Shigella boydii serotype 4 (strain Sb227) GN=rnhA PE=3 SV=1 RNH_SHIB3 - Ribonuclease H OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=rnhA PE=3 SV=1 RNH_ECO24 - Ribonuclease H OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=rnhA PE=3 SV=1 gi\|83570286 - gi\|83570286\|ref\|ZP_00921732.1\| COG0328: Ribonuclease HI [Shigella dysenteriae 1012] gi\|194438212, gi... - gi\|83586294\|ref\|ZP_00924929.1\| COG0328: Ribonuclease HI [Escherichia coli 101-1], gi\|194438212\|ref\|Z... gi\|75513656, gi\|... - gi\|75513656\|ref\|ZP_00736047.1\| COG0328: Ribonuclease HI [Escherichia coli 53638], gi\|188495937\|ref\|Z... RNH_SHISS - Ribonuclease H OS=Shigella sonnei (strain Ss046) GN=rnhA PE=3 SV=1 gi\|190902905, gi... - gi\|75229807\|ref\|ZP_00716334.1\| COG0328: Ribonuclease HI [Escherichia coli B7A], gi\|191167012\|ref\|ZP_... gi\|75238912, gi\|... - gi\|75238912\|ref\|ZP_00722894.1\| COG0328: Ribonuclease HI [Escherichia coli E110019], gi\|193067575\|ref... RNH_ECOLC - Ribonuclease H OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=rnhA PE=3 SV=1 gi\|168763422, gi... - gi\|189366386\|gb\|EDU84802.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4501], gi\|168763422\|ref\|... gi\|168769977, gi... - gi\|189361084\|gb\|EDU79503.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4486], gi\|168769977\|ref\|... gi\|168776182, gi... - gi\|187768426\|gb\|EDU32270.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4196], gi\|168776182\|ref\|... gi\|168782939, gi... - gi\|188999616\|gb\|EDU68602.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4076], gi\|168782939\|ref\|... gi\|168789657, gi... - gi\|189370760\|gb\|EDU89176.1\| ribonuclease H [Escherichia coli O157:H7 str. EC869], gi\|168789657\|ref\|Z... gi\|189377335, gi... - gi\|189377335\|gb\|EDU95751.1\| ribonuclease H [Escherichia coli O157:H7 str. EC508], gi\|168800384\|ref\|Z... RNH_ECODH - Ribonuclease H OS=Escherichia coli (strain K12 / DH10B) GN=rnhA PE=3 SV=1 RNH_ECOSM - Ribonuclease H OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=rnhA PE=3 SV=1 gi\|161485946 - gi\|161485946\|ref\|NP_706155.2\| ribonuclease H [Shigella flexneri 2a str. 301] gi\|188015545, gi... - gi\|188015545\|gb\|EDU53667.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4113], gi\|168750162\|ref\|... gi\|168757207, gi... - gi\|189355700\|gb\|EDU74119.1\| ribonuclease H [Escherichia coli O157:H7 str. EC4401], gi\|168757207\|ref\|... RNH_SHIFL - Ribonuclease HI OS=Shigella flexneri GN=rnhA PE=3 SV=1 gi\|4902951, gi\|8... - gi\|89107089\|ref\|AP_000869.1\| ribonuclease HI, degrades RNA of DNA-RNA hybrids [Escherichia coli str.... gi\|30061766, gi\|... - gi\|30061766\|ref\|NP_835937.1\| ribonuclease H [Shigella flexneri 2a str. 2457T], gi\|30040008\|gb\|AAP157... gi\|15829464, gi\|... - gi\|15829464\|ref\|NP_308237.1\| ribonuclease H [Escherichia coli O157:H7 str. Sakai], gi\|13359666\|dbj\|B... EG10860 - ribonuclease HI, degrades RNA of DNA-RNA hybrids / RNase HI; participates in DNA replication RNH_ECO57 - Ribonuclease HI OS=Escherichia coli O157:H7 GN=rnhA PE=3 SV=1 EG10860 - ribonuclease HI, degrades RNA of DNA-RNA hybrids / RNase HI; participates in DNA replication gi\|15799890, gi\|... - gi\|15799890\|ref\|NP_285902.1\| ribonuclease H [Escherichia coli O157:H7 EDL933], gi\|12512942\|gb\|AAG545... RNH_ECOLI - Ribonuclease HI (EC 3.1.26.4) (RNase HI) (Ribonuclease H) (RNase H) - Escherichia coli RNH_ECOL6 - Ribonuclease HI OS=Escherichia coli O6 GN=rnhA PE=3 SV=1 gi\|254791341, gi... - gi\|254791341\|ref\|YP_003076178.1\| ribonuclease HI, degrades RNA of DNA-RNA hybrids [Escherichia coli ... gi\|254160328, gi... - gi\|254160328\|ref\|YP_003043436.1\| ribonuclease H [Escherichia coli B str. REL606], gi\|253972229\|gb\|AC... gi\|253325808, gi... - gi\|254287131\|ref\|YP_003052879.1\| ribonuclease H [Escherichia coli BL21(DE3)], gi\|253976438\|gb\|ACT421... gi\|242376044, gi... - gi\|251783771\|ref\|YP_002998075.1\| hypothetical protein B21_00212 [Escherichia coli BL21], gi\|24237604... RNH_ECOBW - Ribonuclease H OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=rnhA PE=3 SV=1 RNH_ECOL6 - Ribonuclease HI OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=rnhA PE=3 SV=1	1.0E-47	[1..154]	[1..154]

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Predicted Domain #1

Region A:
Residues: [1-154]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTKQVEIFTD GSCLGNPGPG GYGAILRYKQ HEKTFSAGYY LTTNNRMELM AAIVALEALT  60
   61 SPCEVTLSTD SQYVRQGITQ WIHNWKKRGW KTADRKPVRN VDLWQRLDLA IQSHTIQWEW 120
  121 VKGHAGHPEN ERCDELARQG ANSPTLDDTG YNPD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.221849
Match:	1rbrA
Description:	STRUCTURAL STUDY OF MUTANTS OF ESCHERICHIA COLI RIBONUCLEASE HI WITH ENHANCED THERMOSTABILITY
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ribonuclease activity	3.91517707500372	bayes_pls_golite062009
endoribonuclease activity	3.00008907756136	bayes_pls_golite062009
ribonuclease H activity	2.37346218921366	bayes_pls_golite062009
hydrolase activity	2.30893115816458	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.26022264830742	bayes_pls_golite062009
nuclease activity	1.81796593394339	bayes_pls_golite062009
endonuclease activity	1.79009816048707	bayes_pls_golite062009
catalytic activity	1.62277843225829	bayes_pls_golite062009
exoribonuclease activity	1.48827607538468	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	1.34153791988846	bayes_pls_golite062009
3'-5'-exoribonuclease activity	0.8085201347205	bayes_pls_golite062009
exonuclease activity	0.39213900591465	bayes_pls_golite062009
endoribonuclease activity, producing 5'-phosphomonoesters	0.13187450705887	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: