YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229695888, gi...
Organism:	Yersinia pestis biovar Orientalis str. PEXU2
Length:	610 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|229695888, gi....

Description	E-value	Query Range	Subject Range
gi\|77956404, gi\|... - gi\|77956404\|ref\|ZP_00820506.1\| COG0514: Superfamily II DNA helicase [Yersinia bercovieri ATCC 43970]...	0.0	[1..610]	[1..610]
gi\|77960560 - gi\|77960560\|ref\|ZP_00824426.1\| COG0514: Superfamily II DNA helicase [Yersinia mollaretii ATCC 43969]	0.0	[14..610]	[1..597]
gi\|77973641, gi\|... - gi\|77973641\|ref\|ZP_00829187.1\| COG0514: Superfamily II DNA helicase [Yersinia frederiksenii ATCC 336...	0.0	[1..610]	[1..610]
gi\|238793565, gi... - gi\|77978530\|ref\|ZP_00833958.1\| COG0514: Superfamily II DNA helicase [Yersinia intermedia ATCC 29909]...	0.0	[1..610]	[1..610]
gi\|50123092, gi\|... - gi\|50123092\|ref\|YP_052259.1\| ATP-dependent DNA helicase RecQ [Pectobacterium atrosepticum SCRI1043],...	0.0	[1..610]	[1..608]
gi\|78195168, gi\|... - gi\|78223913\|ref\|YP_385660.1\| ATP-dependent DNA helicase RecQ [Geobacter metallireducens GS-15], gi\|7...	0.0	[14..603]	[7..599]
gi\|36787875, gi\|... - gi\|37528437\|ref\|NP_931782.1\| ATP-dependent DNA helicase RecQ [Photorhabdus luminescens subsp. laumon...	0.0	[1..607]	[1..606]
gi\|27360504, gi\|... - gi\|27364385\|ref\|NP_759913.1\| ATP-dependent DNA helicase RecQ [Vibrio vulnificus CMCP6], gi\|27360504\|...	0.0	[14..608]	[17..610]
gi\|37681371, gi\|... - gi\|37681371\|ref\|NP_935980.1\| ATP-dependent DNA helicase RecQ [Vibrio vulnificus YJ016], gi\|37200123\|...	0.0	[1..608]	[15..624]
gi\|110617034, gi... - gi\|110807486\|ref\|YP_691006.1\| ATP-dependent DNA helicase RecQ [Shigella flexneri 5 str. 8401], gi\|11...	0.0	[1..610]	[1..608]

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Predicted Domain #1

Region A:
Residues: [1-519]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSTAAVINRE LLAVQVLRDT FGYQQFRPGQ QEIINATLSG QDCLVVMPTG GGKSLCYQIP  60
   61 ALVTDGLTLV VSPLISLMKD QVDQLLAYGV GAGCLNSSQT REQQLAVMDG CRSGQIKLLY 120
  121 IAPERLVMES FLDQLYQWRP ALLAVDEAHC ISQWGHDFRP EYRALGQLKQ RFPDLPVIAL 180
  181 TATADEATRG DIVRLLNLDQ PLIQISSFDR PNIRYTLVEK FKPLDQLWRF VQDQRGKSGI 240
  241 IYCNSRAKVE DTTARLQSRG LSVAAYHAGL DNERRAQVQE AFQRDDLQVV VATVAFGMGI 300
  301 NKPNVRFVVH FDIPRTIESY YQETGRAGRD GLPAEAVLLY DPADMAWLRR CLEEKPAGAQ 360
  361 QDIERHKLNA MGAFAEAQTC RRLVLLNYFG EGKQQPCGNC DICLDPPKRY DGLADAQKAL 420
  421 SCVYRVGQRF GLGYIVEVLR GANNQRIREM GHDKLSVYGI GREQTHEHWV SVLRQLIHLG 480
  481 LLSQNIAQFS ALQLTEAARP VLRAELPLQL AVPRIQSLK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	110.0
Match:	1oywA
Description:	Structure of the RecQ Catalytic Core
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA helicase activity	5.33108843895592	bayes_pls_golite062009
four-way junction helicase activity	5.20361383647271	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.16381244011837	bayes_pls_golite062009
pyrophosphatase activity	2.13284212711072	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.11265775498161	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.11046854230259	bayes_pls_golite062009
single-stranded DNA-dependent ATPase activity	1.8195489846634	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
single-stranded DNA-dependent ATP-dependent DNA helicase activity	1.69315154404254	bayes_pls_golite062009
hydrolase activity	1.66122526893602	bayes_pls_golite062009
ATPase activity	1.53315090215319	bayes_pls_golite062009
RNA helicase activity	1.42791449104435	bayes_pls_golite062009
nucleic acid binding	1.41477043612798	bayes_pls_golite062009
RNA-dependent ATPase activity	1.39335733374328	bayes_pls_golite062009
ATP-dependent RNA helicase activity	1.36724390116598	bayes_pls_golite062009
microtubule motor activity	1.30090199952739	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2155186842031	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
DNA binding	1.11699929651302	bayes_pls_golite062009
motor activity	1.03253378953548	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
transcription regulator activity	0.989226939888218	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.5886142102548	bayes_pls_golite062009
single-stranded DNA binding	0.568457189190858	bayes_pls_golite062009
	0.442119153778711	bayes_pls_golite062009
mismatched DNA binding	0.31144582840038	bayes_pls_golite062009
exodeoxyribonuclease V activity	0.185603938981231	bayes_pls_golite062009
protein binding	0.170837278876362	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
purine nucleotide binding	0.10713474095071	bayes_pls_golite062009
purine ribonucleotide binding	0.0916519414118148	bayes_pls_golite062009
ribonucleotide binding	0.0915913646217636	bayes_pls_golite062009
transcription factor activity	0.0434163635422169	bayes_pls_golite062009
RNA binding	0.0261282189186349	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [520-610]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VRSSANQKSY GGNYDRKLFA KLRKLRKSIA DEGNIPPYVV FNDATLLEMA EQMPITASEL  60
   61 LSVNGVGQRK LERFGAPFMA LIRDHVDNND D

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	26.0
Match:	1wudA
Description:	E. coli RecQ HRDC domain
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: