YRC Public Data Repository - Protein Structure Prediction

Protein:	RUVA_SHEON
Organism:	Shewanella oneidensis MR-1
Length:	205 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 RUVA_SHEON.

Description	E-value	Query Range	Subject Range
gi\|78691306, gi\|... - gi\|78691306\|ref\|ZP_00855929.1\| DNA recombination protein, RuvA [Shewanella sp. MR-7], gi\|78509308\|gb... gi\|78505591, gi\|... - gi\|78686707\|ref\|ZP_00851471.1\| DNA recombination protein, RuvA [Shewanella sp. ANA-3], gi\|78505591\|g...	264.0	[0..1]	[205..26]
gi\|91188507, gi\|... - gi\|91227614\|ref\|ZP_01261918.1\| Holliday junction DNA helicase motor protein [Vibrio alginolyticus 12...	263.0	[0..1]	[205..1]
gi\|86146483, gi\|... - gi\|86146483\|ref\|ZP_01064806.1\| Holliday junction DNA helicase motor protein [Vibrio sp. MED222], gi\|... RUVA_VIBTL - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio tasmaniensis (strain LGP32) GN=ruvA PE=3...	261.0	[0..1]	[205..1]
gi\|84377068, gi\|... - gi\|84388519\|ref\|ZP_00991066.1\| Holliday junction DNA helicase motor protein [Vibrio splendidus 12B01...	260.0	[0..1]	[205..1]
RUVA_VIBVU - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio vulnificus GN=ruvA PE=3 SV=1 RUVA_VIBVY - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio vulnificus (strain YJ016) GN=ruvA PE=3 S... RUVA_VIBVU - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio vulnificus (strain CMCP6) GN=ruvA PE=3 S...	260.0	[0..1]	[205..1]
RUVA_SHESR - Holliday junction ATP-dependent DNA helicase RuvA OS=Shewanella sp. (strain MR-7) GN=ruvA PE=3 SV=1 RUVA_SHESA - Holliday junction ATP-dependent DNA helicase RuvA OS=Shewanella sp. (strain ANA-3) GN=ruvA PE=3 SV=1	260.0	[0..1]	[205..1]
RUVA_SHESM - Holliday junction ATP-dependent DNA helicase RuvA OS=Shewanella sp. (strain MR-4) GN=ruvA PE=3 SV=1	258.0	[0..1]	[205..1]
gi\|208725235, gi... - gi\|208810719\|ref\|ZP_03252595.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. E... sp\|B7USN8\|RUVA_ECO27 - Holliday junction ATP-dependent DNA helicase ruvA OS=Escherichia coli O127:H6 (strain E2348/69 / EPE... gi\|208731265, gi... - gi\|208816922\|ref\|ZP_03258042.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. E... RUVA_ECO5E - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O157:H7 (strain EC4115 / EHEC)... RUVA_ECOSE - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli (strain SE11) GN=ruvA PE=3 SV=... gi\|191173018, gi... - gi\|191173018\|ref\|ZP_03034552.1\| Holliday junction DNA helicase RuvA [Escherichia coli F11], gi\|19090... gi\|193066070, gi... - gi\|193066070\|ref\|ZP_03047127.1\| Holliday junction DNA helicase RuvA [Escherichia coli E22], gi\|19292... gi\|194429662, gi... - gi\|194429662\|ref\|ZP_03062180.1\| Holliday junction DNA helicase RuvA [Escherichia coli B171], gi\|1944... gi\|195940293 - gi\|195940293\|ref\|ZP_03085675.1\| Holliday junction DNA helicase motor protein [Escherichia coli O157:... gi\|189376026, gi... - gi\|189376026\|gb\|EDU94442.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC508... RUVA_ECODH - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli (strain K12 / DH10B) GN=ruvA P... RUVA_ECOSM - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=ru... RUVA_SHIB3 - Holliday junction ATP-dependent DNA helicase RuvA OS=Shigella boydii serotype 18 (strain CDC 3083-94... gi\|189360288, gi... - gi\|189360288\|gb\|EDU78707.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC448... EG10923 - component of RuvABC resolvasome, regulatory subunit / Holliday junction recognition factor, recruits... gi\|187768087, gi... - gi\|187768087\|gb\|EDU31931.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC419... gi\|5107495\|pdb\|1... - Chain A, E. Coli Ruva With Bound Dna Holliday Junction, Alpha Carbons And Phosphate Atoms Only, Chai... gi\|188999499, gi... - gi\|188999499\|gb\|EDU68485.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC407... gi\|189372002, gi... - gi\|189372002\|gb\|EDU90418.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC869... gi\|195182923 - gi\|195182923\|dbj\|BAG66491.1\| Holliday junction helicase subunit B [Escherichia coli O111:H-] RUVA_ECO24 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O139:H28 (strain E24377A / ETE... RUVA_ECOL6 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 70... RUVA_ECO81 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O81 (strain ED1a) GN=ruvA PE=3... RUVA_ECO57 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O157:H7 GN=ruvA PE=3 SV=1 RUVA_ECO55 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli (strain 55989 / EAEC) GN=ruvA ... EG10923 - component of RuvABC resolvasome, regulatory subunit / Holliday junction recognition factor, recruits... RUVA_ECO7I - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) G... gi\|12515917, gi\|... - gi\|15802274\|ref\|NP_288298.1\| Holliday junction DNA helicase motor protein [Escherichia coli O157:H7 ... RUVA_ECOLU - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O17:K52:H18 (strain UMN026 / E... RUVA_ECOLI - Holliday junction ATP-dependent DNA helicase ruvA (EC 3.6.1.-) - Escherichia coli RUVA_ECO27 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O127:H6 (strain E2348/69 / EPE... gi\|217318042, gi... - gi\|217328695\|ref\|ZP_03444776.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. T... RUVA_ECO8A - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O8 (strain IAI1) GN=ruvA PE=3 ... RUVA_ECO45 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN... RUVA_ECOUT - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli (strain UTI89 / UPEC) GN=ruvA ... gi\|15831825, gi\|... - gi\|15831825\|ref\|NP_310598.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. Saka... RUVA_ECOL5 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC)... gi\|89108701, gi\|... - gi\|89108701\|ref\|AP_002481.1\| component of RuvABC resolvasome, regulatory subunit [Escherichia coli s... gi\|188017456, gi... - gi\|188017456\|gb\|EDU55578.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC411... gi\|189355165, gi... - gi\|189355165\|gb\|EDU73584.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC440... RUVA_SHIBS - Holliday junction ATP-dependent DNA helicase RuvA OS=Shigella boydii serotype 4 (strain Sb227) GN=ru... gi\|168762345, gi... - gi\|189367348\|gb\|EDU85764.1\| Holliday junction DNA helicase RuvA [Escherichia coli O157:H7 str. EC450... RUVA_ECOK1 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O1:K1 / APEC GN=ruvA PE=3 SV=1 RUVA_ECOL6 - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli O6 GN=ruvA PE=3 SV=1 gi\|226900572, gi... - gi\|237705815\|ref\|ZP_04536296.1\| holliday junction helicase subunit B [Escherichia sp. 3_2_53FAA], gi... gi\|227885711, gi... - gi\|227885711\|ref\|ZP_04003516.1\| Holliday junction DNA helicase motor protein [Escherichia coli 83972... gi\|254793485, gi... - gi\|254793485\|ref\|YP_003078322.1\| component of RuvABC resolvasome, regulatory subunit [Escherichia co... RUVA_ECOBW - Holliday junction ATP-dependent DNA helicase RuvA OS=Escherichia coli (strain K12 / MC4100 / BW2952)...	257.0	[0..1]	[205..1]
gi\|30041524, gi\|... - gi\|30063272\|ref\|NP_837443.1\| Holliday junction DNA helicase motor protein [Shigella flexneri 2a str....	257.0	[0..1]	[205..1]
gi\|75828632, gi\|... - gi\|75828632\|ref\|ZP_00757998.1\| COG0632: Holliday junction resolvasome, DNA-binding subunit [Vibrio c... RUVA_VIBC3 - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio cholerae serotype O1 (strain ATCC 39541 ... gi\|75814052, gi\|... - gi\|75814052\|ref\|ZP_00744704.1\| COG0632: Holliday junction resolvasome, DNA-binding subunit [Vibrio c... RUVA_VIBCM - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio cholerae serotype O1 (strain M66-2) GN=r... gi\|121591344, gi... - gi\|121591344\|ref\|ZP_01678632.1\| Holliday junction DNA helicase RuvA [Vibrio cholerae 2740-80], gi\|12... gi\|229508057, gi... - gi\|229508057\|ref\|ZP_04397562.1\| holliday junction DNA helicase RuvA [Vibrio cholerae BX 330286], gi\|... gi\|153225609, gi... - gi\|153225609\|ref\|ZP_01954804.1\| Holliday junction DNA helicase RuvA [Vibrio cholerae MAK 757], gi\|12... gi\|229343532, gi... - gi\|229518843\|ref\|ZP_04408286.1\| holliday junction DNA helicase RuvA [Vibrio cholerae RC9], gi\|229343... gi\|229351669, gi... - gi\|229511704\|ref\|ZP_04401183.1\| holliday junction DNA helicase RuvA [Vibrio cholerae B33], gi\|229351... gi\|229607618, gi... - gi\|229607618\|ref\|YP_002878266.1\| holliday junction DNA helicase RuvA [Vibrio cholerae MJ-1236], gi\|2... RUVA_VIBCH - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio cholerae GN=ruvA PE=3 SV=1 RUVA_VIBCH - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio cholerae serotype O1 (strain ATCC 39315 ...	257.0	[0..1]	[205..1]

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Predicted Domain #1

Region A:
Residues: [1-205]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIGRLRGVLI EKQAPEVLID VNGVGYELQM PLTSFYELPE LNQPTTVYTH FVVREDAQLL  60
   61 YGFITKQERS LFRLLIKANG VGPKLALTIL SGMTASEFVG CVERDDIVTL VKLPGVGKKT 120
  121 AERLLVEMRD KLKSLMEASV GSEREFVLQS NYSPAPVVNS AEEDAISALI SLGYKPPQAS 180
  181 KAVSAAFKEG MDSETLIKAA LKSML

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	69.0
Match:	1bdxA
Description:	DNA helicase RuvA subunit, C-terminal domain; DNA helicase RuvA subunit, middle domain; DNA helicase RuvA subunit, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
four-way junction helicase activity	6.5377357736202	bayes_pls_golite062009
DNA helicase activity	4.17140899815273	bayes_pls_golite062009
endodeoxyribonuclease activity	3.43738564958931	bayes_pls_golite062009
helicase activity	3.41619150983834	bayes_pls_golite062009
deoxyribonuclease activity	3.18777140839084	bayes_pls_golite062009
excinuclease ABC activity	2.75922711242844	bayes_pls_golite062009
nucleic acid binding	1.99569639221804	bayes_pls_golite062009
structure-specific DNA binding	1.68542948433544	bayes_pls_golite062009
binding	1.60192408330567	bayes_pls_golite062009
single-stranded DNA binding	1.58506920916947	bayes_pls_golite062009
DNA binding	1.33645375386113	bayes_pls_golite062009
endonuclease activity	1.07194065760938	bayes_pls_golite062009
damaged DNA binding	1.01799678384131	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.01626429465845	bayes_pls_golite062009
structural constituent of ribosome	0.83740886071361	bayes_pls_golite062009
structural molecule activity	0.53636537261201	bayes_pls_golite062009
nuclease activity	0.29926900436997	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0954216620147701	bayes_pls_golite062009
exonuclease activity	0.0152988330656798	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: