YRC Public Data Repository - Protein Structure Prediction

Protein:	RUVB_SHEON
Organism:	Shewanella oneidensis MR-1
Length:	334 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 RUVB_SHEON.

Description	E-value	Query Range	Subject Range
gi\|46143843 - gi\|46143843\|ref\|ZP_00133974.2\| COG2255: Holliday junction resolvasome, helicase subunit [Actinobacil... RUVB_ACTP2 - Holliday junction ATP-dependent DNA helicase RuvB OS=Actinobacillus pleuropneumoniae serotype 5b (st...	237.0	[0..1]	[331..1]
RUVB_ALTMD - Holliday junction ATP-dependent DNA helicase ruvB OS=Alteromonas macleodii (strain DSM 17117 / Deep ...	234.0	[0..1]	[334..1]
RUVB_HAEDU - Holliday junction ATP-dependent DNA helicase ruvB OS=Haemophilus ducreyi GN=ruvB PE=3 SV=1 RUVB_HAEDU - Holliday junction ATP-dependent DNA helicase RuvB OS=Haemophilus ducreyi (strain 35000HP / ATCC 7007...	234.0	[0..1]	[330..1]
RUVB_YERPG - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pestis bv. Antiqua (strain Angola) GN=...	233.0	[0..1]	[334..1]
gi\|149366013, gi... - gi\|149366013\|ref\|ZP_01888048.1\| Holliday junction DNA helicase [Yersinia pestis CA88-4125], gi\|14929... RUVB_YERPP - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pestis (strain Pestoides F) GN=ruvB PE... gi\|229702245, gi... - gi\|229894772\|ref\|ZP_04509952.1\| ATP-dependent DNA helicase, component of RuvABC resolvasome [Yersini... gi\|229897475, gi... - gi\|229897475\|ref\|ZP_04512631.1\| ATP-dependent DNA helicase, component of RuvABC resolvasome [Yersini... RUVB_YERPS - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pseudotuberculosis GN=ruvB PE=3 SV=1 gi\|229898121, gi... - gi\|229898121\|ref\|ZP_04513270.1\| ATP-dependent DNA helicase, component of RuvABC resolvasome [Yersini... gi\|167049119, gi... - gi\|167401423\|ref\|ZP_02306920.1\| Holliday junction DNA helicase RuvB [Yersinia pestis biovar Antiqua ... gi\|167419932, gi... - gi\|167419932\|ref\|ZP_02311685.1\| Holliday junction DNA helicase RuvB [Yersinia pestis biovar Oriental... gi\|167056370, gi... - gi\|167424488\|ref\|ZP_02316241.1\| Holliday junction DNA helicase RuvB [Yersinia pestis biovar Mediaeva... RUVB_YERPY - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pseudotuberculosis serotype O:3 (strai... RUVB_YERPB - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pseudotuberculosis serotype IB (strain... gi\|21959099, gi\|... - gi\|22126138\|ref\|NP_669561.1\| Holliday junction DNA helicase B [Yersinia pestis KIM], gi\|21959099\|gb\|... RUVB_YERPS - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pseudotuberculosis serotype I (strain ... RUVB_YERPN - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pestis bv. Antiqua (strain Nepal516) G... gi\|45441703, gi\|... - gi\|45441703\|ref\|NP_993242.1\| Holliday junction DNA helicase B [Yersinia pestis biovar Microtus str. ... gi\|218929165, gi... - gi\|218929165\|ref\|YP_002347040.1\| Holliday junction DNA helicase RuvB [Yersinia pestis CO92], gi\|1612... RUVB_YERP3 - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pseudotuberculosis serotype O:1b (stra... gi\|165919633, gi... - gi\|165928350\|ref\|ZP_02224182.1\| Holliday junction DNA helicase RuvB [Yersinia pestis biovar Oriental... gi\|165991786, gi... - gi\|166009231\|ref\|ZP_02230129.1\| Holliday junction DNA helicase RuvB [Yersinia pestis biovar Antiqua ... gi\|165913241, gi... - gi\|89104240\|ref\|ZP_01176789.1\| COG2255: Holliday junction resolvasome, helicase subunit [Yersinia pe... RUVB_YERPE - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pestis GN=ruvB PE=3 SV=1 RUVB_YERPA - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN... gi\|166210761, gi... - gi\|166210761\|ref\|ZP_02236796.1\| Holliday junction DNA helicase RuvB [Yersinia pestis biovar Antiqua ...	233.0	[0..1]	[334..1]
RUVB_ECOL6 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 70... sp\|B7USN7\|RUVB_ECO27 - Holliday junction ATP-dependent DNA helicase ruvB OS=Escherichia coli O127:H6 (strain E2348/69 / EPE... RUVB_ECOL6 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O6 GN=ruvB PE=3 SV=1 gi\|75239719, gi\|... - gi\|75239719\|ref\|ZP_00723682.1\| COG2255: Holliday junction resolvasome, helicase subunit [Escherichia... gi\|227837285, gi... - gi\|227885712\|ref\|ZP_04003517.1\| Holliday junction DNA helicase B [Escherichia coli 83972], gi\|227837... RUVB_ECOL5 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC)... RUVB_ECOSM - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=ru... RUVB_ESCF3 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia fergusonii (strain ATCC 35469 / DSM... RUVB_ECO27 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O127:H6 (strain E2348/69 / EPE... RUVB_ECOLU - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O17:K52:H18 (strain UMN026 / E... RUVB_ECO7I - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) G...	233.0	[0..1]	[334..1]
gi\|77973529, gi\|... - gi\|77973529\|ref\|ZP_00829076.1\| COG2255: Holliday junction resolvasome, helicase subunit [Yersinia fr...	233.0	[0..1]	[334..1]
RUVB_METFK - Holliday junction ATP-dependent DNA helicase RuvB OS=Methylobacillus flagellatus (strain KT / ATCC 5...	233.0	[0..1]	[333..1]
gi\|24113210, gi\|... - gi\|24113210\|ref\|NP_707720.1\| Holliday junction DNA helicase B [Shigella flexneri 2a str. 301], gi\|24... gi\|30041523, gi\|... - gi\|30063271\|ref\|NP_837442.1\| Holliday junction DNA helicase B [Shigella flexneri 2a str. 2457T], gi\|... RUVB_SHIFL - Holliday junction ATP-dependent DNA helicase RuvB OS=Shigella flexneri GN=ruvB PE=3 SV=1 RUVB_SHIF8 - Holliday junction ATP-dependent DNA helicase RuvB OS=Shigella flexneri serotype 5b (strain 8401) GN=...	233.0	[0..1]	[334..1]
RUVB_ERWCT - Holliday junction ATP-dependent DNA helicase RuvB OS=Erwinia carotovora subsp. atroseptica GN=ruvB P... RUVB_PECAS - Holliday junction ATP-dependent DNA helicase RuvB OS=Pectobacterium atrosepticum (strain SCRI 1043 /...	232.0	[0..1]	[334..1]

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Predicted Domain #1

Region A:
Residues: [1-334]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIEADRLIQP QLQGQDDVID RAMRPKLLDE YTGQDDTRAQ LKVFIQAAKN REEALDHMLI  60
   61 YGPPGLGKTT LAMIVANEMG VNIKSTSGPV LEKAGDLAAL LTNLEAGDVL FIDEIHRLSP 120
  121 VVEEILYPAM EDYQLDIMIG EGPAARSIKL DLPPFTLVGA TTRAGALTSP LRARFGIPLR 180
  181 LEFYNVKDLS TIVTRSAQVM GLAIDSEGAT EIAKRSRGTP RIANRLLRRV RDYAEVQHDG 240
  241 AVTQNVAELA LNLLDVDGEG FDYMDRKLLL AIIDKFMGGP VGLDNLAAAI GEERETIEDV 300
  301 LEPFLIQQGF IQRTPRGRIA TARAYVHFGM IKPE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	55.0
Match:	1in8A
Description:	Holliday junction helicase RuvB
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
four-way junction helicase activity	6.48256695424298	bayes_pls_golite062009
DNA helicase activity	5.33108843895592	bayes_pls_golite062009
helicase activity	5.10646465062463	bayes_pls_golite062009
ATP-dependent DNA helicase activity	2.88286413334554	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
hydrolase activity	1.66122526893602	bayes_pls_golite062009
ATPase activity	1.53315090215319	bayes_pls_golite062009
binding	1.41264401383678	bayes_pls_golite062009
DNA-dependent ATPase activity	1.1653223755451	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
ATP-dependent 3'-5' DNA helicase activity	0.7649321307396	bayes_pls_golite062009
nucleic acid binding	0.216266069700019	bayes_pls_golite062009
exodeoxyribonuclease V activity	0.185603938981231	bayes_pls_golite062009
ATP-dependent helicase activity	0.156322124775303	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.156322124775303	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

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: