YRC Public Data Repository - Protein Structure Prediction

Protein:	RUVB_YERPB
Organism:	Yersinia pseudotuberculosis PB1/+
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_YERPB.

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...	2.0E-61	[1..331]	[1..331]
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...	8.0E-61	[1..334]	[1..334]
RUVB_METFK - Holliday junction ATP-dependent DNA helicase RuvB OS=Methylobacillus flagellatus (strain KT / ATCC 5...	3.0E-60	[1..333]	[1..334]
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=...	5.0E-60	[1..334]	[1..334]
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...	6.0E-60	[1..334]	[1..334]
RUVB_YERPG - Holliday junction ATP-dependent DNA helicase RuvB OS=Yersinia pestis bv. Antiqua (strain Angola) GN=...	7.0E-60	[1..334]	[1..334]
gi\|124531067, gi... - gi\|124531067\|ref\|ZP_01701452.1\| Holliday junction DNA helicase RuvB [Escherichia coli B], gi\|1244988... gi\|253773183, gi... - gi\|254288708\|ref\|YP_003054456.1\| Holliday junction DNA helicase B [Escherichia coli BL21(DE3)], gi\|2... gi\|251785308, gi... - gi\|251785308\|ref\|YP_002999612.1\| hypothetical protein B21_01819 [Escherichia coli BL21], gi\|24237758... RUVB_ECOBW - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli (strain K12 / MC4100 / BW2952)... gi\|226900571, gi... - gi\|237705814\|ref\|ZP_04536295.1\| holliday junction helicase subunit A [Escherichia sp. 3_2_53FAA], gi... gi\|168747888, gi... - gi\|188017493\|gb\|EDU55615.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. EC411... gi\|189355195, gi... - gi\|189355195\|gb\|EDU73614.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. EC440... gi\|168762346, gi... - gi\|189367355\|gb\|EDU85771.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. EC450... gi\|189360310, gi... - gi\|189360310\|gb\|EDU78729.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. EC448... gi\|217328582, gi... - gi\|217328582\|ref\|ZP_03444663.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. T... RUVB_ECO8A - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O8 (strain IAI1) GN=ruvB PE=3 ... RUVB_ECO45 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN... RUVB_ECO81 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O81 (strain ED1a) GN=ruvB PE=3... RUVB_ECO55 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli (strain 55989 / EAEC) GN=ruvB ... RUVB_ECO57 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O157:H7 GN=ruvB PE=3 SV=1 gi\|195182922 - gi\|195182922\|dbj\|BAG66490.1\| Holliday junction helicase subunit A [Escherichia coli O111:H-] EG10924 - ATP-dependent DNA helicase, component of RuvABC resolvasome / DNA helicase driving branch migration ... gi\|12515916, gi\|... - gi\|15802273\|ref\|NP_288297.1\| Holliday junction DNA helicase B [Escherichia coli O157:H7 EDL933], gi\|... gi\|168783160, gi... - gi\|188999428\|gb\|EDU68414.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. EC407... RUVB_ECODH - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli (strain K12 / DH10B) GN=ruvB P... gi\|194433957, gi... - gi\|194433957\|ref\|ZP_03066229.1\| Holliday junction DNA helicase RuvB [Shigella dysenteriae 1012], gi\|... gi\|195940294 - gi\|195940294\|ref\|ZP_03085676.1\| Holliday junction DNA helicase B [Escherichia coli O157:H7 str. EC40... gi\|208810394, gi... - gi\|208810394\|ref\|ZP_03252270.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. E... gi\|208730956, gi... - gi\|208816613\|ref\|ZP_03257733.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. E... RUVB_ECO5E - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O157:H7 (strain EC4115 / EHEC)... RUVB_ECOSE - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli (strain SE11) GN=ruvB PE=3 SV=... gi\|89108700, gi\|... - gi\|89108700\|ref\|AP_002480.1\| ATP-dependent DNA helicase, component of RuvABC resolvasome [Escherichi... RUVB_ECOUT - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli (strain UTI89 / UPEC) GN=ruvB ... gi\|15831824, gi\|... - gi\|15831824\|ref\|NP_310597.1\| Holliday junction DNA helicase RuvB [Escherichia coli O157:H7 str. Saka... RUVB_ECOLC - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli (strain ATCC 8739 / DSM 1576 /... RUVB_SHIBS - Holliday junction ATP-dependent DNA helicase RuvB OS=Shigella boydii serotype 4 (strain Sb227) GN=ru... RUVB_ECOLI - Holliday junction ATP-dependent DNA helicase ruvB (EC 3.6.1.-) - Escherichia coli RUVB_ECOHS - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O9:H4 (strain HS) GN=ruvB PE=3... gi\|194429647, gi... - gi\|75209094\|ref\|ZP_00709349.1\| COG2255: Holliday junction resolvasome, helicase subunit [Escherichia... gi\|194439048, gi... - gi\|83585539\|ref\|ZP_00924183.1\| COG2255: Holliday junction resolvasome, helicase subunit [Escherichia... RUVB_ECO24 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O139:H28 (strain E24377A / ETE... gi\|75511831, gi\|... - gi\|75511831\|ref\|ZP_00734449.1\| COG2255: Holliday junction resolvasome, helicase subunit [Escherichia... RUVB_SHIDS - Holliday junction ATP-dependent DNA helicase RuvB OS=Shigella dysenteriae serotype 1 (strain Sd197) ... gi\|75235336, gi\|... - gi\|75235336\|ref\|ZP_00719562.1\| COG2255: Holliday junction resolvasome, helicase subunit [Escherichia... gi\|254592884, gi... - gi\|254793484\|ref\|YP_003078321.1\| ATP-dependent DNA helicase, component of RuvABC resolvasome [Escher... EG10924 - ATP-dependent DNA helicase, component of RuvABC resolvasome / DNA helicase driving branch migration ... gi\|75255875, gi\|... - gi\|75255875\|ref\|ZP_00727614.1\| COG2255: Holliday junction resolvasome, helicase subunit [Escherichia... RUVB_ECOK1 - Holliday junction ATP-dependent DNA helicase RuvB OS=Escherichia coli O1:K1 / APEC GN=ruvB PE=3 SV=1 gi\|254161920, gi... - gi\|254161920\|ref\|YP_003045028.1\| Holliday junction DNA helicase B [Escherichia coli B str. REL606], ...	9.0E-60	[1..334]	[1..334]
RUVB_SHIB3 - Holliday junction ATP-dependent DNA helicase RuvB OS=Shigella boydii serotype 18 (strain CDC 3083-94...	1.0E-59	[1..334]	[1..334]
RUVB_SALCH - Holliday junction ATP-dependent DNA helicase RuvB OS=Salmonella choleraesuis GN=ruvB PE=3 SV=1 RUVB_SALCH - Holliday junction ATP-dependent DNA helicase RuvB OS=Salmonella choleraesuis (strain SC-B67) GN=ruvB... RUVB_SALPC - Holliday junction ATP-dependent DNA helicase RuvB OS=Salmonella paratyphi C (strain RKS4594) GN=ruvB... gi\|194454980, gi... - gi\|194468616\|ref\|ZP_03074600.1\| holliday junction DNA helicase RuvB [Salmonella enterica subsp. ente... RUVB_SALHS - Holliday junction ATP-dependent DNA helicase RuvB OS=Salmonella heidelberg (strain SL476) GN=ruvB PE... RUVB_SALNS - Holliday junction ATP-dependent DNA helicase RuvB OS=Salmonella newport (strain SL254) GN=ruvB PE=3 ... gi\|168820717, gi... - gi\|205342660\|gb\|EDZ29424.1\| holliday junction DNA helicase RuvB [Salmonella enterica subsp. enterica... gi\|168462575, gi... - gi\|195634281\|gb\|EDX52633.1\| holliday junction DNA helicase RuvB [Salmonella enterica subsp. enterica... gi\|205339368, gi... - gi\|205339368\|gb\|EDZ26132.1\| holliday junction DNA helicase RuvB [Salmonella enterica subsp. enterica... gi\|238912046 - gi\|238912046\|ref\|ZP_04655883.1\| Holliday junction DNA helicase RuvB [Salmonella enterica subsp. ente... gi\|205331956, gi... - gi\|205331956\|gb\|EDZ18720.1\| holliday junction DNA helicase RuvB [Salmonella enterica subsp. enterica... gi\|205322862, gi... - gi\|205322862\|gb\|EDZ10701.1\| holliday junction DNA helicase RuvB [Salmonella enterica subsp. enterica... RUVB_SALCH - Holliday junction ATP-dependent DNA helicase ruvB OS=Salmonella choleraesuis GN=ruvB PE=3 SV=1	1.0E-59	[1..334]	[1..334]
RUVB_RHIL3 - Holliday junction ATP-dependent DNA helicase RuvB OS=Rhizobium leguminosarum bv. viciae (strain 3841... gi\|240860095, gi... - gi\|241206205\|ref\|YP_002977301.1\| Holliday junction DNA helicase RuvB [Rhizobium leguminosarum bv. tr...	1.0E-59	[1..334]	[1..332]

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Predicted Domain #1

Region A:
Residues: [1-334]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIEADRLISA AVINDEESID RAIRPKLLTE YVGQPHVREQ MEIFIQAAKQ RGDALDHVLI  60
   61 FGPPGLGKTT LANIIANEMG VNLRTTSGPV LEKAGDLAAM LTNLEPHDVL FIDEIHRLSP 120
  121 VVEEILYPAM EDYQLDIMIG EGPAARSIKL DLPPFTLIGA TTRAGSLTSP LRDRFGIVQR 180
  181 LEFYQVADLE HIVSRSAKCL GLELTPEGAH QLARRSRGTP RITNRLLRRV RDFAEVRADG 240
  241 AINGEVAMKA LDMLNVDAEG FDFMDRKLLL AVIDKFMGGP VGLDNLAAAI GEERETIEDV 300
  301 LEPYLIQQGF IQRTPRGRIA TNHAYKHFGI TREE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	52.09691
Match:	1j7kA
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: