YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29140641, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	968 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|29140641, gi|....

Description	E-value	Query Range	Subject Range
lcl\|NC_016856.1_... - [gene=hepA] [protein=ATP-dependent helicase HepA] [protein_id=YP_005235749.1] [location=complement(1... RAPA_SALTY - RNA polymerase-associated protein rapA OS=Salmonella typhimurium GN=rapA PE=3 SV=3 RAPA_SALTY - RNA polymerase-associated protein RapA OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 70072... RAPA_SALTY - RNA polymerase-associated protein rapA OS=Salmonella typhimurium GN=rapA PE=3 SV=3 gi\|205331308, gi... - gi\|205331308\|gb\|EDZ18072.1\| RNA polymerase associated protein RapA [Salmonella enterica subsp. enter...	0.0	[1..968]	[1..968]
RAPA_ECO27 - RNA polymerase-associated protein RapA OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=rapA ... RAPA_ECOSM - RNA polymerase-associated protein RapA OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=rapA PE=3 SV=... gi\|75236944, gi\|... - gi\|75236944\|ref\|ZP_00721003.1\| COG0553: Superfamily II DNA/RNA helicases, SNF2 family [Escherichia c... RAPA_ECO7I - RNA polymerase-associated protein RapA OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=rapA PE=3... sp\|B7UIA5\|RAPA_ECO27 - RNA polymerase-associated protein rapA OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=rapA ... RAPA_ECOL6 - RNA polymerase-associated protein RapA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC... RAPA_ECOL6 - RNA polymerase-associated protein rapA OS=Escherichia coli O6 GN=rapA PE=3 SV=3 RAPA_ECOL5 - RNA polymerase-associated protein RapA OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=rapA PE...	0.0	[1..968]	[1..968]
RAPA_SHIDS - RNA polymerase-associated protein RapA OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rapA PE=...	0.0	[1..968]	[1..968]
RAPA_SALCH - RNA polymerase-associated protein RapA OS=Salmonella choleraesuis (strain SC-B67) GN=rapA PE=3 SV=1 RAPA_SALCH - RNA polymerase-associated protein rapA OS=Salmonella choleraesuis GN=rapA PE=3 SV=1 RAPA_SALCH - RNA polymerase-associated protein rapA OS=Salmonella choleraesuis GN=rapA PE=3 SV=1	0.0	[1..968]	[1..968]
gi\|208738365, gi... - gi\|208818242\|ref\|ZP_03258562.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str... gi\|208735160, gi... - gi\|208813883\|ref\|ZP_03255212.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str... gi\|226902115, gi... - gi\|237704203\|ref\|ZP_04534684.1\| RNA polymerase-associated protein rapA [Escherichia sp. 3_2_53FAA], ... gi\|217324831, gi... - gi\|217324831\|ref\|ZP_03440915.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str... RAPA_ECOBW - RNA polymerase-associated protein RapA OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=rapA PE... RAPA_ECOSE - RNA polymerase-associated protein RapA OS=Escherichia coli (strain SE11) GN=rapA PE=3 SV=1 gi\|251783623, gi... - gi\|251783623\|ref\|YP_002997927.1\| hypothetical protein B21_00060 [Escherichia coli BL21], gi\|24237589... RAPA_ECO55 - RNA polymerase-associated protein RapA OS=Escherichia coli (strain 55989 / EAEC) GN=rapA PE=3 SV=1 gi\|253976292, gi... - gi\|254286985\|ref\|YP_003052733.1\| ATP-dependent helicase HepA [Escherichia coli BL21(DE3)], gi\|253976... RAPA_ECO45 - RNA polymerase-associated protein RapA OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=rapA PE=3 ... gi\|254160182, gi... - gi\|254160182\|ref\|YP_003043290.1\| ATP-dependent helicase HepA [Escherichia coli B str. REL606], gi\|25... gi\|254791197, gi... - gi\|254791197\|ref\|YP_003076034.1\| RNA polymerase-associated helicase protein (ATPase and RNA polymera... RAPA_ECOLU - RNA polymerase-associated protein RapA OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=ra... gi\|15829317, gi\|... - gi\|15829317\|ref\|NP_308090.1\| ATP-dependent helicase HepA [Escherichia coli O157:H7 str. Sakai], gi\|1... gi\|189365906, gi... - gi\|189365906\|gb\|EDU84322.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str. EC... EG11083 - RNA polymerase remodeling /recycling factor ATPase; RNA polymerase-associated, ATP-dependent RNA tran... gi\|189357101, gi... - gi\|189357101\|gb\|EDU75520.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str. EC... gi\|189370827, gi... - gi\|189370827\|gb\|EDU89243.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str. EC... gi\|187767748, gi... - gi\|187767748\|gb\|EDU31592.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str. EC... gi\|194434414, gi... - gi\|194434414\|ref\|ZP_03066676.1\| RNA polymerase associated protein RapA [Shigella dysenteriae 1012], ... gi\|189376375, gi... - gi\|189376375\|gb\|EDU94791.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str. EC... gi\|89106943, gi\|... - gi\|89106943\|ref\|AP_000723.1\| RNA polymerase-associated helicase protein [Escherichia coli str. K-12 ... gi\|208728573, gi... - gi\|208808772\|ref\|ZP_03251109.1\| RNA polymerase associated protein RapA [Escherichia coli O157:H7 str... RAPA_ECOUT - RNA polymerase-associated protein RapA OS=Escherichia coli (strain UTI89 / UPEC) GN=rapA PE=3 SV=1 gi\|195939275 - gi\|195939275\|ref\|ZP_03084657.1\| ATP-dependent helicase HepA [Escherichia coli O157:H7 str. EC4024] gi\|193065903, gi... - gi\|75256067\|ref\|ZP_00727780.1\| COG0553: Superfamily II DNA/RNA helicases, SNF2 family [Escherichia c... RAPA_ECOLC - RNA polymerase-associated protein RapA OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN... gi\|83585217 - gi\|83585217\|ref\|ZP_00923867.1\| COG0553: Superfamily II DNA/RNA helicases, SNF2 family [Escherichia c... gi\|194429367, gi... - gi\|75209419\|ref\|ZP_00709651.1\| COG0553: Superfamily II DNA/RNA helicases, SNF2 family [Escherichia c... RAPA_ECOLI - RNA polymerase-associated protein rapA (EC 3.6.1.-) (ATP-dependent helicase hepA) - Escherichia coli gi\|124530628, gi... - gi\|124530628\|ref\|ZP_01701212.1\| SNF2-related protein [Escherichia coli B], gi\|124499052\|gb\|EAY46548.... EG11083 - RNA polymerase remodeling /recycling factor ATPase; RNA polymerase-associated, ATP-dependent RNA tran... RAPA_ECO57 - RNA polymerase-associated protein RapA OS=Escherichia coli O157:H7 GN=rapA PE=3 SV=2 gi\|15799743, gi\|... - gi\|15799743\|ref\|NP_285755.1\| ATP-dependent helicase HepA [Escherichia coli O157:H7 EDL933], gi\|12512...	0.0	[1..968]	[1..968]
RAPA_ECOHS - RNA polymerase-associated protein RapA OS=Escherichia coli O9:H4 (strain HS) GN=rapA PE=3 SV=1	0.0	[1..968]	[1..968]
gi\|24050256, gi\|... - gi\|24111503\|ref\|NP_706013.1\| ATP-dependent helicase HepA [Shigella flexneri 2a str. 301], gi\|2405025... RAPA_SHIFL - RNA polymerase-associated protein RapA OS=Shigella flexneri GN=rapA PE=3 SV=3 RAPA_SHIF8 - RNA polymerase-associated protein RapA OS=Shigella flexneri serotype 5b (strain 8401) GN=rapA PE=3 S...	0.0	[1..968]	[1..968]
RAPA_SALPA - RNA polymerase-associated protein RapA OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=rapA... RAPA_SALPA - RNA polymerase-associated protein rapA OS=Salmonella paratyphi A GN=rapA PE=3 SV=1 RAPA_SALPK - RNA polymerase-associated protein RapA OS=Salmonella paratyphi A (strain AKU_12601) GN=rapA PE=3 SV=...	0.0	[1..968]	[1..968]
gi\|192955842, gi... - gi\|75234298\|ref\|ZP_00718676.1\| COG0553: Superfamily II DNA/RNA helicases, SNF2 family [Escherichia c...	0.0	[1..968]	[1..968]
gi\|30039866, gi\|... - gi\|30061624\|ref\|NP_835795.1\| ATP-dependent helicase HepA [Shigella flexneri 2a str. 2457T], gi\|30039...	0.0	[1..968]	[1..968]

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Predicted Domain #1

Region A:
Residues: [1-142]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPFTLGQRWI SDTESELGLG TVVAMDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT  60
   61 ITSHEGWQLH IDEVKEENGL LVYVGTRLDT EETNVTLREV LLDSKLVFSK PQDRLFAGQI 120
  121 DRMDRFALRY RARKFQSEQY RM

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [143-658]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PYSGLRGQRT NLIPHQLNIA HDVGRRHAPR VLLADEVGLG KTIEAGMILH QQLLSGAAER  60
   61 VLIIVPETLQ HQWLVEMLRR FNLRFALFDD ERYTEAQHDA YNPFETEQLV ICSLDFARRN 120
  121 KQRLEHLCDA EWDLLVVDEA HHLVWSTDAP SREYMAIEQL AERVPGVLLL TATPEQLGME 180
  181 SHFARLRLLD PNRFHDFEQF VEEQKNYRPV ADAVAMLLAG NKLSNDELNR LGDLIGEQDI 240
  241 EPLLQAANSD RDDAQAARDE LVSMLMDRHG TSRVLFRNTR NGVKGFPKRE LHTVKLPLPT 300
  301 QYQTAIKVSG IMGARKSAED RARDMLYPEQ IYQEFEGDTG TWWNFDPRVE WLMGYLTSHR 360
  361 SQKVLVICAK ATTALQLEQV LREREGIRAA VFHEGMSIIE RDRAAAWFAE EDTGAQVLLC 420
  421 SEIGSEGRNF QFASNLVMFD LPFNPDLLEQ RIGRLDRIGQ AHDIQIHVPY LEKTAQSVLV 480
  481 RWYHEGLDAF EHTCPTGRAI YDSAYASLIN YLAAPE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	61.0
Match:	1z3iX
Description:	Structure of the SWI2/SNF2 chromatin remodeling domain of eukaryotic Rad54
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	1.82891461927498	bayes_pls_golite062009
catalytic activity	1.37148167194523	bayes_pls_golite062009
transcription regulator activity	0.530058973650498	bayes_pls_golite062009
nucleic acid binding	0.483287504056289	bayes_pls_golite062009
DNA binding	0.215388441407425	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [659-771]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ETDGFDDLIK SCREQHEALK AQLEQGRDRL LEINSNGGEK AQQLAQSIEE QDDDTNLIAF  60
   61 AMNLFDIVGI NQDDRGDNLI VLTPSDHMLV PDFPGLPEDG CTITFERDVA LSR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	18.39794
Match:	2v1xA
Description:	No description for 2v1xA was found.

Predicted Domain #4

Region A:
Residues: [772-968]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EDAQFITWEH PLIRNGLDLI LSGDTGSSTI SLLKNKALPV GTLLVELVYV VEAQAPKQLQ  60
   61 LNRFLPPTPV RMLLDKNGNN LAAQVEFETF NRQLSAVNRH TGSKLVNAVQ QDVHAILQLG 120
  121 ETQIEQSARA LIDNARREAD EKLSGELSRL EALRAVNPNI RDDELAAIDS NRQQVLESLN 180
  181 QAGWRLDALR LIVVTHQ

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

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: