YRC Public Data Repository - Protein Structure Prediction

Protein:	RAPA_ECOLI
Organism:	Escherichia coli
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 RAPA_ECOLI.

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...	729.0	[0..1]	[968..1]
RAPA_SHIDS - RNA polymerase-associated protein RapA OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rapA PE=...	729.0	[0..1]	[968..1]
gi\|29140641, gi\|... - gi\|29140641\|ref\|NP_803983.1\| ATP-dependent helicase HepA [Salmonella enterica subsp. enterica serova... gi\|16759091 - gi\|16759091\|ref\|NP_454708.1\| ATP-dependent helicase HepA [Salmonella enterica subsp. enterica serova... RAPA_SALTI - RNA polymerase-associated protein rapA OS=Salmonella typhi GN=rapA PE=3 SV=3 RAPA_SALTI - RNA polymerase-associated protein RapA OS=Salmonella typhi GN=rapA PE=3 SV=3 gi\|214001243 - gi\|214001243\|ref\|ZP_03411978.1\| ATP-dependent helicase HepA [Salmonella enterica subsp. enterica ser... gi\|213161695 - gi\|213161695\|ref\|ZP_03347405.1\| ATP-dependent helicase HepA [Salmonella enterica subsp. enterica ser...	728.0	[0..1]	[968..1]
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	728.0	[0..1]	[968..1]
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...	728.0	[0..1]	[968..1]
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=...	728.0	[0..1]	[968..1]
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...	728.0	[0..1]	[968..1]
RAPA_ECOHS - RNA polymerase-associated protein RapA OS=Escherichia coli O9:H4 (strain HS) GN=rapA PE=3 SV=1	727.0	[0..1]	[968..1]
gi\|192955842, gi... - gi\|75234298\|ref\|ZP_00718676.1\| COG0553: Superfamily II DNA/RNA helicases, SNF2 family [Escherichia c...	727.0	[0..1]	[968..1]
gi\|30039866, gi\|... - gi\|30061624\|ref\|NP_835795.1\| ATP-dependent helicase HepA [Shigella flexneri 2a str. 2457T], gi\|30039...	727.0	[0..1]	[968..1]

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Predicted Domain #1

Region A:
Residues: [1-141]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPFTLGQRWI SDTESELGLG TVVAVDARTV TLLFPSTGEN RLYARSDSPV TRVMFNPGDT  60
   61 ITSHDGWQMQ VEEVKEENGL LTYIGTRLDT EESGVALREV FLDSKLVFSK PQDRLFAGQI 120
  121 DRMDRFALRY RARKYSSEQF R

[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: [142-710]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPYSGLRGQR TSLIPHQLNI AHDVGRRHAP RVLLADEVGL GKTIEAGMIL HQQLLSGAAE  60
   61 RVLIIVPETL QHQWLVEMLR RFNLRFALFD DERYAEAQHD AYNPFDTEQL VICSLDFARR 120
  121 SKQRLEHLCE AEWDLLVVDE AHHLVWSEDA PSREYQAIEQ LAEHVPGVLL LTATPEQLGM 180
  181 ESHFARLRLL DPNRFHDFAQ FVEEQKNYRP VADAVAMLLA GNKLSNDELN MLGEMIGEQD 240
  241 IEPLLQAANS DSEDAQSARQ ELVSMLMDRH GTSRVLFRNT RNGVKGFPKR ELHTIKLPLP 300
  301 TQYQTAIKVS GIMGARKSAE DRARDMLYPE RIYQEFEGDN ATWWNFDPRV EWLMGYLTSH 360
  361 RSQKVLVICA KAATALQLEQ VLREREGIRA AVFHEGMSII ERDRAAAWFA EEDTGAQVLL 420
  421 CSEIGSEGRN FQFASHMVMF DLPFNPDLLE QRIGRLDRIG QAHDIQIHVP YLEKTAQSVL 480
  481 VRWYHEGLDA FEHTCPTGRT IYDSVYNDLI NYLASPDQTE GFDDLIKNCR EQHEALKAQL 540
  541 EQGRDRLLEI HSNGGEKAQA LAESIEEQD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	62.045757
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: [711-767]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDTNLIAFAM NLFDIIGINQ DDRGDNMIVL TPSDHMLVPD FPGLSEDGIT ITFDREV

[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 #4

Region A:
Residues: [768-826]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ALAREDAQFI TWEHPLIRNG LDLILSGDTG SSTISLLKNK ALPVGTLLVE LIYVVEAQA

[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 #5

Region A:
Residues: [827-968]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PKQLQLNRFL PPTPVRMLLD KNGNNLAAQV EFETFNRQLN AVNRHTGSKL VNAVQQDVHA  60
   61 ILQLGEAQIE KSARALIDAA RNEADEKLSA ELSRLEALRA VNPNIRDDEL TAIESNRQQV 120
  121 MESLDQAGWR LDALRLIVVT HQ

[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: