YRC Public Data Repository - Protein Structure Prediction

Protein:	RP54_PSEAE
Organism:	Pseudomonas aeruginosa PAO1
Length:	497 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 RP54_PSEAE.

Description	E-value	Query Range	Subject Range
gi\|434702, gi\|10... - gi\|434702\|gb\|AAA19793.1\| rpoN [Pseudomonas aeruginosa], pir\|\|A53373 rpoN protein - Pseudomonas aerug...	0.0	[1..497]	[1..497]
RP54_PSEPK - RNA polymerase sigma-54 factor OS=Pseudomonas putida (strain KT2440) GN=rpoN PE=1 SV=1 RP54_PSEPU - RNA polymerase sigma-54 factor OS=Pseudomonas putida GN=rpoN PE=3 SV=1 gi\|148546234, gi... - gi\|82735975\|ref\|ZP_00898836.1\| Sigma-54 factor [Pseudomonas putida F1], gi\|82716962\|gb\|EAP52015.1\| S...	0.0	[1..497]	[1..497]
gi\|77457084, gi\|... - gi\|77457084\|ref\|YP_346589.1\| RNA polymerase factor sigma-54 [Pseudomonas fluorescens Pf0-1], gi\|7738...	0.0	[1..497]	[1..497]
gi\|70728297, gi\|... - gi\|70728297\|ref\|YP_258046.1\| RNA polymerase factor sigma-54 [Pseudomonas fluorescens Pf-5], gi\|68342...	0.0	[1..497]	[1..497]
gi\|7434786, gi\|45733 - pir\|\|T01753 transcription initiation factor sigma rpoN - Pseudomonas putida, gi\|45733\|emb\|CAA34494.1...	0.0	[1..497]	[1..497]
gi\|33359228 - gi\|33359228\|gb\|AAQ17035.1\| sigma factor RpoN [Pseudomonas fluorescens]	0.0	[1..497]	[1..497]
gi\|28871588, gi\|... - gi\|28871588\|ref\|NP_794207.1\| RNA polymerase factor sigma-54 [Pseudomonas syringae pv. tomato str. DC... tr\|Q87WU0\|Q87WU0... - RNA polymerase sigma-54 factor OS=Pseudomonas syringae pv. tomato (strain DC3000) GN=rpoN PE=3 SV=1	0.0	[1..497]	[1..497]
gi\|84316985 - gi\|84316985\|ref\|ZP_00965442.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|84323006 - gi\|84323006\|ref\|ZP_00971083.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|32039678 - gi\|32039678\|ref\|ZP_00137950.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma... gi\|107099953 - gi\|107099953\|ref\|ZP_01363871.1\| hypothetical protein PaerPA_01000974 [Pseudomonas aeruginosa PACS2]	0.0	[9..497]	[1..489]
gi\|23266970 - gi\|23266970\|gb\|AAN16366.1\| sigma 54 [Pseudomonas alcaligenes]	0.0	[3..497]	[1..495]
gi\|6851304 - gi\|6851304\|gb\|AAF29509.1\|AF199600_1 alternative sigma factor RpoN [Pseudomonas syringae pv. maculico...	0.0	[1..497]	[1..497]

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Predicted Domain #1

Region A:
Residues: [1-122]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKPSLVLKMG QQLTMTPQLQ QAIRLLQLST LDLQQEIQEA LESNPMLERQ EDGDDFDNSD  60
   61 PLADGAEQAA SAPQESPLQE SATPSVESLD DDQWSERIPS ELPVDTAWED IYQTSASSLP 120
  121 SN

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [123-278]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDDEWDFTAR TSSGESLHSH LLWQVNLAPM SDTDRMIAVT IIDSINNDGY LEESLEEILA  60
   61 AIDPELDVEL DEVEVVLRRI QQLEPAGIGA RNLRECLLLQ LRQLPSTTPW LNEALRLVSD 120
  121 YLDLLGGRDY SQLMRRMKLK EDELRQVIEL IQCLHP

[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 #3

Region A:
Residues: [279-428]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RPGSQIESSE AEYIVPDVIV RKDNERWLVE LNQEAMPRLR VNATYAGMVR RADSSADNTF  60
   61 MRNQLQEARW FIKSLQSRNE TLMKVATQIV EHQRGFLDYG EEAMKPLVLH DIAEAVGMHE 120
  121 STISRVTTQK YMHTPRGIFE LKYFFSSHVS

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	15.309804
Match:	PF04552.4
Description:	No description for PF04552.4 was found.

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [429-497]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TAEGGECSST AIRAIIKKLV AAENAKKPLS DSKIAGLLEA QGIQVARRTV AKYRESLGIA  60
   61 PSSERKRLV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.09691
Match:	2ahqA
Description:	Solution Structure of the C-terminal RpoN Domain of Sigma-54 from Aquifex aeolicus
Matching Structure (courtesy of the PDB):

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