YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24375448, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	491 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|24375448, gi|....

Description	E-value	Query Range	Subject Range
gi\|2342480 - gi\|2342480\|dbj\|BAA21883.1\| RNA polymerase sigma factor N [Vibrio alginolyticus] gi\|75856327, gi\|... - gi\|75856327\|ref\|ZP_00763957.1\| COG1508: DNA-directed RNA polymerase specialized sigma subunit, sigma...	701.0	[0..1]	[491..1]
gi\|91189706, gi\|... - gi\|91225586\|ref\|ZP_01260660.1\| DNA-directed RNA polymerase subunit N [Vibrio alginolyticus 12G01], g...	698.0	[0..1]	[491..1]
gi\|156527492, gi... - gi\|156975898\|ref\|YP_001446805.1\| RNA polymerase factor sigma-54 [Vibrio harveyi ATCC BAA-1116], gi\|1... gi\|8118094 - gi\|8118094\|gb\|AAF72887.1\|AF227983_2 alternative sigma factor RpoN [Vibrio harveyi]	692.0	[0..1]	[491..1]
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...	690.0	[0..1]	[491..1]
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	689.0	[0..1]	[491..1]
gi\|90438492, gi\|... - gi\|90580190\|ref\|ZP_01235997.1\| DNA-directed RNA polymerase subunit N [Vibrio angustum S14], gi\|90438...	687.0	[0..1]	[491..1]
gi\|7434786, gi\|45733 - pir\|\|T01753 transcription initiation factor sigma rpoN - Pseudomonas putida, gi\|45733\|emb\|CAA34494.1...	687.0	[0..1]	[491..1]
gi\|63258081, gi\|... - gi\|66047374\|ref\|YP_237215.1\| RNA polymerase factor sigma-54 [Pseudomonas syringae pv. syringae B728a...	686.0	[0..1]	[491..15]
gi\|77457084, gi\|... - gi\|77457084\|ref\|YP_346589.1\| RNA polymerase factor sigma-54 [Pseudomonas fluorescens Pf0-1], gi\|7738...	686.0	[0..1]	[491..1]
gi\|71557168, gi\|... - gi\|71736615\|ref\|YP_276273.1\| RNA polymerase factor sigma-54 [Pseudomonas syringae pv. phaseolicola 1...	686.0	[0..1]	[491..1]

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Predicted Domain #1

Region A:
Residues: [1-119]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKASLQLKLG QQLTMTPQLQ QAIRLLQLSS LELQQEIQQA LDSNPLLELE EEQFDAPSER  60
   61 KQDLADTDFS ETSAQPQEQD NSTVDIAESL TKESLPEELP MDTTWDEVFT ASPNSGSGA

[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: [120-324]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SREDDMPFQG ETSEGLYEHL EWQKNLTPFS ETDLAIATAI IDAIDDQGYL TQSTEDILEA  60
   61 MGNPEIELDE VEAVLKRIQH FDPVGVAARD LSECLLIQLS HFSPDTPHLE NARMLIKDHL 120
  121 DLIAARDFRL LMRKTKLKED ELRDSIALIQ TLNPRPGLLI TAVDEEYVVP DVSVSKKNGR 180
  181 WVVELNPDCM PKINVNQQYA AMARS

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	110.173925
Match:	PF04963.4
Description:	No description for PF04963.4 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 #3

Region A:
Residues: [325-423]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SKNQADSQFI RGHLQEAKWF IKSLESRNET LLKVANCIVQ YQQGFFEYGE EAMKPMVLND  60
   61 IAEAVEMHES TISRVTTQKY MHTPKGLFEL KYFFSSHVG

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	12.356547
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: [424-491]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TDDGGECSST AIRAFIKKLV AAENQKKPLS DSKMAQLLAE QGINVARRTI AKYREAMLIP  60
   61 PSNQRKSL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.0
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