YRC Public Data Repository - Protein Structure Prediction

Protein:	SIGC_ARATH
Organism:	Arabidopsis thaliana
Length:	571 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 SIGC_ARATH.

Description	E-value	Query Range	Subject Range
gi\|71795952, gi\|... - gi\|71891846\|ref\|YP_277575.1\| RNA polymerase sigma-70 factor [Candidatus Blochmannia pennsylvanicus s...	406.0	[0..71]	[570..100]
gi\|45437587, gi\|... - gi\|45442721\|ref\|NP_994260.1\| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus str. ...	401.0	[0..71]	[570..117]
gi\|33519536, gi\|... - gi\|33519536\|ref\|NP_878368.1\| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus], gi\|...	400.0	[0..71]	[570..101]
gi\|21960500, gi\|... - gi\|22127411\|ref\|NP_670834.1\| RNA polymerase sigma factor RpoD [Yersinia pestis KIM], gi\|21960500\|gb\|...	400.0	[0..71]	[570..118]
gi\|77974118 - gi\|77974118\|ref\|ZP_00829660.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	399.0	[0..71]	[570..120]
gi\|238719206, gi... - gi\|77962309\|ref\|ZP_00826131.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	399.0	[0..71]	[570..120]
gi\|77959510 - gi\|77959510\|ref\|ZP_00823529.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	399.0	[0..71]	[570..120]
gi\|77977904 - gi\|77977904\|ref\|ZP_00833342.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	397.0	[0..71]	[570..120]
gi\|71736970, gi\|... - gi\|71736970\|ref\|YP_272918.1\| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. phaseolicola...	396.0	[0..71]	[571..98]
gi\|1072030 - gi\|1072030\|gb\|AAB60181.1\| RNA polymerase sigma-subunit [Escherichia coli]	396.0	[0..71]	[570..96]

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Predicted Domain #1

Region A:
Residues: [1-91]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MASFNSFPIP KQIVGSSSSS SSSTSRPRIL VRSSLTSSMT STNSMLVFVH PHPLIKHWLS  60
   61 LLRSDQTSFP IFVRIPMTSV VATRWSFLSS V

[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: [92-189]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KEESRIYQND SLKACGCASV SPYTAQNNVY VELKDPKENI GVGSAERSYS SRSMLQYNLL  60
   61 AKNLLALEET FVALDSVRME RDIMLQMGKL GAAELFKT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	53.09691
Match:	1sigA
Description:	CRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA COLI RNA POLYMERASE
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [190-571]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 CLSRYRGSSI TSCLSDTTEL VDTTPNQQVF VSSRRKVKKK ARRSSVTAEN GDQSSLPIGL  60
   61 RTTWNNIDVP RVRRPPKYRK KRERISRNET EMSTGVKIVA DMERIRTQLE EESGKVASLS 120
  121 CWAAAAGMNE KLLMRNLHYG WYCRDELVKS TRSLVLFLAR NYRGLGIAHE DLIQAGYVGV 180
  181 LQGAERFDHT RGYKFSTYVQ YWIRKSMSTM VSRHARGVHI PSSIIRTINH IQKARKTLKT 240
  241 SHGIKYAADE EIAKLTGHSV KKIRAANQCL KVVGSIDKKV GDCFTTKFLE FTPDTTMESP 300
  301 EEAVMRQSAR RDIHDLLEGL EPREKQVMVL RYGLQDYRPK SLEEIGKLLK VSKEWIRKIE 360
  361 RRAMAKLRDQ PNAEDLRYYL NQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	65.522879
Match:	1l9zH
Description:	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits
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