YRC Public Data Repository - Protein Structure Prediction

Protein:	SIGB_ARATH
Organism:	Arabidopsis thaliana
Length:	572 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 SIGB_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...	428.0	[0..15]	[569..16]
gi\|33519536, gi\|... - gi\|33519536\|ref\|NP_878368.1\| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus], gi\|...	427.0	[0..15]	[569..16]
gi\|25288442, gi\|... - gi\|25288442\|pir\|\|AB0893 RNA polymerase sigma-70 factor [imported] - Salmonella enterica subsp. enter... gi\|29143472, gi\|... - gi\|29143472\|ref\|NP_806814.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s... gi\|16761985 - gi\|16761985\|ref\|NP_457602.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	426.0	[0..15]	[569..61]
gi\|62181728, gi\|... - gi\|62181728\|ref\|YP_218145.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	426.0	[0..15]	[569..61]
gi\|205333914, gi... - gi\|205358509\|ref\|ZP_02656872.2\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|205343355, gi... - gi\|205359720\|ref\|ZP_02831723.2\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... lcl\|NC_016856.1_... - [gene=rpoD] [protein=RNA polymerase sigma factor RpoD] [protein_id=YP_005239387.1] [location=3394519... gi\|16421768 - gi\|16421768\|gb\|AAL22085.1\| sigma D factor of RNA polymerase [Salmonella enterica subsp. enterica ser... gi\|197095558, gi... - gi\|197364081\|ref\|YP_002143718.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|56415151, gi\|... - gi\|56415151\|ref\|YP_152226.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	425.0	[0..15]	[569..61]
gi\|45437587, gi\|... - gi\|45442721\|ref\|NP_994260.1\| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus str. ...	424.0	[0..15]	[569..35]
gi\|21960500, gi\|... - gi\|22127411\|ref\|NP_670834.1\| RNA polymerase sigma factor RpoD [Yersinia pestis KIM], gi\|21960500\|gb\|...	423.0	[0..15]	[569..36]
gi\|238719206, gi... - gi\|77962309\|ref\|ZP_00826131.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	422.0	[0..15]	[569..38]
gi\|77959510 - gi\|77959510\|ref\|ZP_00823529.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	422.0	[0..15]	[569..38]
gi\|77974118 - gi\|77974118\|ref\|ZP_00829660.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	421.0	[0..15]	[569..38]

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Predicted Domain #1

Region A:
Residues: [1-99]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSCLLPQFK CPPDSFSIHF RTSFCAPKHN KGSVFFQPQC AVSTSPALLT SMLDVAKLRL  60
   61 PSFDTDSDSL ISDRQWTYTR PDGPSTEAKY LEALASETL

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.510	a.7.14	Description not found.
View	Download	0.495	a.253.1	Description not found.
View	Download	0.471	d.52.7	Ribosome-binding factor A, RbfA
View	Download	0.444	d.375.1	Description not found.
View	Download	0.434	a.69.4	Description not found.
View	Download	0.427	d.74.3	RBP11-like subunits of RNA polymerase
View	Download	0.426	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators
View	Download	0.418	a.68.1	Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
View	Download	0.402	d.109.1	Actin depolymerizing proteins

Predicted Domain #2

Region A:
Residues: [100-189]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LTSDEAVVVA AAAEAVALAR AAVKVAKDAT LFKNSNNTNL LTSSTADKRS KWDQFTEKER  60
   61 AGILGHLAVS DNGIVSDKIT ASASNKESIG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	46.522879
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: [190-572]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DLESEKQEEV ELLEEQPSVS LAVRSTRQTE RKARRAKGLE KTASGIPSVK TGSSPKKKRL  60
   61 VAQEVDHNDP LRYLRMTTSS SKLLTVREEH ELSAGIQDLL KLERLQTELT ERSGRQPTFA 120
  121 QWASAAGVDQ KSLRQRIHHG TLCKDKMIKS NIRLVISIAK NYQGAGMNLQ DLVQEGCRGL 180
  181 VRGAEKFDAT KGFKFSTYAH WWIKQAVRKS LSDQSRMIRL PFHMVEATYR VKEARKQLYS 240
  241 ETGKHPKNEE IAEATGLSMK RLMAVLLSPK PPRSLDQKIG MNQNLKPSEV IADPEAVTSE 300
  301 DILIKEFMRQ DLDKVLDSLG TREKQVIRWR FGMEDGRMKT LQEIGEMMGV SRERVRQIES 360
  361 SAFRKLKNKK RNNHLQQYLV AQS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	72.69897
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