YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|39998144, gi\|...
Organism:	Geobacter sulfurreducens PCA
Length:	250 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|39998144, gi|....

Description	E-value	Query Range	Subject Range
gi\|55739378, gi\|... - gi\|55823393\|ref\|YP_141834.1\| RNA polymerase sigma factor RpoD [Streptococcus thermophilus CNRZ1066],... gi\|116101464, gi... - gi\|62527015\|ref\|ZP_00388317.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)... gi\|55739378 - gb\|AAV63019.1\| DNA directed RNA polymerase sigma 42 protein [Streptococcus thermophilus CNRZ1066]	182.0	[0..2]	[250..114]
gi\|55737450, gi\|... - gi\|55821465\|ref\|YP_139907.1\| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMG 18311]... gi\|55737450 - gb\|AAV61092.1\| DNA directed RNA polymerase sigma 42 protein [Streptococcus thermophilus LMG 18311]	181.0	[0..2]	[250..114]
gi\|88912059, gi\|... - gi\|88931788\|ref\|ZP_01137481.1\| Carbamoyl-phosphate synthase L chain, ATP-binding [Acidothermus cellu...	180.0	[0..4]	[249..225]
gi\|109644065, gi... - gi\|109646116\|ref\|ZP_01370036.1\| RNA polymerase, sigma 38 subunit, RpoS [Desulfitobacterium hafniense...	178.0	[0..3]	[250..139]
gi\|213960104, gi... - gi\|213960104\|ref\|ZP_03388387.1\| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137], gi... gi\|50840117, gi\|... - gi\|50842515\|ref\|YP_055742.1\| RNA polymerase sigma factor [Propionibacterium acnes KPA171202], gi\|508...	178.0	[0..3]	[249..253]
gi\|66867712, gi\|... - gi\|66966421\|ref\|ZP_00413980.1\| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70 region...	178.0	[0..1]	[249..186]
gi\|76563399, gi\|... - gi\|76788342\|ref\|YP_330069.1\| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909], gi\|76... gi\|77159097, gi\|... - gi\|77414847\|ref\|ZP_00790961.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515], gi\|771... gi\|22537572, gi\|... - gi\|22537572\|ref\|NP_688423.1\| RNA polymerase sigma factor RpoD [Streptococcus agalactiae 2603V/R], gi... gi\|77161430, gi\|... - gi\|77412516\|ref\|ZP_00788814.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111], gi\|... gi\|77409561, gi\|... - gi\|77409561\|ref\|ZP_00786243.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1], gi\|77... gi\|25011538, gi\|... - gi\|25011538\|ref\|NP_735933.1\| RNA polymerase sigma factor RpoD [Streptococcus agalactiae NEM316], gi\|...	178.0	[0..2]	[250..114]
gi\|77406972, gi\|... - gi\|77406972\|ref\|ZP_00783989.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B], gi\|77...	177.0	[0..2]	[250..114]
gi\|223932503, gi... - gi\|81096984\|ref\|ZP_00875303.1\| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70 regi... gi\|146321288, gi... - gi\|146321288\|ref\|YP_001200999.1\| RNA polymerase sigma factor RpoD [Streptococcus suis 98HAH33], gi\|1... gi\|145689888, gi... - gi\|146319082\|ref\|YP_001198794.1\| RNA polymerase sigma factor RpoD [Streptococcus suis 05ZYH33], gi\|1... gi\|251820209, gi... - gi\|253753963\|ref\|YP_003027104.1\| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7], gi\|2518... gi\|251816427, gi... - gi\|253752138\|ref\|YP_003025279.1\| RNA polymerase sigma factor RpoD [Streptococcus suis SC84], gi\|2518... gi\|253755898, gi... - gi\|253755898\|ref\|YP_003029038.1\| RNA polymerase sigma factor RpoD [Streptococcus suis BM407], gi\|251...	177.0	[0..2]	[248..117]
gi\|254997617 - gi\|254997617\|dbj\|BAH88218.1\| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans NN2025... SIGA_STRMU - RNA polymerase sigma factor SigA OS=Streptococcus mutans serotype c (strain ATCC 700610 / UA159) GN=... RPOD_STRMU - RNA polymerase sigma factor rpoD OS=Streptococcus mutans GN=rpoD PE=3 SV=1	177.0	[0..2]	[250..116]

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Predicted Domain #1

Region A:
Residues: [1-250]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNCMLKAYEQ EAQRSVAQTR DELIVNHLPL VKFLVGRIAS QLPPHLDQED LMSAAIIGLI  60
   61 TAAERFDPTR GVQFKTFAEQ RIRGTIIDEL RSQDWLTRSL RDKFKKLEKE FVLLEHQLGR 120
  121 NPTSEEVATA LKMSVDEYYQ MLEEIHLLSF VSLDESWEDD DGSPFGLLDI LADTSIENPQ 180
  181 SQLMARQMLD SLTESIESLP EKERLVITLY YYEELNLKEI GAVLELSESR ISQLHSQAIV 240
  241 RLRAKMKNMR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.69897
Match:	1rp3A
Description:	Cocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription initiation factor activity	5.71806750193815	bayes_pls_golite062009
sigma factor activity	5.58029806879061	bayes_pls_golite062009
transcription regulator activity	3.67872017549582	bayes_pls_golite062009
binding	0.503184853376433	bayes_pls_golite062009

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: