YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|42519241, gi\|...
Organism:	Lactobacillus johnsonii NCC 533
Length:	372 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|42519241, gi|....

Description	E-value	Query Range	Subject Range
gi\|116494985, gi... - gi\|116494985\|ref\|YP_806719.1\| RNA polymerase sigma factor RpoD [Lactobacillus casei ATCC 334], gi\|11... gi\|191638497, gi... - gi\|191638497\|ref\|YP_001987663.1\| RNA polymerase sigma factor RpoD [Lactobacillus casei BL23], gi\|190... gi\|224453634 - gi\|224453634\|ref\|ZP_03662107.1\| RNA polymerase sigma factor RpoD [Lactobacillus paracasei subsp. par... gi\|227187324, gi... - gi\|227535009\|ref\|ZP_03965058.1\| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus paraca...	310.0	[0..13]	[372..63]
gi\|227894905, gi... - gi\|227894905\|ref\|ZP_04012710.1\| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp. pla... gi\|28271441, gi\|... - gi\|28378605\|ref\|NP_785497.1\| RNA polymerase sigma factor RpoD [Lactobacillus plantarum WCFS1], gi\|28...	308.0	[0..1]	[372..1]
gi\|116514229, gi... - gi\|116514229\|ref\|YP_813135.1\| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp. bul...	308.0	[0..1]	[372..1]
gi\|104774139, gi... - gi\|104774139\|ref\|YP_619119.1\| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp. bul...	307.0	[0..1]	[372..1]
gi\|92089653, gi\|... - gi\|92089653\|ref\|ZP_01274588.1\| RNA polymerase sigma factor RpoD-like [Lactobacillus reuteri 100-23],...	307.0	[0..1]	[372..9]
gi\|89079310, gi\|... - gi\|89090874\|ref\|ZP_01163909.1\| Sigma-70 factor [Lactobacillus reuteri JCM 1112], gi\|89079310\|gb\|EAR5... gi\|227364887, gi... - gi\|227364887\|ref\|ZP_03848933.1\| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus reuter... gi\|227531077, gi... - gi\|227531077\|ref\|ZP_03961126.1\| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus reuter...	307.0	[0..1]	[372..9]
gi\|58254795, gi\|... - gi\|58337478\|ref\|YP_194063.1\| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus NCFM], gi\|5...	307.0	[0..30]	[372..14]
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]	307.0	[0..6]	[372..2]
gi\|81428494, gi\|... - gi\|81428494\|ref\|YP_395494.1\| RNA polymerase sigma factor RpoD [Lactobacillus sakei subsp. sakei 23K]...	307.0	[0..7]	[372..5]
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\|...	306.0	[0..8]	[372..4]

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Predicted Domain #1

Region A:
Residues: [1-372]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAESKTTKET TMTLDKKVKE VVKEVKKDKQ ITEKEFTAQL IKPYDLQGKA VDQLVQEFED  60
   61 NGISIVDENG EPSKLALKKQ KDVEKAELKD MSAPSSVRMN DPVRMYLKEI GRVSLLNADQ 120
  121 EIALAKRIES GDEEAKQELA EANLRLVVSI AKRYVGRGMS FLDLIQEGNM GLMKAVDKFD 180
  181 YRLGFKFSTY ATWWIRQAIT RAIADQARTI RIPVHMVETI NKLIRIQRQL LQDLGREPTP 240
  241 EEIGAEMDMP TDKVREILKI AQEPVSLETP IGEEDDSHLG DFIEDKDATS PEQHASYELL 300
  301 KEQLEEVLDT LTDREENVLR LRFGLDDGRT RTLEEVGKVF GVTRERIRQI EAKALRKLRH 360
  361 PSRSNQLKDF LD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	60.522879
Match:	1iw7F
Description:	Sigma70
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