YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|225854569, gi...
Organism:	Streptococcus pneumoniae JJA
Length:	369 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|225854569, 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]	338.0	[0..2]	[369..1]
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\|...	338.0	[0..2]	[369..1]
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]	336.0	[0..2]	[369..1]
gi\|77406972, gi\|... - gi\|77406972\|ref\|ZP_00783989.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B], gi\|77...	336.0	[0..2]	[369..1]
gi\|139474032, gi... - gi\|139474032\|ref\|YP_001128748.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str. Manfr... gi\|209559154, gi... - gi\|209559154\|ref\|YP_002285626.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131], gi... gi\|13621959, gi\|... - gi\|15674827\|ref\|NP_269001.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes M1 GAS], gi\|13... gi\|50913963, gi\|... - gi\|50913963\|ref\|YP_059935.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10394], gi... gi\|94992161, gi\|... - gi\|94992161\|ref\|YP_600260.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS2096], gi\|... gi\|94541793, gi\|... - gi\|94988285\|ref\|YP_596386.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS9429], gi\|... gi\|71853195, gi\|... - gi\|71910413\|ref\|YP_281963.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS5005], gi\|... gi\|94994083, gi\|... - gi\|94994083\|ref\|YP_602181.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10750], gi... gi\|71903245, gi\|... - gi\|71903245\|ref\|YP_280048.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS6180], gi\|... gi\|94543672, gi\|... - gi\|94990164\|ref\|YP_598264.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10270], gi...	336.0	[0..2]	[369..1]
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...	335.0	[0..3]	[369..6]
gi\|19745866, gi\|... - gi\|19748016\|gb\|AAL97501.1\| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes MGAS8232...	334.0	[0..2]	[369..1]
gi\|21910055, gi\|... - gi\|21910055\|ref\|NP_664323.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS315], gi\|2... gi\|28811498, gi\|... - gi\|28896247\|ref\|NP_802597.1\| RNA polymerase sigma factor RpoD [Streptococcus pyogenes SSI-1], gi\|288...	332.0	[0..2]	[369..1]
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...	330.0	[0..2]	[368..1]
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...	330.0	[0..7]	[368..18]

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Predicted Domain #1

Region A:
Residues: [1-369]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MATKQKEVTT FDVQVAEFIR NHKQKGTATD DEINASLVIP FTLDADGIED LLQRIQDAGI  60
   61 SITDNEGNPS ARVLSNEEEP ELSDEDLIGS TSAKVNDPVR MYLKEIGVVP LLTNEEEKEL 120
  121 ALAVEAGDIE AKQRLAEANL RLVVSIAKRY VGRGMQFLDL IQEGNMGLMK AVDKFDYSKG 180
  181 FKFSTYATWW IRQAITRAIA DQARTIRIPV HMVETINKLV REQRNLLQEL GQDPTPEQIA 240
  241 ERMDMTPDKV REILKIAQEP VSLETPIGEE DDSHLGDFIE DEVIENPVDY TTRIVLREQL 300
  301 DEILDTLTDR EENVLRLRFG LDDGKMRTLE DVGKVFNVTR ERIRQIEAKA LRKLRQPSRS 360
  361 KPLRDFIED

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	61.045757
Match:	1l9uH
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