YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29143472, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	660 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|29143472, gi|....

Description	E-value	Query Range	Subject Range
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...	0.0	[1..660]	[1..660]
gi\|62181728, gi\|... - gi\|62181728\|ref\|YP_218145.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	0.0	[1..660]	[1..658]
gi\|238719206, gi... - gi\|77962309\|ref\|ZP_00826131.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	0.0	[28..660]	[5..634]
gi\|77959510 - gi\|77959510\|ref\|ZP_00823529.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	0.0	[28..660]	[5..634]
gi\|45437587, gi\|... - gi\|45442721\|ref\|NP_994260.1\| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus str. ...	0.0	[28..660]	[2..631]
gi\|77977904 - gi\|77977904\|ref\|ZP_00833342.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	0.0	[28..660]	[5..634]
gi\|77974118 - gi\|77974118\|ref\|ZP_00829660.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	0.0	[28..660]	[5..634]
gi\|21960500, gi\|... - gi\|22127411\|ref\|NP_670834.1\| RNA polymerase sigma factor RpoD [Yersinia pestis KIM], gi\|21960500\|gb\|...	0.0	[28..660]	[3..632]
gi\|33519536, gi\|... - gi\|33519536\|ref\|NP_878368.1\| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus], gi\|...	0.0	[46..660]	[1..616]
RPOD_SALTY - RNA polymerase sigma factor rpoD OS=Salmonella typhimurium GN=rpoD PE=3 SV=1 RPOD_SALTI - RNA polymerase sigma factor rpoD OS=Salmonella typhi GN=rpoD PE=3 SV=1 RPOD_SALTY - RNA polymerase sigma factor RpoD OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=... gi\|168262827, gi... - gi\|205348629\|gb\|EDZ35260.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|168243042, gi... - gi\|205337819\|gb\|EDZ24583.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|197289083, gi... - gi\|197289083\|gb\|EDY28452.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|205331247, gi... - gi\|205331247\|gb\|EDZ18011.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|238910014 - gi\|238910014\|ref\|ZP_04653851.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|194472915, gi... - gi\|194472915\|ref\|ZP_03078899.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|194451693, gi... - gi\|194451693\|ref\|YP_002047209.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|194445988, gi... - gi\|194445988\|ref\|YP_002042478.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|168463576, gi... - gi\|195633147\|gb\|EDX51561.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|167551873, gi... - gi\|205323318\|gb\|EDZ11157.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|161616204, gi... - gi\|161616204\|ref\|YP_001590169.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|213865054 - gi\|213865054\|ref\|ZP_03387173.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|213646106 - gi\|213646106\|ref\|ZP_03376159.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|213586893 - gi\|213586893\|ref\|ZP_03368719.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... RPOD_SALTI - RNA polymerase sigma factor RpoD OS=Salmonella typhi GN=rpoD PE=3 SV=1 gi\|198242489, gi... - gi\|198242489\|ref\|YP_002217192.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... RPOD_SALTY - RNA polymerase sigma factor rpoD OS=Salmonella typhimurium GN=rpoD PE=3 SV=1 gi\|197264102, gi... - gi\|197264102\|ref\|ZP_03164176.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|197215575, gi... - gi\|197251872\|ref\|YP_002148141.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|194736124, gi... - gi\|194736124\|ref\|YP_002116168.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|213425630 - gi\|213425630\|ref\|ZP_03358380.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|207858469, gi... - gi\|207858469\|ref\|YP_002245120.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|204322416, gi... - gi\|204928094\|ref\|ZP_03219294.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|200389116, gi... - gi\|200389116\|ref\|ZP_03215728.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric...	0.0	[46..660]	[1..615]

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Predicted Domain #1

Region A:
Residues: [1-156]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPHIVREAPD SRSERQRPKY KYALALNVDS YTVDTNQTNK CGYRLMEQNP QSQLKLLVTR  60
   61 GKEQGYLTYA EVNDHLPEDI VDSDQIEDII QMINDMGIQV MEEAPDADDL LLAENTTSTD 120
  121 EDAEEAAAQV LSSVESEIGR TTDPVRMYMR EMGTVE

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.88
Match:	1l9zH
Description:	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [157-255]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LLTREGEIDI AKRIEDGINQ VQCSVAEYPE AITYLLEQYD RVEAEEARLS DLITGFVDPN  60
   61 AEEEMAPTAT HVGSELSQED LDDDEDEDEE DGDDDAADD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	62.69897
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: [256-660]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DNSIDPELAR EKFAELRAQY VVTRDTIKAK GRSHAAAQEE ILKLSEVFKQ FRLVPKQFDY  60
   61 LVNSMRVMMD RVRTQERLIM KLCVEQCKMP KKNFITLFTG NETSETWFNA AIAMNKPWSE 120
  121 KLHDVAEEVQ RCLQKLRQIE EETGLTIEQV KDINRRMSIG EAKARRAKKE MVEANLRLVI 180
  181 SIAKKYTNRG LQFLDLIQEG NIGLMKAVDK FEYRRGYKFS TYATWWIRQA ITRSIADQAR 240
  241 TIRIPVHMIE TINKLNRISR QMLQEMGREP TPEELAERML MPEDKIRKVL KIAKEPISME 300
  301 TPIGDDEDSH LGDFIEDTTL ELPLDSATTE SLRAATHDVL AGLTAREAKV LRMRFGIDMN 360
  361 TDHTLEEVGK QFDVTRERIR QIEAKALRKL RHPSRSEVLR SFLDD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	61.522879
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