YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29136458, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	514 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|29136458, gi|....

Description	E-value	Query Range	Subject Range
gi\|167992687, gi... - gi\|205329100\|gb\|EDZ15864.1\| transcriptional activator CadC [Salmonella enterica subsp. enterica sero... gi\|168243346, gi... - gi\|205337683\|gb\|EDZ24447.1\| transcriptional activator CadC [Salmonella enterica subsp. enterica sero... gi\|205325245, gi... - gi\|205325245\|gb\|EDZ13084.1\| transcriptional activator CadC [Salmonella enterica subsp. enterica sero... lcl\|NC_016856.1_... - [gene=cadC] [protein=DNA-binding transcriptional activator CadC] [protein_id=YP_005238663.1] [locati... gi\|16421103, gi\|... - gi\|16765877\|ref\|NP_461492.1\| DNA-binding transcriptional activator CadC [Salmonella typhimurium LT2]... gi\|207857965, gi... - gi\|207857965\|ref\|YP_002244616.1\| DNA-binding transcriptional activator CadC [Salmonella enterica sub... gi\|194444192, gi... - gi\|194444192\|ref\|YP_002041820.1\| transcriptional activator CadC [Salmonella enterica subsp. enterica... gi\|194407346, gi... - gi\|194449042\|ref\|YP_002046619.1\| DNA-binding transcriptional activator CadC [Salmonella enterica sub...	0.0	[1..514]	[1..514]
gi\|62181122, gi\|... - gi\|62181122\|ref\|YP_217539.1\| DNA-binding transcriptional activator CadC [Salmonella enterica subsp. ...	0.0	[1..514]	[1..514]
gi\|13958023\|gb\|A... - lysine decarboxylase regulator CadC [Salmonella typhimurium] gi\|13958023 - gi\|13958023\|gb\|AAK50764.1\|AF360364_1 lysine decarboxylase regulator CadC [Salmonella typhimurium]	1.0E-99	[1..514]	[1..512]
gi\|85676886, gi\|... - gi\|89110855\|ref\|AP_004635.1\| DNA-binding transcriptional activator [Escherichia coli str. K-12 subst... EG10133 - cadBA operon transcriptional activator / Transcriptional activator for cadBA, low external pH-, low ... EG10133 - cadBA operon transcriptional activator / Transcriptional activator for cadBA, low external pH-, low ... gi\|170083583, gi... - gi\|170083583\|ref\|YP_001732903.1\| DNA-binding transcriptional activator [Escherichia coli str. K-12 s... gi\|170021869, gi... - gi\|170021869\|ref\|YP_001726823.1\| DNA-binding transcriptional activator CadC [Escherichia coli ATCC 8... gi\|226840251, gi... - gi\|254037145\|ref\|ZP_04871222.1\| transcriptional activator cadC [Escherichia sp. 1_1_43], gi\|22684025... gi\|238860884, gi... - gi\|238903242\|ref\|YP_002929038.1\| DNA-binding transcriptional activator [Escherichia coli BW2952], gi... CADC_ECOLI - Transcriptional activator cadC - Escherichia coli	9.0E-89	[1..514]	[1..512]
gi\|209750582, gi... - pir\|\|A86109 transcription activator of cad operon [imported] - Escherichia coli (strain O157:H7, sub... gi\|15804726, gi\|... - gi\|15804726\|ref\|NP_290767.1\| DNA-binding transcriptional activator CadC [Escherichia coli O157:H7 ED... gi\|13364592, gi\|... - gi\|15834369\|ref\|NP_313142.1\| DNA-binding transcriptional activator CadC [Escherichia coli O157:H7 st... gi\|13364592, gi\|... - gi\|15834369\|ref\|NP_313142.1\| transcriptional activator of cad operon [Escherichia coli O157:H7], gi\|... gi\|208812292, gi... - gi\|208812292\|ref\|ZP_03253621.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4045... gi\|208738833, gi... - gi\|208818710\|ref\|ZP_03259030.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4042... gi\|209398414, gi... - gi\|209398414\|ref\|YP_002273680.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC411... gi\|217326511, gi... - gi\|217326511\|ref\|ZP_03442595.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. TW1458... gi\|189374930, gi... - gi\|189374930\|gb\|EDU93346.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC869], gi... gi\|194437159, gi... - gi\|194437159\|ref\|ZP_03069257.1\| transcriptional activator CadC [Escherichia coli 101-1], gi\|19442371... gi\|251787387, gi... - gi\|251787387\|ref\|YP_003001691.1\| hypothetical protein B21_03966 [Escherichia coli BL21], gi\|24237966... gi\|195935923 - gi\|195935923\|ref\|ZP_03081305.1\| DNA-binding transcriptional activator CadC [Escherichia coli O157:H7... gi\|208805930, gi... - gi\|208805930\|ref\|ZP_03248267.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4206... gi\|168760997, gi... - gi\|189368516\|gb\|EDU86932.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4501], g... gi\|254796156, gi... - gi\|254796156\|ref\|YP_003080993.1\| DNA-binding transcriptional activator [Escherichia coli O157:H7 str... gi\|168766407, gi... - gi\|189364169\|gb\|EDU82588.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4486], g... gi\|168774506, gi... - gi\|187769835\|gb\|EDU33679.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4196], g... gi\|253980123, gi... - gi\|254290816\|ref\|YP_003056564.1\| DNA-binding transcriptional activator [Escherichia coli BL21(DE3)],... gi\|189001675, gi... - gi\|189001675\|gb\|EDU70661.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4076], g... gi\|254164066, gi... - gi\|254164066\|ref\|YP_003047174.1\| DNA-binding transcriptional activator [Escherichia coli B str. REL6... gi\|168748007, gi... - gi\|188017570\|gb\|EDU55692.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4113], g... gi\|168755317, gi... - gi\|189357424\|gb\|EDU75843.1\| transcriptional activator CadC [Escherichia coli O157:H7 str. EC4401], g...	1.0E-88	[1..514]	[1..512]
gi\|18265910 - gi\|18265910\|gb\|AAL67383.1\|AF447814_51 transcriptional activator [Escherichia coli] gi\|26111382, gi\|... - gi\|26250950\|ref\|NP_756990.1\| DNA-binding transcriptional activator CadC [Escherichia coli CFT073], g...	2.0E-88	[1..514]	[1..512]
gi\|227886825, gi... - gi\|227886825\|ref\|ZP_04004630.1\| DNA-binding transcriptional activator CadC [Escherichia coli 83972],... gi\|191173374, gi... - gi\|191173374\|ref\|ZP_03034903.1\| transcriptional activator CadC [Escherichia coli F11], gi\|190906350\|... gi\|226901636, gi... - gi\|237703724\|ref\|ZP_04534205.1\| transcriptional activator CadC [Escherichia sp. 3_2_53FAA], gi\|22690... gi\|115515542, gi... - gi\|117626418\|ref\|YP_859741.1\| DNA-binding transcriptional activator CadC [Escherichia coli APEC O1],... gi\|218367990, gi... - gi\|218561221\|ref\|YP_002394134.1\| DNA-binding transcriptional activator CadC [Escherichia coli S88], ...	3.0E-88	[1..514]	[1..512]
gi\|110346084, gi... - gi\|110644492\|ref\|YP_672222.1\| DNA-binding transcriptional activator CadC [Escherichia coli 536], gi\|...	3.0E-88	[1..514]	[1..512]
gi\|91213683, gi\|... - gi\|91213683\|ref\|YP_543669.1\| DNA-binding transcriptional activator CadC [Escherichia coli UTI89], gi...	4.0E-88	[1..514]	[1..512]
gi\|33358316 - gi\|33358316\|gb\|AAQ16629.1\| CadC [Escherichia coli]	5.0E-88	[1..514]	[1..512]

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Predicted Domain #1

Region A:
Residues: [1-103]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQQPVVRIGE WLVTPSVNQI SRQGRQITLE PRLIDLLMYF AHHPDEVLSR DNIIDHVWMR  60
   61 TIVTNHVVTQ SISELRKSLR DGGDSNAEYI VTVPKRGYKL TAP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	29.0
Match:	2oqrA
Description:	No description for 2oqrA was found.

Predicted Domain #2

Region A:
Residues: [104-197]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VIWCEENSDE IDNLSTSPPP PIAATNAEPT EGVPAAAPVP PASLQTPTKK AKKPRIAAFW  60
   61 TWVMFLLSLA TLVVFIVMSV VDHNAAVTKT RLLL

[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	0.819	g.41.5	Rubredoxin-like
View	Download	0.721	g.41.5	Rubredoxin-like
View	Download	0.663	g.37.1	C2H2 and C2HC zinc fingers
View	Download	0.635	g.15.1	Ovomucoid/PCI-1 like inhibitors
View	Download	0.631	d.10.1	DNA-binding domain

Predicted Domain #3

Region A:
Residues: [198-514]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NPRDIDVRFE GGNSCNNWVS QESYAIGLGG LITDLLNTYS TFMVHDKTNY RVNEPSNSGK  60
   61 TLTIQFVNQR HYRAQQCFMS VVLIDNADGS TMLDKRYFVT NTNQLSIQDD LFNSLSFVLT 120
  121 QPWPNRMREQ LALFRTPQNT ALMRFYEARQ LILSGDAQAL SKAGDILNGI IKETPDFNYA 180
  181 YEYKVLVDVL RQSQQPFDKE QVAALNEEFK KIDQIPGVEK TSVYYKIKTV DLLGKGDIDA 240
  241 AYEEINKSIE LEMSWFNYVL LGKVYEMKGE NRLAADAYLT AFNLRPGENT LYWIENGVFQ 300
  301 TSVQKIVPYL NSFLAED

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.69897
Match:	1w3bA
Description:	The superhelical TPR domain of O-linked GlcNAc transferase reveals structural similarities to importin alpha.
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	1.38012107359817	bayes_pls_golite062009
protein binding	0.90942498397011	bayes_pls_golite062009
transcription regulator activity	0.802322336220332	bayes_pls_golite062009
nucleic acid binding	0.41617031570549	bayes_pls_golite062009
DNA binding	0.29647638972446	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: