YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29140366, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Length:	657 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|29140366, gi|....

Description	E-value	Query Range	Subject Range
gi\|197365143, gi... - gi\|197365143\|ref\|YP_002144780.1\| putative BglB-family transcriptional antiterminator [Salmonella ent... gi\|56130477, gi\|... - gi\|56416220\|ref\|YP_153295.1\| BglB family transcriptional antiterminator [Salmonella enterica subsp. ...	0.0	[1..657]	[1..657]
gi\|167991230, gi... - gi\|205330279\|gb\|EDZ17043.1\| HTH domain protein [Salmonella enterica subsp. enterica serovar 4,[5],12... lcl\|NC_016856.1_... - [gene=STM14_5339] [protein=phosphotransferase system mannitol/fructose-specific IIA component] [prot... gi\|16767694, gi\|... - gi\|16767694\|ref\|NP_463309.1\| phosphotransferase system mannitol/fructose-specific IIA component [Sal...	0.0	[21..657]	[1..637]
gi\|62130506, gi\|... - gi\|62182873\|ref\|YP_219290.1\| phosphotransferase system mannitol/fructose-specific IIA component [Sal...	0.0	[34..636]	[1..603]
LICR_BACSU - Probable licABCH operon regulator OS=Bacillus subtilis (strain 168) GN=licR PE=1 SV=1 LICR_BACSU - Probable licABCH operon regulator OS=Bacillus subtilis GN=licR PE=1 SV=1 gi\|221321064 - gi\|221321064\|ref\|ZP_03602358.1\| transcriptional regulator [Bacillus subtilis subsp. subtilis str. JH... gi\|221316153 - gi\|221316153\|ref\|ZP_03597958.1\| transcriptional regulator [Bacillus subtilis subsp. subtilis str. NC... gi\|221325349 - gi\|221325349\|ref\|ZP_03606643.1\| transcriptional regulator [Bacillus subtilis subsp. subtilis str. SM...	3.0E-96	[22..654]	[1..639]
gi\|238726972, gi... - gi\|77978723\|ref\|ZP_00834148.1\| COG3711: Transcriptional antiterminator [Yersinia intermedia ATCC 299...	5.0E-95	[35..656]	[5..631]
gi\|77973428 - gi\|77973428\|ref\|ZP_00828976.1\| COG3711: Transcriptional antiterminator [Yersinia frederiksenii ATCC ...	4.0E-94	[35..656]	[5..631]
gi\|52787767, gi\|... - gi\|52787767\|ref\|YP_093596.1\| LicR [Bacillus licheniformis ATCC 14580], gi\|52350269\|gb\|AAU42903.1\| Li...	2.0E-93	[22..652]	[1..640]
gi\|77959963 - gi\|77959963\|ref\|ZP_00823872.1\| COG3711: Transcriptional antiterminator [Yersinia mollaretii ATCC 439...	4.0E-93	[35..656]	[5..631]
gi\|77958824 - gi\|77958824\|ref\|ZP_00822851.1\| COG3711: Transcriptional antiterminator [Yersinia bercovieri ATCC 439...	2.0E-92	[35..656]	[5..631]
gi\|254938021 - gi\|254938021\|ref\|ZP_05269718.1\| hypothetical protein LmonF6_12874 [Listeria monocytogenes F6900] gi\|126942179, gi... - gi\|254900651\|ref\|ZP_05260575.1\| hypothetical protein LmonJ_12584 [Listeria monocytogenes J0161], gi\|... gi\|127766638, gi... - gi\|254913648\|ref\|ZP_05263660.1\| hypothetical protein LmonJ2_12654 [Listeria monocytogenes J2818], gi... gi\|47015053, gi\|... - gi\|47096593\|ref\|ZP_00234182.1\| PRD/PTS system IIA 2 domain protein [Listeria monocytogenes str. 1/2a...	2.0E-91	[22..656]	[3..643]

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Predicted Domain #1

Region A:
Residues: [1-193]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MCVSYSLSSG RVSANHEERD VRFPNQRLAQ LFAMLQNETL PQDELAQRLS VSTRTVRADI  60
   61 AALNMLLTPH GAQFTLSRGN GYQLKIDDPA RYQSLQTQQS PTLARGPRTS QERIHYLLAR 120
  121 FLTSAFSLKL EDLADEWFVS RATLQNDMAD VREHLLRYHL TLETRPRHGM KLFGGEMAIR 180
  181 ACLTDLLWTL VQQ

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.21
Match:	1z05A
Description:	Crystal structure of the ROK family transcriptional regulator, homolog of E.coli MLC protein.
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	0.767809642840856	bayes_pls_golite062009
catalytic activity	0.678979500792059	bayes_pls_golite062009
transcription regulator activity	0.559234574371335	bayes_pls_golite062009
sequence-specific DNA binding	0.266645609122554	bayes_pls_golite062009
nucleic acid binding	0.265833800805762	bayes_pls_golite062009
transcription repressor activity	0.259857063944388	bayes_pls_golite062009
protein binding	0.190636486069194	bayes_pls_golite062009
DNA binding	0.0724048374846005	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [194-416]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPSHPLIVST TLNTEVSQRL QSLLPDIFSH CQIRLTDEGE LFLRLYCAVA VRRIREGYPL  60
   61 SECVAEEVDE KVRHAAHEIA ELLQQLADKP LSEPEVSWLK VHIAARQVQE IAPSAINADD 120
  121 EEALVHYILN FINTQYNYNL LNDKQLHADL LTHIKTMITR VRYQIMIPNP LLENIKQHYP 180
  181 MAWDMTLAAI SSWGKYTPYT ISENEIGFLV LHIGVGLERS YNI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	31.30103
Match:	1tlvA
Description:	Structure of the native and inactive LicT PRD from B. subtilis
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	2.56369131794526	bayes_pls_golite062009
transcription antiterminator activity	1.04498481068613	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [417-508]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GYQRQPQVLL VCDAGNAMVR MIEAVLARKY PQIEIARTLT LRDYEARDSM VEDFVISTAR  60
   61 IGEKDKPVIM IAPFPTDYQL EQIGKLVLVD RT

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	3.42
Match:	1tvmA
Description:	NMR structure of enzyme GatB of the galactitol-specific phosphoenolpyruvate-dependent phosphotransferase system
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [509-657]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RPWMLDKYFD ASHFRIVEGE INQQTLFKTL CDQLHEEGFV DAAFLDSVIE REAIVSTLLG  60
   61 DGIALPHALG LLAKKTVVYT VLAPQGIAWG DETAHVIFLL AISKSEYEEA MAIYDIFVTF 120
  121 LRERAMTRLC ACQNFTQFKT VAMECVSRF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	26.154902
Match:	1a3aA
Description:	Phosphotransferase IIa-mannitol
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	0.789390286938302	bayes_pls_golite062009
catalytic activity	0.547925219495929	bayes_pls_golite062009
binding	0.396676636991646	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:

Predicted functions:

Predicted functions: