YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24348818, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	1145 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|24348818, gi|....

Description	E-value	Query Range	Subject Range
gi\|152987761, gi... - gi\|94412802\|ref\|ZP_01292705.1\| hypothetical protein PaerP_01005415 [Pseudomonas aeruginosa PA7], gi\|...	573.0	[0..1]	[1142..1]
gi\|107102802 - gi\|107102802\|ref\|ZP_01366720.1\| hypothetical protein PaerPA_01003870 [Pseudomonas aeruginosa PACS2] gi\|218770759, gi... - gi\|218890536\|ref\|YP_002439400.1\| putative two-component sensor [Pseudomonas aeruginosa LESB58], gi\|2... gi\|46164135, gi\|... - gi\|46164135\|ref\|ZP_00204983.1\| COG0591: Na+/proline symporter [Pseudomonas aeruginosa UCBPP-PA14], g...	573.0	[0..1]	[1142..1]
gi\|11352377 - pir\|\|E83237 probable two-component sensor PA3271 [imported] - Pseudomonas aeruginosa (strain PAO1) gi\|15598467, gi\|... - gi\|9949396\|gb\|AAG06659.1\|AE004749_8 probable two-component sensor [Pseudomonas aeruginosa PAO1], gi\|...	573.0	[0..1]	[1142..1]
gi\|194547219, gi... - gi\|84319851\|ref\|ZP_00968238.1\| COG0591: Na+/proline symporter [Pseudomonas aeruginosa C3719], gi\|254...	571.0	[0..1]	[1142..1]
gi\|67155128, gi\|... - gi\|67155128\|ref\|ZP_00416756.1\| Response regulator receiver:ATP-binding region, ATPase-like:Histidine... gi\|67155128, gi\|... - gi\|67155128\|ref\|ZP_00416756.1\| Response regulator receiver:ATP-binding region, ATPase-like:Histidine...	566.0	[0..1]	[1142..1]
gi\|68346058, gi\|... - gi\|70731759\|ref\|YP_261501.1\| sensory box histidine kinase/response regulator [Pseudomonas fluorescen...	562.0	[0..1]	[1142..1]
gi\|48728471, gi\|... - gi\|77457887\|ref\|YP_347392.1\| periplasmic sensor hybrid histidine kinase [Pseudomonas fluorescens Pf0...	559.0	[0..1]	[1142..1]
gi\|28871052, gi\|... - gi\|28871052\|ref\|NP_793671.1\| sensory box histidine kinase/response regulator [Pseudomonas syringae p... tr\|Q87YA1\|Q87YA1... - Sensory box histidine kinase/response regulator OS=Pseudomonas syringae pv. tomato (strain DC3000) G...	556.0	[0..1]	[1142..1]
gi\|63255537, gi\|... - gi\|66044830\|ref\|YP_234671.1\| response regulator receiver:ATP-binding region, ATPase-like:histidine k...	556.0	[0..1]	[1142..1]
gi\|95109576 - gi\|95109576\|emb\|CAK14277.1\| putative sensory box histidine kinase/response regulator hybrid [Pseudom... gi\|95109576, gi\|... - gi\|95109576\|emb\|CAK14277.1\| putative sensory box histidine kinase/response regulator hybrid [Pseudom...	554.0	[0..1]	[1142..1]

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Predicted Domain #1

Region A:
Residues: [1-176]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNLTLVVAVI AICYVSLLFL LAWGAERWFS GVTKKLQVVI YGLSLAVYCS SWSFLGTVGQ  60
   61 SAKDFWSFIP IFVGPILIFT LGFGMLRKMV LVSKAQNITS VADFIAARYG KSQTLAAIVT 120
  121 LIAMFGIMPY IALQLKAMVF SLNLFQPADD PLNGVTIALL ITALLAIFAI LFGTRK

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [177-360]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LDATEHNPGM MLAIAFESLV KLAAFLLVGI VISFGVFDGF GDIWQQASDK SLIHHPNPRI  60
   61 ETLMPELLVG MAAFLCMPRQ FHVMVVECAD ESVLSKGRWL FPLYLALFGL FVGPLALAGK 120
  121 LILGDSVAAD TYVINLPLAL DHPLLAVIAL LGTLSAATGM VIVAVVTISV MVSNEWLVPV 180
  181 VLRT

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [361-465]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GNIREKNFSQ FSQMLLNARR LAIVIILGLG YGSYLALADS DSLSHLGMLS FGAFAQLAPA  60
   61 LVGGLYWKHG NRAGVFLGLS VGFSLWFYIM LSGMTGNQSP AALMS

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [466-561]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SNIDLLDAIT PNVRDALTAL FANIACYVLG SIWFRAGVAE RIQASAFVSP GKLKNNASKK  60
   61 SGPISQQDLL ILASRFVSPT RAYESFSRFS TEAVKS

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #5

Region A:
Residues: [562-755]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DSWHKAATPE LIAHTERLLA GVLGASSASL VMDSVLQGRD LALDEVFSLV DEASSKIMLS  60
   61 QDMLRGAIEH AYEGMSVIDS DLNLVAWNYK YVELYQYPEG FLQQGMPISE VIRFNAARGY 120
  121 CGSGAIEQQV EKRVQHMRNG TPHTSERQRK DGKVIKIQGN PMPDGGFVMT FTDITQYRQQ 180
  181 ERALLEANET LESR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.154902
Match:	1d06A
Description:	Histidine kinase FixL heme domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ion transmembrane transporter activity	3.69867247360436	bayes_pls_golite062009
cation transmembrane transporter activity	3.34503630083118	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	3.33645564261978	bayes_pls_golite062009
metal ion transmembrane transporter activity	2.99554083986799	bayes_pls_golite062009
voltage-gated cation channel activity	2.93659587419536	bayes_pls_golite062009
voltage-gated ion channel activity	2.92160783463114	bayes_pls_golite062009
voltage-gated channel activity	2.91342394807702	bayes_pls_golite062009
voltage-gated potassium channel activity	2.90751147392211	bayes_pls_golite062009
potassium channel activity	2.89031641462295	bayes_pls_golite062009
cation channel activity	2.78342406299841	bayes_pls_golite062009
ion channel activity	2.75684553022783	bayes_pls_golite062009
gated channel activity	2.70149874833471	bayes_pls_golite062009
substrate-specific channel activity	2.65172440531618	bayes_pls_golite062009
passive transmembrane transporter activity	2.65059750992297	bayes_pls_golite062009
channel activity	2.65059750992297	bayes_pls_golite062009
binding	2.49204215574815	bayes_pls_golite062009
transporter activity	1.90984485953892	bayes_pls_golite062009
transmembrane transporter activity	1.79183331267186	bayes_pls_golite062009
molecular transducer activity	1.75430109151481	bayes_pls_golite062009
signal transducer activity	1.75430109151481	bayes_pls_golite062009
protein binding	1.73179783495389	bayes_pls_golite062009
substrate-specific transporter activity	1.49360338620162	bayes_pls_golite062009
DNA binding	1.20377980878212	bayes_pls_golite062009
nucleic acid binding	1.06245381658836	bayes_pls_golite062009
two-component response regulator activity	0.840018959681963	bayes_pls_golite062009
transcription factor activity	0.709293174791556	bayes_pls_golite062009
protein heterodimerization activity	0.511943063452644	bayes_pls_golite062009
transcription factor binding	0.484038243106157	bayes_pls_golite062009
receptor binding	0.46842316980276	bayes_pls_golite062009
protein dimerization activity	0.456885330585442	bayes_pls_golite062009
inward rectifier potassium channel activity	0.388335970048431	bayes_pls_golite062009
ligand-gated ion channel activity	0.3429235361445	bayes_pls_golite062009
ligand-gated channel activity	0.3429235361445	bayes_pls_golite062009
protein kinase activity	0.293236516800064	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.169353506810019	bayes_pls_golite062009
kinase activity	0.110903778398436	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.0645871948870329	bayes_pls_golite062009
receptor activity	0.0276617751945334	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.0029357667432216	bayes_pls_golite062009

Predicted Domain #6

Region A:
Residues: [756-1009]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VKERTFELAM LNSELLEAKA QEEMANASKS RFLAAVGHDL MQPLNAARLF TASLSQYPNL  60
   61 DREARTTLSH VNSSLKTAGE LLTDLLDISK LDSGMVDVNR RDFAISELLN GLSVEFEAMA 120
  121 ADNQIRFKMI PCSATVNSDP SLLRRVLQNF LTNAYRYARG GRVLFGCRHR GSELEIQVLD 180
  181 TGCGIDEHET HEIFKEFKRL NNPRSKSVSG LGLGLAIADR ISRVLNHGIQ VSSQLGRGSV 240
  241 FSITVPLGET VRQP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	46.154902
Match:	2c2aA
Description:	Structure of the entire cytoplasmic portion of a sensor histidine kinase protein
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [1010-1145]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QVKALPSLLQ PLSGIKVLCI DNEEAILAGL ESLLSRWQCE VICAKDLADA RIKLGLKGVA  60
   61 PDIVLADFHL DDGQNGVDAM DGIRSLYGKD LPGILITANT RKELVEDVQR RGYHYMAKMI 120
  121 KPAALRALIS SLVKKA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.69897
Match:	1mvoA
Description:	PhoP receiver domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
two-component response regulator activity	6.41182973389827	bayes_pls_golite062009
signal transducer activity	5.8299268563449	bayes_pls_golite062009
molecular transducer activity	5.8299268563449	bayes_pls_golite062009
transcription regulator activity	2.23448171655589	bayes_pls_golite062009
binding	1.92400975854452	bayes_pls_golite062009
protein histidine kinase activity	1.60632989169905	bayes_pls_golite062009
two-component sensor activity	1.58303578136745	bayes_pls_golite062009
DNA binding	1.58172125522651	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	1.45748315828993	bayes_pls_golite062009
nucleic acid binding	1.43938837585555	bayes_pls_golite062009
protein kinase activity	1.37509495611612	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	1.08466995707718	bayes_pls_golite062009
transcription factor activity	0.970571914515176	bayes_pls_golite062009
kinase activity	0.9339032594202	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.642205665485028	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: