YRC Public Data Repository - Protein Structure Prediction

Protein:	VBA4_YEAST
Organism:	Saccharomyces cerevisiae S288c
Length:	768 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 VBA4_YEAST.

Description	E-value	Query Range	Subject Range
VBA4 - Protein of unknown function with proposed role as a basic amino acid permease based on phylogeny; GF... VBA4_YEAST - Vacuolar basic amino acid transporter 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=...	0.0	[1..768]	[1..768]
gi\|15927932, gi\|... - gi\|15927932\|ref\|NP_375465.1\| hypothetical protein SA2142 [Staphylococcus aureus subsp. aureus N315],... gi\|253314692 - gi\|253314692\|ref\|ZP_04837905.1\| hypothetical protein SauraC_00665 [Staphylococcus aureus subsp. aure... gi\|12003106, gi\|... - pir\|\|C90035 hypothetical protein SA2142 [imported] - Staphylococcus aureus (strain N315), gi\|120031... gi\|255007128 - gi\|255007128\|ref\|ZP_05145729.2\| hypothetical protein SauraM_11685 [Staphylococcus aureus subsp. aure... gi\|14248126, gi\|... - gi\|15925342\|ref\|NP_372876.1\| multidrug resistance protein [Staphylococcus aureus subsp. aureus Mu50]... gi\|269203983\|ref... - EmrB/QacA family drug resistance transporter [Staphylococcus aureus subsp. aureus ED98] gi\|90583610, gi\|... - gi\|90583610\|ref\|ZP_01239364.1\| Drug resistance transporter EmrB/QacA subfamily [Staphylococcus aureu... gi\|147741858, gi... - gi\|90585929\|ref\|ZP_01241634.1\| Drug resistance transporter EmrB/QacA subfamily [Staphylococcus aureu... gi\|156980667, gi... - gi\|156980667\|ref\|YP_001442926.1\| hypothetical protein SAHV_2336 [Staphylococcus aureus subsp. aureus...	2.0E-99	[144..767]	[32..634]
gi\|21225257, gi\|... - gi\|7649556\|emb\|CAB89031.1\| putative membrane transport protein. [Streptomyces coelicolor A3(2)], gi\|...	3.0E-99	[227..762]	[12..522]
gi\|19551627, gi\|... - gi\|62389280\|ref\|YP_224682.1\| major facilitator superfamily permease [Corynebacterium glutamicum ATCC...	1.0E-95	[234..764]	[29..543]
gi\|14389419 - gi\|14389419\|gb\|AAF64435.2\|AF238225_1 DHA14-like major facilitator [Botryotinia fuckeliana]	3.0E-93	[164..763]	[14..592]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	7.0E-92	[228..764]	[1..509]
gi\|16944692 - gi\|16944692\|emb\|CAC28808.2\| related to tetracycline efflux protein (otrb) [Neurospora crassa]	2.0E-91	[205..754]	[2..550]
lcl\|NC_016856.1_... - [gene=emrB] [protein=putative multidrug transport protein] [protein_id=YP_005238915.1] [location=298... gi\|16766126, gi\|... - gi\|16766126\|ref\|NP_461741.1\| putative multidrug transport protein [Salmonella typhimurium LT2], gi\|1... gi\|167992539, gi... - gi\|205329344\|gb\|EDZ16108.1\| multidrug resistance protein B [Salmonella enterica subsp. enterica sero...	3.0E-91	[242..756]	[6..500]
gi\|16761596 - gi\|16761596\|ref\|NP_457213.1\| multidrug resistance protein B [Salmonella enterica subsp. enterica ser... gi\|25306158, gi\|... - gi\|25306158\|pir\|\|AG0842 multidrug resistance protein B [imported] - Salmonella enterica subsp. enter... gi\|29138709, gi\|... - gi\|29143076\|ref\|NP_806418.1\| multidrug resistance protein B [Salmonella enterica subsp. enterica ser... gi\|213850377 - gi\|213850377\|ref\|ZP_03381275.1\| multidrug resistance protein B [Salmonella enterica subsp. enterica ... gi\|214000013 - gi\|214000013\|ref\|ZP_03410748.1\| multidrug resistance protein B [Salmonella enterica subsp. enterica ...	4.0E-91	[242..756]	[6..500]

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Predicted Domain #1

Region A:
Residues: [1-74]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGKKDRQRKK LREFAKLKNR QRNLRKSVQT LKNEVQREAK VPRTSNQIAL GNDKIEEINE  60
   61 NSPLLSAPSK QEEV

[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 #2

Region A:
Residues: [75-244]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SIPKAVDIDT IDAQPLHEGP KIDDSPQDEV NSIKGKPADK ANEDDLKPPS QHEACGNSAL  60
   61 QSSITDFSDR SVSPLQSITS CNTPMSEHEL PVSSSNSFER ADDMPVVQAD NQTSSSKSLH 120
  121 IVAPSPEVPV SGDEITSYGY GSIPQSIGDV ENGLNPPYVE NTSSDELVHD

[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 functions:

Term	Confidence	Notes
transporter activity	1.47137690164233	bayes_pls_golite062009
transmembrane transporter activity	1.05831640191854	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.04845870423152	bayes_pls_golite062009
substrate-specific transporter activity	1.01835310550526	bayes_pls_golite062009
binding	0.0875556388382674	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [245-427]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LTRRRIFSSC MCTYLFFIAM DSSIILVIAS KIASEFHELW RLSLVISAYL LSNAIGQLVF  60
   61 LKLSLISSVK LLLCIAQFSF ILGGYLSWSS AHFWTFIFAR CVTGFGGGSL IALKSTIMNR 120
  121 FSQKNDSRYS LSASMITFAM GVVIGPFMMN LFDSSHGSGW RNAFLIPVPF CLVNASIMLA 180
  181 DMY

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [509-632]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNSVISMSLQ GDKRLIWTMI GISFCFAALM CIIPFGTTYF IIVLNLSTLQ LAERLSPFFF  60
   61 SIVLGYFSVS YFWKSKGQNF LLKFVLSGAT LLLYVALMGV SLNLPVWKQY ICLSLPFLGS 120
  121 SMIL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.39794
Match:	1ja5A_
Description:	No description for 1ja5A_ was found.

Predicted Domain #4

Region A:
Residues: [428-508]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SVKSTLYGRP TPTLWKRFKN TLLSPDLYEI LTLTLFLLCF VQVTSLDLTG LKNNTMIQAL  60
   61 LFSVIIVCGI LFFLIETSDT Y

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.39794
Match:	1ja5A_
Description:	No description for 1ja5A_ was found.

Predicted Domain #5

Region A:
Residues: [633-768]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TLLSNLYHEY HEQRKSPISG SIVYCFGAVG GTVGISLGGY VFHKTLIKLM HEKVMPFSKQ  60
   61 GYLKKDLLKI IKHATESSDW VHESAPKFVF QTLIECYLQA CRNVFKLSTL FFTITVVAIF 120
  121 IFNRIHCRSQ NCLSLS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	3.30103
Match:	1kplA_
Description:	Clc chloride channel
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

Predicted functions: