YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29387053, gi\|...
Organism:	Mus musculus
Length:	243 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|29387053, gi|....

Description	E-value	Query Range	Subject Range
VAPB_MOUSE - Vesicle-associated membrane protein-associated protein B OS=Mus musculus GN=Vapb PE=1 SV=3	279.0	[0..1]	[243..1]
VAPB_BOVIN - Vesicle-associated membrane protein-associated protein B OS=Bos taurus GN=VAPB PE=2 SV=1	272.0	[0..1]	[243..1]
gi\|73992635 - gi\|73992635\|ref\|XP_534466.2\| PREDICTED: similar to Vesicle-associated membrane protein-associated pr...	272.0	[0..1]	[243..1]
VAPB_RAT - Vesicle-associated membrane protein-associated protein B OS=Rattus norvegicus GN=Vapb PE=1 SV=3	271.0	[0..1]	[243..1]
gi\|109091456 - gi\|109091456\|ref\|XP_001085676.1\| PREDICTED: VAMP (vesicle-associated membrane protein)-associated pr...	265.0	[0..1]	[243..1]
gi\|109091460, gi... - gi\|109091460\|ref\|XP_001085791.1\| PREDICTED: VAMP (vesicle-associated membrane protein)-associated pr... CCDS33498.1_1 - null gi\|60655589, gi\|... - gi\|60655589\|gb\|AAX32358.1\| VAMP-associated protein B and C [synthetic construct], gi\|60655587\|gb\|AAX... gi\|90080367 - gi\|90080367\|dbj\|BAE89665.1\| unnamed protein product [Macaca fascicularis] gi\|114682798, gi... - gi\|114682798\|ref\|XP_001135464.1\| PREDICTED: VAMP-associated protein B/C isoform 3 [Pan troglodytes],... VAPB - VAMP (vesicle-associated membrane protein)-associated protein B and C	265.0	[0..1]	[243..1]
gi\|57529406, gi\|... - gi\|57529406\|ref\|NP_001006296.1\| VAMP (vesicle-associated membrane protein)-associated protein B and ...	252.0	[0..1]	[243..1]

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Predicted Domain #1

Region A:
Residues: [1-127]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAKVEQVLSL EPQHELKFRG PFTDVVTTNL KLGNPTDRNV CFKVKTTAPR RYCVRPNSGV  60
   61 IDAGASLNVS VMLQPFDYDP NEKSKHKFMV QSMFAPPDTS DMEAVWKEAK PEDLMDSKLR 120
  121 CVFELPA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.0
Match:	2criA
Description:	Solution structure of the MSP domain of mouse VAMP-associated proteinA
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [128-243]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ENAKPHDVEI NKIIPTSASK TEAPAAAKSL TSPLDDTEVK KVMEECRRLQ GEVQRLREES  60
   61 RQLKEEDGLR VRKAMPSNSP VAALAATGKE EGLSARLLAL VVLFFIVGVI IGKIAL

[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.

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