YRC Public Data Repository - Protein Structure Prediction

Protein:	VAPB
Organism:	Homo sapiens
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 VAPB.

Description	E-value	Query Range	Subject Range
gi\|73992635 - gi\|73992635\|ref\|XP_534466.2\| PREDICTED: similar to Vesicle-associated membrane protein-associated pr...	7.0E-75	[1..243]	[1..243]
VAPB_BOVIN - Vesicle-associated membrane protein-associated protein B OS=Bos taurus GN=VAPB PE=2 SV=1	1.0E-74	[1..243]	[1..243]
gi\|29387053, gi\|... - gi\|34785640\|gb\|AAH57123.1\| Vesicle-associated membrane protein, associated protein B and C [Mus musc...	2.0E-73	[1..243]	[1..243]
gi\|109091456 - gi\|109091456\|ref\|XP_001085676.1\| PREDICTED: VAMP (vesicle-associated membrane protein)-associated pr...	3.0E-73	[1..243]	[1..243]
VAPB_RAT - Vesicle-associated membrane protein-associated protein B OS=Rattus norvegicus GN=Vapb PE=1 SV=3	1.0E-72	[1..243]	[1..243]
gi\|7677066 - gi\|7677066\|gb\|AAF67013.1\|AF160212_1 VAMP-associated 33 kDa protein [Homo sapiens]	5.0E-72	[1..243]	[1..243]
gi\|57529406, gi\|... - gi\|57529406\|ref\|NP_001006296.1\| VAMP (vesicle-associated membrane protein)-associated protein B and ...	3.0E-67	[1..243]	[1..243]

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Predicted Domain #1

Region A:
Residues: [1-153]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAKVEQVLSL EPQHELKFRG PFTDVVTTNL KLGNPTDRNV CFKVKTTAPR RYCVRPNSGI  60
   61 IDAGASINVS VMLQPFDYDP NEKSKHKFMV QSMFAPTDTS DMEAVWKEAK PEDLMDSKLR 120
  121 CVFELPAEND KPHDVEINKI ISTTASKTET PIV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	40.30103
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: [154-243]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SKSLSSSLDD TEVKKVMEEC KRLQGEVQRL REENKQFKEE DGLRMRKTVQ SNSPISALAP  60
   61 TGKEEGLSTR LLALVVLFFI VGVIIGKIAL

[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.

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