YRC Public Data Repository - Protein Structure Prediction

Protein:	VAM3
Organism:	Saccharomyces cerevisiae
Length:	283 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 VAM3.

Description	E-value	Query Range	Subject Range
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	3.0E-46	[34..281]	[1..254]
gi\|3123708, gi\|9... - gi\|9625039\|ref\|NP_062506.1\| syntaxin 1B1 [Mus musculus], gi\|3123708\|dbj\|BAA25986.1\| syntaxin1B [Mus ...	3.0E-45	[1..281]	[1..282]
STX1B_MOUSE - Syntaxin-1B OS=Mus musculus GN=Stx1b PE=1 SV=1 gi\|251471 - gi\|251471\|gb\|AAB22526.1\| syntaxin, P35B [rats, brain, Peptide, 288 aa] ENSCJAT00000005845 - null gi\|114662156 - gi\|114662156\|ref\|XP_001145497.1\| PREDICTED: similar to syntaxin B [Pan troglodytes] STX1B - syntaxin 1B STX1B_RAT - Syntaxin-1B OS=Rattus norvegicus GN=Stx1b PE=1 SV=1	4.0E-45	[6..281]	[1..282]
gi\|447739 - gi\|447739\|prf\|\|1915304A nylB upstream ORF	1.0E-44	[6..281]	[1..282]
gi\|18859443, gi\|... - gi\|7107406\|gb\|AAF36403.1\|AF229154_1 syntaxin 1B [Danio rerio], gi\|18859443\|ref\|NP_571598.1\| syntaxin...	2.0E-44	[6..281]	[1..282]
gi\|7595847, gi\|7... - gi\|7595847\|gb\|AAF64478.1\| syntaxin 1A [Macaca mulatta], gi\|74136291\|ref\|NP_001028037.1\| syntaxin 1B ...	7.0E-44	[9..281]	[6..283]

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Predicted Domain #1

Region A:
Residues: [1-121]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSFFDIEAQS SKGNSQQEPQ FSTNQKTKEL SNLIETFAEQ SRVLEKECTK IGSKRDSKEL  60
   61 RYKIETELIP NCTSVRDKIE SNILIHQNGK LSADFKNLKT KYQSLQQSYN QRKSLFPLKT 120
  121 P

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	395.30103
Match:	1hs7A_
Description:	Vam3p N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
phosphatidic acid binding	4.54790612451186	bayes_pls_golite062009
SNAP receptor activity	3.50393203740159	bayes_pls_golite062009
binding	2.18404492932496	bayes_pls_golite062009
protein binding	1.82422117934251	bayes_pls_golite062009
transporter activity	1.74189664015129	bayes_pls_golite062009
substrate-specific transporter activity	1.2360389745429	bayes_pls_golite062009
transmembrane transporter activity	1.13101548288086	bayes_pls_golite062009
protein transporter activity	0.81087535212264	bayes_pls_golite062009
SNARE binding	0.71459772253941	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.398018181744571	bayes_pls_golite062009
ion transmembrane transporter activity	0.0981818568206971	bayes_pls_golite062009
phospholipid binding	0.0172309833091902	bayes_pls_golite062009
cytoskeletal protein binding	0.00476738027966683	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [122-185]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ISPGTSKERK DIHPRTEAVR QDPESSYISI KVNEQSPLLH NEGQHQLQLQ EEQEQQQQGL  60
   61 SQEE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.616	d.9.1	Interleukin 8-like chemokines
View	Download	0.599	d.58.3	Protease propeptides/inhibitors
View	Download	0.384	d.58.17	Metal-binding domain
View	Download	0.391	d.58.10	Acylphosphatase-like
View	Download	0.462	d.58.23	Probable ACP-binding domain of malonyl-CoA ACP transacylase
View	Download	0.381	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.354	d.58.7	RNA-binding domain, RBD
View	Download	0.334	d.58.5	GlnB-like
View	Download	0.334	a.4.1	Homeodomain-like
View	Download	0.310	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.306	a.64.2	Bacteriocin AS-48
View	Download	0.288	d.186.1	Head-to-tail joining protein W, gpW
View	Download	0.287	a.64.1	Saposin
View	Download	0.271	d.88.1	SRF-like
View	Download	0.253	a.4.1	Homeodomain-like
View	Download	0.244	a.163.1	Crustacean CHH/MIH/GIH neurohormone
View	Download	0.229	a.4.1	Homeodomain-like
View	Download	0.220	a.159.1	Protein serine/threonine phosphatase 2C, C-terminal domain
View	Download	0.220	a.4.1	Homeodomain-like
View	Download	0.203	d.57.1	DNA damage-inducible protein DinI

Predicted functions:

Term	Confidence	Notes
phosphatidic acid binding	3.99289411123023	bayes_pls_golite062009
SNAP receptor activity	2.87584659156593	bayes_pls_golite062009
binding	2.10865031355861	bayes_pls_golite062009
protein binding	1.71065434412329	bayes_pls_golite062009
transporter activity	1.70608335538771	bayes_pls_golite062009
substrate-specific transporter activity	1.17569067269837	bayes_pls_golite062009
transmembrane transporter activity	1.13402377922348	bayes_pls_golite062009
protein transporter activity	0.593122950767464	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.396657939634767	bayes_pls_golite062009
SNARE binding	0.387098576112631	bayes_pls_golite062009
ion transmembrane transporter activity	0.0934422877951697	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [186-283]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LDFQTIIHQE RSQQIGRIHT AVQEVNAIFH QLGSLVKEQG EQVTTIDENI SHLHDNMQNA  60
   61 NKQLTRADQH QRDRNKCGKV TLIIIIVVCM VVLLAVLS

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	13.98
Match:	1gl2B
Description:	Syntaxin 7
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:

Predicted functions: