YRC Public Data Repository - Protein Structure Prediction

Protein:	VPS29
Organism:	Saccharomyces cerevisiae
Length:	282 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 VPS29.

Description	E-value	Query Range	Subject Range
VPS29_YEAST - Vacuolar protein sorting-associated protein 29 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S28... VPS29 - Endosomal protein that is a subunit of the membrane-associated retromer complex essential for endoso... gi\|151943954 - gi\|151943954\|gb\|EDN62247.1\| vacuolar sorting protein [Saccharomyces cerevisiae YJM789]	6.0E-74	[1..282]	[1..282]
gi\|14520324, gi\|... - gi\|5457539\|emb\|CAB49030.1\| Predicted phosphohydrolase, putative [Pyrococcus abyssi GE5], gi\|14520324... gi\|5457539, gi\|7... - pir\|\|G75197 lacz expression regulatory protein (icc) PAB2278 - Pyrococcus abyssi (strain Orsay), gi\|...	1.0E-45	[1..252]	[4..296]
gi\|14590054, gi\|... - gi\|3256490\|dbj\|BAA29173.1\| 505aa long hypothetical protein [Pyrococcus horikoshii OT3], gi\|14590054\|... gi\|7518470 - pir\|\|F71230 hypothetical protein PH0104 - Pyrococcus horikoshii	2.0E-45	[1..252]	[4..296]
gi\|18976460, gi\|... - gi\|18976460\|ref\|NP_577817.1\| icc related protein [Pyrococcus furiosus DSM 3638], gi\|18891999\|gb\|AAL8...	6.0E-45	[1..252]	[1..293]
gi\|76638993\|ref\|... - PREDICTED: similar to Vacuolar protein sorting 29 (Vesicle protein sorting 29) isoform 6 [Bos taurus... gi\|114646926 - gi\|114646926\|ref\|XP_001143634.1\| PREDICTED: similar to vacuolar sorting protein VPS29 isoform 2 [Pan... VPS29_MOUSE - Vacuolar protein sorting-associated protein 29 OS=Mus musculus GN=Vps29 PE=1 SV=1 gi\|73994600 - gi\|73994600\|ref\|XP_861583.1\| PREDICTED: similar to Vacuolar protein sorting 29 (Vesicle protein sort... gi\|149720676 - gi\|149720676\|ref\|XP_001495130.1\| PREDICTED: similar to vacuolar sorting protein VPS29 isoform 1 [Equ... gi\|109098718 - gi\|109098718\|ref\|XP_001107873.1\| PREDICTED: similar to Vacuolar protein sorting 29 (Vesicle protein ...	2.0E-34	[1..197]	[1..182]
gi\|7435078 - pir\|\|G72200 phosphoesterase-related protein TM1876 [similarity] - Thermotoga maritima (strain MSB8) gi\|15644619, gi\|... - gi\|4982462\|gb\|AAD36938.1\|AE001824_7 conserved hypothetical protein [Thermotoga maritima MSB8], gi\|15... gi\|214040024, gi... - gi\|254485363\|ref\|ZP_05098574.1\| phosphodiesterase, family [Marinitoga piezophila KA3], gi\|224398183\|... gi\|119827843, gi... - gi\|148270055\|ref\|YP_001244515.1\| phosphodiesterase [Thermotoga petrophila RKU-1], gi\|147735599\|gb\|AB...	2.0E-34	[1..196]	[1..226]
VPS29 - vacuolar protein sorting 29 homolog (S. cerevisiae)	2.0E-34	[1..197]	[1..182]

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Predicted Domain #1

Region A:
Residues: [1-222]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLLLALSDAH IPDRATDLPV KFKKLLSVPD KISQVALLGN STKSYDFLKF VNQISNNITI  60
   61 VRGEFDNGHL PSTKKDKASD NSRPMEEIPM NSIIRQGALK IGCCSGYTVV PKNDPLSLLA 120
  121 LARQLDVDIL LWGGTHNVEA YTLEGKFFVN PGSCTGAFNT DWPIVFDVED SDEAVTSEVD 180
  181 KPTKENQSED DDAKGGSTGK EQPGSYTPKE GTAGERENEN ES

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.221849
Match:	1ii7A_
Description:	Mre11
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	2.15398287574737	bayes_pls_golite062009
protein transporter activity	1.31841400137462	bayes_pls_golite062009
transporter activity	1.24767072239634	bayes_pls_golite062009
phosphoric ester hydrolase activity	1.23826159413064	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	1.13357344565764	bayes_pls_golite062009
protein serine/threonine phosphatase activity	1.09206313505563	bayes_pls_golite062009
phosphatase activity	1.08894272596476	bayes_pls_golite062009
binding	1.0086165150304	bayes_pls_golite062009
substrate-specific transporter activity	0.783004917746429	bayes_pls_golite062009
phosphoprotein phosphatase activity	0.521298686118866	bayes_pls_golite062009
protein binding	0.306836734324834	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [223-282]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NVKPENQFKE DEVDMSDSDI NGSNSPSFCL LDIQGNTCTL YIYLYVNGEV KVDKVVYEKE  60
   61

[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.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.941	b.122.1	PUA domain-like

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: