YRC Public Data Repository - Protein Structure Prediction

Protein:	SEC28
Organism:	Saccharomyces cerevisiae
Length:	359 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 SEC28.

Description	E-value	Query Range	Subject Range
COPE_BOVIN - Coatomer subunit epsilon OS=Bos taurus GN=COPE PE=1 SV=3	0.0	[62..358]	[15..307]
COPE_MOUSE - Coatomer subunit epsilon OS=Mus musculus GN=Cope PE=1 SV=3	0.0	[62..358]	[15..307]
COPE - coatomer protein complex, subunit epsilon gi\|114676186, gi... - gi\|114676186\|ref\|XP_512517.2\| PREDICTED: similar to epsilon-COP protein isoform 10 [Pan troglodytes]... gi\|117646338, gi... - gi\|124000451\|gb\|ABM87734.1\| coatomer protein complex, subunit epsilon [synthetic construct], gi\|1239...	0.0	[62..358]	[15..307]
COPE_CRIGR - Coatomer subunit epsilon OS=Cricetulus griseus GN=COPE PE=2 SV=2	0.0	[62..358]	[15..307]
gi\|190406291 - gi\|190406291\|gb\|EDV09558.1\| epsilon-COP coatomer subunit [Saccharomyces cerevisiae RM11-1a] SEC28 - Epsilon-COP subunit of the coatomer; regulates retrograde Golgi-to-ER protein traffic; stabilizes Co... COPE_YEAST - Coatomer subunit epsilon OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SEC28 PE=1 SV=2 gi\|151943087 - gi\|151943087\|gb\|EDN61422.1\| epsilon-COP coatomer subunit [Saccharomyces cerevisiae YJM789]	5.0E-96	[64..359]	[1..296]
COPE1_ARATH - Coatomer subunit epsilon-1 OS=Arabidopsis thaliana GN=At1g30630 PE=2 SV=1	7.0E-94	[64..356]	[8..292]
gi\|7670062 - gi\|7670062\|dbj\|BAA94964.1\| epsilon1-COP [Glycine max]	1.0E-92	[64..355]	[5..288]

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Predicted Domain #1

Region A:
Residues: [1-114]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQRLQWDKDI LFLIFKVILI FCWFFFSFLS SEKLQFLQKN TSSYSIRTDC EELGGEHRNR  60
   61 QKIMDYFNIK QNYYTGNFVQ CLQEIEKFSK VTDNTLLFYK AKTLLALGQY QSQD

[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 functions:

Term	Confidence	Notes
binding	2.07128880832802	bayes_pls_golite062009
protein binding	1.72061787550863	bayes_pls_golite062009
signal sequence binding	0.144756387712192	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [115-212]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PTSKLGKVLD LYVQFLDTKN IEELENLLKD KQNSPYELYL LATAQAILGD LDKSLETCVE  60
   61 GIDNDEAEGT TELLLLAIEV ALLNNNVSTA STIFDNYT

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [325-359]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TNQLVKLDHE HAFIKHHQEI DAKFDELVRK YDTSN

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.83
Match:	1hh8A
Description:	Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [213-260]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NAIEDTVSGD NEMILNLAES YIKFATNKET ATSNFYYYEE LSQTFPTW

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.83
Match:	1hh8A
Description:	Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [261-324]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KTQLGLLNLH LQQRNIAEAQ GIVELLLSDY YSVEQKENAV LYKPTFLANQ ITLALMQGLD  60
   61 TEDL

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.83
Match:	1hh8A
Description:	Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
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: