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 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	0.328	a.1.1	Globin-like
View	Download	0.329	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.306	d.52.3	Prokaryotic type KH domain (KH-domain type II)
View	Download	0.409	a.60.10	Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain
View	Download	0.326	d.58.9	RuBisCO, large subunit, small (N-terminal) domain
View	Download	0.278	a.7.5	Tubulin chaperone cofactor A
View	Download	0.237	a.7.5	Tubulin chaperone cofactor A
View	Download	0.233	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.223	d.110.1	Profilin (actin-binding protein)
View	Download	0.218	a.47.2	t-snare proteins
View	Download	0.212	a.61.1	Retroviral matrix proteins
View	Download	0.202	a.121.1	Tetracyclin repressor-like, C-terminal 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: