YRC Public Data Repository - Protein Structure Prediction

Protein:	YPP1
Organism:	Saccharomyces cerevisiae
Length:	817 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 YPP1.

Description	E-value	Query Range	Subject Range
YPP1 - Cargo-transport protein involved in endocytosis; interacts with phosphatidylinositol-4-kinase Stt4; ... YPP1_YEAST - Cargo-transport protein YPP1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=YPP1 PE=1 S...	0.0	[1..817]	[1..817]
SEC_ARATH - Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SEC OS=Arabidopsis thalian...	3.0E-63	[252..775]	[42..539]
gi\|13775066 - gi\|13775066\|gb\|AAK39123.1\|AF363030_1 UDP-N-acetylglucosaminyltransferase [Mus musculus]	1.0E-62	[240..712]	[22..473]
OGT1_RAT - UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit OS=Rattus norvegicu...	2.0E-62	[244..712]	[16..463]
OGT - O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylgluco... gi\|123993895, gi... - gi\|224487755\|dbj\|BAH24112.1\| O-linked N-acetylglucosamine (GlcNAc) transferase [synthetic construct]...	3.0E-62	[244..712]	[16..463]
gi\|5052534 - gi\|5052534\|gb\|AAD38597.1\|AF145622_1 BcDNA.GH04245 [Drosophila melanogaster]	2.0E-61	[249..712]	[53..502]
gi\|13472042, gi\|... - gi\|14022787\|dbj\|BAB49395.1\| mll2209 [Mesorhizobium loti MAFF303099], gi\|13472042\|ref\|NP_103609.1\| hy...	8.0E-58	[263..738]	[58..509]
ogt-1 - status:Confirmed UniProt:O18158 protein_id:AAA62535.2	1.0E-57	[194..711]	[66..576]

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Predicted Domain #1

Region A:
Residues: [1-179]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPNSNVRIPP TVPSKIIDVV DQALRARLLG GSTFNSGFDS LDSVLNLQFR LHYHVIGSNG  60
   61 PAKPVCDVLL KESQNLEKNM SMMEELNDYP EITKLVEKIL FNCLGILFFH RGQFQESQRC 120
  121 LLHSLKIHNN TASQKTALME QYDRYLIVEN LYYRGLVSQD INIMQNVFYK ELLAHVDTI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	15.221849
Match:	1elwA_
Description:	Hop
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
signal sequence binding	2.68460419248567	bayes_pls_golite062009
binding	2.29041171814244	bayes_pls_golite062009
protein binding	1.6279032205159	bayes_pls_golite062009
transcription regulator activity	1.36301889945421	bayes_pls_golite062009
nucleic acid binding	1.04482640570705	bayes_pls_golite062009
DNA binding	1.03582297487751	bayes_pls_golite062009
peroxisome targeting sequence binding	1.01220052237687	bayes_pls_golite062009
ligase activity	0.825764637499128	bayes_pls_golite062009
RNA binding	0.540255067346835	bayes_pls_golite062009
transcription factor activity	0.39224150319016	bayes_pls_golite062009
signal transducer activity	0.279505673062022	bayes_pls_golite062009
molecular transducer activity	0.279505673062022	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [180-257]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PPESNGLLFE YISLIVAKLR FNQIQDLAEN FKTTVENPFI LFLYMIKKFQ SPLKKHIDND  60
   61 DLYLKFGQNV LLKAKFPT

[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 Domain #3

Region A:
Residues: [258-403]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ASETNDEALE HFNVFLQYYF KFTHIKKIKV NPSWYNFIIS SMEKTFQSIE VSKTAMFLFQ  60
   61 NLSDNSNDEI KKKTFKRESI LNFVNFVKYN DKYYQLHDNS HRDIISFIDA YSFILQNSSK 120
  121 TDSIENVFDY DNTVSTFATS LNSFYK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.0
Match:	1fchA_
Description:	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [404-471]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EYNLPLMSQS ESLDWLENST RCVYPGNISK VLTNAWSTLY EIRKYQLDFL VSNNLTSYLC  60
   61 NAMMLSTK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.0
Match:	1fchA_
Description:	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [472-608]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EKDNADVEEQ EEGEEEKALR ELQFKYSYTL AQQRHIETAI KTLESLILSK NPNYYKAWHL  60
   61 LALCRSVQED KEMSYKIVCS VLEAMNESLQ NNTLLLNDRW QFIHLKLTQL ALIEEIFGTL 120
  121 EALETLPEVF ELYATLF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.0
Match:	1fchA_
Description:	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [609-817]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PDSQPELNSM GPKYSQTKEY LLQMVWIFAA NMYMRTKDND EDAKAAIKEA SNVESKFKNL  60
   61 NCNIANGYLS IIKDEPGVAL KEFETVLYYD ENNLDALVGF AELIFPEELG VEETNLERYY 120
  121 TLSLDKKPGK RAKLTFVNDT DRSAAYARLK FLLECAILES IEAYYSPEVW WYLSLIYEKY 180
  181 QDDEYKNSLL KCIKYQELNP IRSLRYCNY

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident 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

Predicted functions: