YRC Public Data Repository - Protein Structure Prediction

Protein:	MIP6
Organism:	Saccharomyces cerevisiae
Length:	659 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 MIP6.

Description	E-value	Query Range	Subject Range
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	0.0	[102..560]	[2..450]
PABP1_BOVIN - Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1 gi\|109087089 - gi\|109087089\|ref\|XP_001098239.1\| PREDICTED: poly(A) binding protein, cytoplasmic 1 isoform 2 [Macaca... gi\|123993665, gi... - gi\|168278070\|dbj\|BAG11013.1\| polyadenylate-binding protein 1 [synthetic construct], gi\|123999981\|gb\|... gi\|194036975 - gi\|194036975\|ref\|XP_001927782.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-bind... PABPC1 - poly(A) binding protein, cytoplasmic 1 gi\|73974130, gi\|... - gi\|73974178\|ref\|XP_857695.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-binding ...	0.0	[102..560]	[2..450]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	0.0	[102..560]	[2..450]
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	0.0	[102..550]	[2..441]
gi\|64970 - gi\|64970\|emb\|CAA40721.1\| polyA binding protein [Xenopus laevis]	0.0	[102..560]	[2..448]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	0.0	[105..545]	[5..435]
gi\|7528270 - gi\|7528270\|gb\|AAF63202.1\|AF240679_1 poly(A)-binding protein [Cucumis sativus]	0.0	[87..556]	[5..461]

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Predicted Domain #1

Region A:
Residues: [1-96]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPNSHGNVLN NISLNSKQNP RSISKSCPND KDARQKSFKT ISAQALVRVQ GAGYKLGDVK  60
   61 LKDAEVKEKN SLKKYDCKNA TQEKKEQEQV FEKTVA

[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 #2

Region A:
Residues: [97-189]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KGSVQKYITK TSKTNSLFIG NLKSTVTEEM LRKIFKRYQS FESAKVCRDF LTKKSLGYGY  60
   61 LNFKDKNDAE SARKEFNYTV FFGQEVKIMP SMK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	262.533179
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	4.43921816934576	bayes_pls_golite062009
binding	3.49612884560266	bayes_pls_golite062009
mRNA binding	3.1794312979994	bayes_pls_golite062009
nucleocytoplasmic transporter activity	2.51546867995401	bayes_pls_golite062009
nucleic acid binding	2.34356093608328	bayes_pls_golite062009
protein binding	1.32954276279597	bayes_pls_golite062009
transporter activity	1.15189574940599	bayes_pls_golite062009
transmembrane transporter activity	1.06701715708589	bayes_pls_golite062009
single-stranded RNA binding	0.851308060174055	bayes_pls_golite062009
substrate-specific transporter activity	0.796360682730618	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.540791176419082	bayes_pls_golite062009
mRNA 3'-UTR binding	0.414871108842203	bayes_pls_golite062009
nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity	0.212405663170905	bayes_pls_golite062009
poly-purine tract binding	0.15653271757169	bayes_pls_golite062009
poly-pyrimidine tract binding	0.11509546367801	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.096231856558874	bayes_pls_golite062009
pyrophosphatase activity	0.059732432409948	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.0510390778764699	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.0484248928275733	bayes_pls_golite062009
poly(A) RNA binding	0.0459878286238641	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [190-294]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NTLFRKNIGT NVFFSNLPLE NPQLTTRSFY LIMIEYGNVL SCLLERRKNI GFVYFDNDIS  60
   61 ARNVIKKYNN QEFFGNKIIC GLHFDKEVRT RPEFTKRKKM IGSDI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	262.533179
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	4.43921816934576	bayes_pls_golite062009
binding	3.49612884560266	bayes_pls_golite062009
mRNA binding	3.1794312979994	bayes_pls_golite062009
nucleocytoplasmic transporter activity	2.51546867995401	bayes_pls_golite062009
nucleic acid binding	2.34356093608328	bayes_pls_golite062009
protein binding	1.32954276279597	bayes_pls_golite062009
transporter activity	1.15189574940599	bayes_pls_golite062009
transmembrane transporter activity	1.06701715708589	bayes_pls_golite062009
single-stranded RNA binding	0.851308060174055	bayes_pls_golite062009
substrate-specific transporter activity	0.796360682730618	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.540791176419082	bayes_pls_golite062009
mRNA 3'-UTR binding	0.414871108842203	bayes_pls_golite062009
nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity	0.212405663170905	bayes_pls_golite062009
poly-purine tract binding	0.15653271757169	bayes_pls_golite062009
poly-pyrimidine tract binding	0.11509546367801	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.096231856558874	bayes_pls_golite062009
pyrophosphatase activity	0.059732432409948	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.0510390778764699	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.0484248928275733	bayes_pls_golite062009
poly(A) RNA binding	0.0459878286238641	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [295-389]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VIEDELLASN NLSDNARSKT ILVKNLPSDT TQEEVLDYFS TIGPIKSVFI SEKQANTPHK  60
   61 AFVTYKNEEE SKKAQKCLNK TIFKNHTIWV GPGKD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	85.056057
Match:	1b7fA_
Description:	Sex-lethal protein
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [390-543]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPVHNQIGTN KKTKVYLKNL SFNCNKEFIS QLCLQEKIRF SEIKITNYNS LNWTFCGHVE  60
   61 CFSRSDAERL FNILDRRLIG SSLVEASWSK NNDNILNEID YDDGNNNENY KKLINISSMM 120
  121 RFRTQELSAH QKGLTSQFQQ VVSPFSSYSN SYTN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	85.056057
Match:	1b7fA_
Description:	Sex-lethal protein
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [544-659]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNSLVATPMK PHPAFNLITN TVDEKLHQPK RTKQENAEIL ESLKKIINRN LQRISISGLN  60
   61 KEENLRSISE FIFDVFWEHD SERLSHFLLM TNTSLESQKI LQKQVTRAAE SLGFTV

[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.

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: