YRC Public Data Repository - Protein Structure Prediction

Protein:	SKI3
Organism:	Saccharomyces cerevisiae
Length:	1432 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 SKI3.

Description	E-value	Query Range	Subject Range
gi\|558147 - gi\|558147\|gb\|AAA50573.1\| antiviral protein [Saccharomyces cerevisiae]	0.0	[1..1432]	[1..1432]
gi\|20904523, gi\|... - gi\|21226280\|ref\|NP_632202.1\| hypothetical protein MM_0178 [Methanosarcina mazei Go1], gi\|20904523\|gb...	0.0	[2..1416]	[334..1699]
gi\|33640682, gi\|... - gi\|33862569\|ref\|NP_894129.1\| TPR repeat-containing protein [Prochlorococcus marinus str. MIT 9313], ...	0.0	[423..1431]	[53..1023]
gi\|20090471, gi\|... - gi\|20090471\|ref\|NP_616546.1\| TPR domain-containing protein [Methanosarcina acetivorans C2A], gi\|1991...	0.0	[5..1370]	[6..1264]
SKI3_SCHPO - Superkiller protein 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ski3 PE=3 SV=1 SPCC1919.05 - TPR repeat protein Ski3	0.0	[4..1428]	[2..1375]

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Predicted Domain #1

Region A:
Residues: [1-179]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDIKQLLKE AKQELTNRDY EETIEISEKV LKLDPDNYFA HIFLGKALSS LPASNNVSSN  60
   61 RNLERATNHY VSAAKLVPDN LLAWKGLFLL FRTTEVVPDI LSYDEYFDLC GQYADALLKQ 120
  121 EQSQVELIND IKLLKKTHPD CQKAFYQHLK PGSLMAETIG RHLSTPQDAL LNLIKILSN

[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.

Predicted functions:

Term	Confidence	Notes
binding	1.415772038524	bayes_pls_golite062009
protein binding	0.816793912043238	bayes_pls_golite062009
RNA binding	0.663379880504337	bayes_pls_golite062009
nucleic acid binding	0.272790651314508	bayes_pls_golite062009
hydrolase activity	0.271487362607254	bayes_pls_golite062009
transcription regulator activity	0.22530421898958	bayes_pls_golite062009
DNA binding	9.99975086740101E-4	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [180-386]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IETTEIGKTL SQNRLKLKAS DPDYQIKLNS FSWEIIKNSE IDQLYNQLVN ILADDQKRSE  60
   61 IENQWLEYRI KVLKSMPLDV KKDFFTKVKE MVEDMVLVNH QSLLAWQKYF EWTDYEDLDN 120
  121 MDAPLIIKYF KKFPKDPLAM ILYSWLSSKL SKYDIKSLES ANKPPEGHKK TEKETDIKDV 180
  181 DETNEDEVKD RVEDEVKDRV EDEVKDQ

[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.

Predicted Domain #3

Region A:
Residues: [387-732]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DEEAKEDEEE DLDDIEIGLL EEEVVTVLTE NIVKCKNNIL AHRILCQYYL LTKEYEAALP  60
   61 YIKNGISLIA YNIKDLGVHL PLTKREFSLD LATVYTYVDA PKDHNAALKL YDNILSGDFS 120
  121 NIQAKMGKGI IFIERKNWKD AMTLLTQVHE QSPNNLEVLS ELSWSKAHMG YMDEALAGLD 180
  181 TVIKGIKGMD LRSIDFRALN LWRQAKVYIM KHASINDAKQ ENVKCAFKLL IQSIKILDTF 240
  241 APGFSTLGDI YCHYYKDHLR AFKCYFKAFD LDAGDYTAAK YITETYASKP NWQAASSIAS 300
  301 RLIKGEKAKA ELRSNNWPFR VVGIAHLEKQ EESDSIEWFQ SALRVD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	20.0
Match:	1fchA_
Description:	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	1.48701537593139	bayes_pls_golite062009
protein binding	0.931467806305272	bayes_pls_golite062009
RNA binding	0.675746721046834	bayes_pls_golite062009
hydrolase activity	0.252678932946087	bayes_pls_golite062009
nucleic acid binding	0.25258244124997	bayes_pls_golite062009
transcription regulator activity	0.221255948377457	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [733-849]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PNDVESWVGL GQAYHACGRI EASIKVFDKA IQLRPSHTFA QYFKAISLCD VGEYLESLDI  60
   61 LEKVCQEAAT EESFQIGLVE VLMRCSLDLY SQGFLLKSVS IAKDTIERIK IIISELK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	18.0
Match:	1na0A_
Description:	Designed protein cTPR3
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [850-935]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 CENQQVWIYL SQVLRLFIWI ESKVDTLPVE SLVSIFENSQ FSGSEEIDSV DNIKIDTLLD  60
   61 STTDDNVSIA CKFLILASKY SVSDQK

[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 #6

Region A:
Residues: [936-1149]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FTDIAGTVRA SYWYNIGISE LTAFITLKEP QYRDAAIFAF KKSIQLQSNT SETWIGLGIA  60
   61 TMDINFRVSQ HCFIKATALE PKATNTWFNL AMLGLKKKDT EFAQQVLNKL QSLAPQDSSP 120
  121 WLGMALILEE QGDIIGSSKL FAHSFILSNG RSKAAQFMYA KNVLENHINN GDDERDIETV 180
  181 EKLTTASIAL EQFFKKSPDS QFALQCALLT LERL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.69897
Match:	1d8dA_
Description:	Protein farnesyltransferase alpha-subunit
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [1150-1221]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HHYENANELA NRLIGILEKK FEKTQDEREL FNFAIIKGQF ARIHLGLGNF ELSIENADLS  60
   61 QGIISESSDE KS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.39794
Match:	1elrA_
Description:	Hop
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [1222-1432]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKTKISNHIC LGLSYFFLND FDQTLNQFQE LLSISKDSKH LVVLIAKVLY DVGESDTKEI  60
   61 ALQELTEYIA TSGADLLVTL TIAAMSILDD KREDLSIILE ELKALPLSKQ IIDKHKDAPY 120
  121 LIEEITKRLY RNDTGKQVWQ RSAYFFPNNL KVWERLDKNI QRRIASNGQN KVTAEEMSKL 180
  181 YCESKNLRSI QRGMFLCPWN VTAVKALNEC F

[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:

Predicted functions: