YRC Public Data Repository - Protein Structure Prediction

Protein:	YKU80
Organism:	Saccharomyces cerevisiae
Length:	629 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 YKU80.

Description	E-value	Query Range	Subject Range
gi\|190408335 - gi\|190408335\|gb\|EDV11600.1\| yeast Ku80 protein [Saccharomyces cerevisiae RM11-1a] KU80_YEAST - ATP-dependent DNA helicase II subunit 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=... YKU80 - Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, struct...	0.0	[1..629]	[1..629]
XRCC6 - X-ray repair complementing defective repair in Chinese hamster cells 6 gi\|190690795, gi... - gi\|190690795\|gb\|ACE87172.1\| X-ray repair complementing defective repair in Chinese hamster cells 6 (...	0.0	[3..595]	[35..604]
gi\|19548754, gi\|... - gi\|74138092\|dbj\|BAE25441.1\| unnamed protein product [Mus musculus], gi\|19548756\|gb\|AAL90775.1\| Ku70 ...	0.0	[3..594]	[33..601]
gi\|18181882, gi\|... - gi\|21717799\|ref\|NP_620780.1\| thyroid autoantigen [Rattus norvegicus], gi\|18181882\|dbj\|BAB83858.1\| G2...	0.0	[3..595]	[33..602]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[3..594]	[20..588]
gi\|1836065 - gi\|1836065\|gb\|AAB46854.1\| Ku70=DNA-dependent protein kinase 70 kda DNA-binding subunit/DNA-PK Ku70 s...	0.0	[3..595]	[33..602]
XRCC6_CHICK - X-ray repair cross-complementing protein 5 OS=Gallus gallus GN=XRCC6 PE=2 SV=1	0.0	[3..596]	[56..627]
gi\|4630797 - gi\|4630797\|dbj\|BAA76953.1\| human Ku70 autoantigen homologue [Xenopus laevis]	0.0	[3..596]	[34..606]

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Predicted Domain #1

Region A:
Residues: [1-244]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSESTTFIV DVSPSMMKNN NVSKSMAYLE YTLLNKSKKS RKTDWISCYL ANCPVSENSQ  60
   61 EIPNVFQIQS FLAPVTTTAT IGFIKRLKQY CDQHSHDSSN EGLQSMIQCL LVVSLDIKQQ 120
  121 FQARKILKQI VVFTDNLDDL DITDEEIDLL TEELSTRIIL IDCGKDTQEE RKKSNWLKLV 180
  181 EAIPNSRIYN MNELLVEITS PATSVVKPVR VFSGELRLGA DILSTQTSNP SGSMQDENCL 240
  241 CIKV

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [269-288]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KKERYVGVKS IIEYEIHNEG

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [481-513]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDTDELPEIP LGNYYQPIGE VTTDTTLPLP SLN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	158.0
Match:	1jeqA_
Description:	DNA binding C-terminal domain of ku70; Ku70 subunit
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
double-stranded telomeric DNA binding	8.64621483095491	bayes_pls_golite062009
DNA-dependent protein kinase activity	7.33495559751688	bayes_pls_golite062009
telomeric DNA binding	5.16364366157397	bayes_pls_golite062009
transcription regulator activity	3.05720838352689	bayes_pls_golite062009
binding	2.75824485094584	bayes_pls_golite062009
nucleic acid binding	2.08531850924748	bayes_pls_golite062009
promoter binding	1.97164983798318	bayes_pls_golite062009
DNA binding	1.91667917801679	bayes_pls_golite062009
transcription repressor activity	1.69798374416156	bayes_pls_golite062009
transcription activator activity	1.54159704189366	bayes_pls_golite062009
protein binding	1.53311876872122	bayes_pls_golite062009
transcription factor activity	1.37299910766941	bayes_pls_golite062009
DNA-dependent ATPase activity	0.985753648509262	bayes_pls_golite062009
single-stranded DNA binding	0.814975395718076	bayes_pls_golite062009
DNA helicase activity	0.720743494912414	bayes_pls_golite062009
transcription corepressor activity	0.702777559747981	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.506640285146188	bayes_pls_golite062009
protein dimerization activity	0.45109468643752	bayes_pls_golite062009
structure-specific DNA binding	0.450760554291027	bayes_pls_golite062009
structural molecule activity	0.375125487765613	bayes_pls_golite062009
transporter activity	0.371057816653329	bayes_pls_golite062009
protein complex binding	0.31789779419928	bayes_pls_golite062009
transcription factor binding	0.184852480703492	bayes_pls_golite062009
protein C-terminus binding	0.15516806759612	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [245-268]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EAFPATKAVS GLNRKTAVEV EDSQ

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [289-445]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NKKNVSEDDQ SGSSYIPVTI SKDSVTKAYR YGADYVVLPS VLVDQTVYES FPGLDLRGFL  60
   61 NREALPRYFL TSESSFITAD TRLGCQSDLM AFSALVDVML ENRKIAVARY VSKKDSEVNM 120
  121 CALCPVLIEH SNINSEKKFV KSLTLCRLPF AEDERVT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	158.0
Match:	1jeqA_
Description:	DNA binding C-terminal domain of ku70; Ku70 subunit
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [446-480]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DFPKLLDRTT TSGVPLKKET DGHQIDELME QFVDS

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [514-629]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KDQEENKKDP LRIPTVFVYR QQQVLLEWIH QLMINDSREF EIPELPDSLK NKISPYTHKK  60
   61 FDSTKLVEVL GIKKVDKLKL DSELKTELER EKIPDLETLL KRGEQHSRGS PNNSNN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	158.0
Match:	1jeqA_
Description:	DNA binding C-terminal domain of ku70; Ku70 subunit
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: