YRC Public Data Repository - Protein Structure Prediction

Protein:	YKU70
Organism:	Saccharomyces cerevisiae
Length:	602 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 YKU70.

Description	E-value	Query Range	Subject Range
gi\|207342065 - gi\|207342065\|gb\|EDZ69944.1\| YMR284Wp-like protein [Saccharomyces cerevisiae AWRI1631] YKU70 - Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, struct... KU70_YEAST - ATP-dependent DNA helicase II subunit 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=...	0.0	[1..602]	[1..602]
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	[12..566]	[18..555]
gi\|1836065 - gi\|1836065\|gb\|AAB46854.1\| Ku70=DNA-dependent protein kinase 70 kda DNA-binding subunit/DNA-PK Ku70 s...	0.0	[12..563]	[16..550]
gi\|19548754, gi\|... - gi\|74138092\|dbj\|BAE25441.1\| unnamed protein product [Mus musculus], gi\|19548756\|gb\|AAL90775.1\| Ku70 ...	0.0	[12..566]	[16..553]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[12..566]	[3..540]
gi\|18181882, gi\|... - gi\|21717799\|ref\|NP_620780.1\| thyroid autoantigen [Rattus norvegicus], gi\|18181882\|dbj\|BAB83858.1\| G2...	0.0	[12..566]	[16..553]
XRCC6_CHICK - X-ray repair cross-complementing protein 5 OS=Gallus gallus GN=XRCC6 PE=2 SV=1	0.0	[13..566]	[40..577]

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Predicted Domain #1

Region A:
Residues: [1-260]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRSVTNAFGN SGELNDQVDE TGYRKFDIHE GILFCIELSE TMFKESSDLE YKSPLLEILE  60
   61 SLDELMSQLV ITRPGTAIGC YFYYCNREDA KEGIYELFPL RDINATFMKK LNDLLEDLSS 120
  121 GRISLYDYFM FQQTGSEKQV RLSVLFTFML DTFLEEIPGQ KQLSNKRVFL FTDIDKPQEA 180
  181 QDIDERARLR RLTIDLFDNK VNFATFFIGY ADKPFDNEFY SDILQLGSHT NENTGLDSEF 240
  241 DGPSTKPIDA KYIKSRILRK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [289-313]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MYTHEKAGVR YKLVYEHEDI RQEAY

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [476-602]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NMKKVTQSIM GYFNLRDGYN PSDFKNPLLQ KHYKVLHDYL LQIETTFDEN ETPNTKKDRM  60
   61 MREDDSLRKL YYIRNKILES EKSEDPIIQR LNKYVKIWNM FYKKFNDDNI SIKEEKKPFD 120
  121 KKPKFNI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	207.0
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
promoter binding	3.01492777192913	bayes_pls_golite062009
transcription activator activity	2.87080577911324	bayes_pls_golite062009
binding	2.75824485094584	bayes_pls_golite062009
protein binding	2.58357303743968	bayes_pls_golite062009
nucleic acid binding	2.08531850924748	bayes_pls_golite062009
DNA binding	1.91667917801679	bayes_pls_golite062009
transcription repressor activity	1.69798374416156	bayes_pls_golite062009
transcription factor activity	1.37299910766941	bayes_pls_golite062009
DNA-dependent ATPase activity	0.985753648509262	bayes_pls_golite062009
protein complex binding	0.94234534987624	bayes_pls_golite062009
sequence-specific DNA binding	0.914051610867509	bayes_pls_golite062009
single-stranded DNA binding	0.814975395718076	bayes_pls_golite062009
protein dimerization activity	0.73404855126602	bayes_pls_golite062009
DNA helicase activity	0.720743494912414	bayes_pls_golite062009
transcription corepressor activity	0.702777559747981	bayes_pls_golite062009
protein heterodimerization activity	0.64812784969409	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.506640285146188	bayes_pls_golite062009
structure-specific DNA binding	0.450760554291027	bayes_pls_golite062009
structural molecule activity	0.375125487765613	bayes_pls_golite062009
receptor binding	0.234020194580985	bayes_pls_golite062009
transcription factor binding	0.184852480703492	bayes_pls_golite062009
protein C-terminus binding	0.15516806759612	bayes_pls_golite062009
identical protein binding	0.125363466534611	bayes_pls_golite062009
collagen binding	0.113837148027681	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [261-288]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KEVKRIMFQC PLILDEKTNF IVGVKGYT

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [314-475]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SKRKFLNPIT GEDVTGKTVK VYPYGDLDIN LSDSQDQIVM EAYTQKDAFL KIIGFRSSSK  60
   61 SIHYFNNIDK SSFIVPDEAK YEGSIRTLAS LLKILRKKDK IAILWGKLKS NSHPSLYTLS 120
  121 PSSVKDYNEG FYLYRVPFLD EIRKFPSLLS YDDGSEHKLD YD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	207.0
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: