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View Structure Prediction Details

Protein: CDC9
Organism: Saccharomyces cerevisiae
Length: 755 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 CDC9.

Description E-value Query
Range
Subject
Range
gi|151941840 - gi|151941840|gb|EDN60196.1| DNA ligase [Saccharomyces cerevisiae YJM789]
DNLI1_YEAST - DNA ligase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CDC9 PE=1 SV=2
CDC9 - DNA ligase found in the nucleus and mitochondria, an essential enzyme that joins Okazaki fragments d...
0.0 [1..755] [1..755]
DNLI1_SCHPO - DNA ligase 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cdc17 PE=3 SV=1
cdc17 - ATP-dependent DNA ligase Cdc17
0.0 [18..750] [21..751]
DNLI1_ARATH - DNA ligase 1 OS=Arabidopsis thaliana GN=LIG1 PE=2 SV=2
0.0 [24..753] [48..779]
DNLI1_XENLA - DNA ligase 1 OS=Xenopus laevis GN=lig1 PE=2 SV=1
0.0 [9..755] [305..1058]
LIG1 - ligase I, DNA, ATP-dependent
0.0 [10..755] [149..905]
DNLI1_MOUSE - DNA ligase 1 OS=Mus musculus GN=Lig1 PE=1 SV=2
0.0 [9..749] [146..897]
DNLI1_RAT - DNA ligase 1 OS=Rattus norvegicus GN=Lig1 PE=1 SV=1
0.0 [5..749] [150..899]
gi|16905197, gi|... - gi|40539108|gb|AAR87364.1| putative DNA ligase [Oryza sativa (japonica cultivar-group)], gi|37535574...
0.0 [8..751] [70..796]

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Predicted Domain #1
Region A:
Residues: [1-143]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN KPTEGTPSPK  60
   61 KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM GSNFSSIPSS APSSGVADSP 120
  121 QQSQRLVGEV EDALSSNNND HYS

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 7.99
Match: 1ldvA
Description: No description for 1ldvA was found.

Predicted Domain #2
Region A:
Residues: [144-330]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SNIPYSEVCE VFNKIEAISS RLEIIRICSD FFIKIMKQSS KNLIPTTYLF INRLGPDYEA  60
   61 GLELGLGENL LMKTISETCG KSMSQIKLKY KDIGDLGEIA MGARNVQPTM FKPKPLTVGE 120
  121 VFKNLRAIAK TQGKDSQLKK MKLIKRMLTA CKGIEAKFLI RSLESKLRIG LAEKTVLISL 180
  181 SKALLLH

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 7.17
Match: 1lshA
Description: Lipovitellin-phosvitin complex, superhelical domain; Lipovitellin-phosvitin complex; beta-sheet shell regions
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
DNA ligase activity 5.12640522664474 bayes_pls_golite062009
ligase activity, forming phosphoric ester bonds 5.0464977640909 bayes_pls_golite062009
DNA ligase (ATP) activity 3.18914513915107 bayes_pls_golite062009
DNA ligase (NAD+) activity 3.1488483282989 bayes_pls_golite062009
ligase activity 2.36807839237461 bayes_pls_golite062009
catalytic activity 2.15370807854636 bayes_pls_golite062009
nucleotidyltransferase activity 2.06695360101593 bayes_pls_golite062009
nucleic acid binding 1.4725380374617 bayes_pls_golite062009
binding 1.23714137231717 bayes_pls_golite062009
DNA binding 1.1855473374207 bayes_pls_golite062009
protein binding 0.0772495917382868 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [331-391]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DENREDSPDK DVPMDVLESA QQKIRDAFCQ VPNYEIVINS CLEHGIMNLD KYCTLRPGIP  60
   61 L

[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 #4
Region A:
Residues: [392-419]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPMLAKPTKA INEVLDRFQG ETFTSEYK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [548-599]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TQITTNNLDE LQKFLDESVN HSCEGLMVKM LEGPESHYEP SKRSRNWLKL KK

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 38.30103
Match: 1a0i__
Description: ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5
Region A:
Residues: [420-547]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YDGERAQVHL LNDGTMRIYS RNGENMTERY PEINITDFIQ DLDTTKNLIL DCEAVAWDKD  60
   61 QGKILPFQVL STRKRKDVEL NDVKVKVCLF AFDILCYNDE RLINKSLKER REYLTKVTKV 120
  121 VPGEFQYA

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [600-755]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DYLEGVGDSL DLCVLGAYYG RGKRTGTYGG FLLGCYNQDT GEFETCCKIG TGFSDEMLQL  60
   61 LHDRLTPTII DGPKATFVFD SSAEPDVWFE PTTLFEVLTA DLSLSPIYKA GSATFDKGVS 120
  121 LRFPRFLRIR EDKGVEDATS SDQIVELYEN QSHMQN

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 38.30103
Match: 1a0i__
Description: ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
Matching Structure (courtesy of the PDB):

YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle