Clamp Protein


    DNA Polymerase Processivity Factor (PDB code: 1axc):


    Distant Homology Indetification by Universal Discrete State-space Models

    Zhang, S., Zuccola, H.J., Szustakowski, J.D., Hogle, J., Smith, T.F.

    Proteins with structural and functional similarities may have little primary sequence identity. Conventional sequence comparison methods are unable to identify remote homologs for these protein families. We developed a method for identifying distant homologs of such protein families using a universal Discrete State-space Model (uDSM). A uDSM is constructed as a covering model over a set of DSMs of representative family members. The uDSM of DNA polymerase processivity factor family is constructed. Good sensitivity and specificity are obtained for this fold. Homology identification using this strategy were performed and hits from difference databases are listed here.


    YNL063W YMR241W YLR208W YAL037W YBR088C YGR096W YIL053W YNL003C YNL210W YDR315C

    C. elegans:

    CEF55C9_10 CET20H9_4 CEY63D3A_9 CEY119D3_462_C CET17A3_7 CEC03A3_3 CEF55C9_4 CEC09B8_4 CEC52E2_I CET27E4_1 CET17A3_6 CEK07B1_5 CEW03D2_4 CEC15C6_2B CEC32B5_8 CEK03E5_1 CEF54F7_6 CEC41G11_1 CEY45F10D_7 CEF18G5_5 CEF45C12_11 CEC08G5_2


    GP-AAC95182_1 GP-AAC17630_1 GP-AAD20409_1 GP-AAB91986_1 GP-BAA23158_1 GP-AAB91985_1 GP-AAD03459_1 GP-AAC28215_1 GP-AAB64021_1 SW-CX32_ARATH GP-AAB61044_1 GP-BAA74838_1 GP-AAD21692_1 GP-AC006955_19 GP-CAB37535_1 GP-AC006580_11 PIR-S55244 GP-AC007134_20 GP-AC007576_23 GP-AC007659_8 GP-AC006220_4 PIR-A39357 GP-CAA19696_1 GP-AAB97694_1 GP-CAA11757_1 GP-AC007063_11 GP-AAD12694_1 GP-AC007267_4 GP-AAC78513_1 GP-AAB64023_1 GP-AAC13620_1 GP-CAA77109_1 GP-AAC98041_1 GP-AAD13708_1 GP-CAA17555_1 GP-AAC25929_1 GP-AAD18122_1 GP-CAB39795_1

    CMV(human cytomegalovirus):

    gi|1780822|emb|CAA35403.1 gi|2647982|emb|CAA74075.1 gi|1780955|emb|CAA35291.1 gi|1780832|emb|CAA35413.1 gi|1813970|emb|CAA35363.1

    EBV (Epstein-Barr virus):

    gi|1334858|emb|CAA24844.1|_(V01555) gi|1334902|emb|CAA24794.1|_(V01555) gi|330332|gb|AAA45866.1|_(M11923)

    CCV (channel catfish herpes virus):

    gi|331277|gb|AAA88171 gi|331233|gb|AAA88126 gi|331281|gb|AAA88175 gi|331283|gb|AAA88177 gi|331280|gb|AAA88174 gi|331267|gb|AAA88160

    Varola Virus:

    gi|438989|gb|AAA60819 gi|4049873|gb|AAC97833 gi|438929|gb|AAA60759


    CT8431 CT38631 CT36731 CT25340 CT17654 CT27906 CT35120 CT26256 CT3959 CT23860 CT32101 CT31887 CT28825 CT17698 CT26072 CT19041 CT37199 CT15469 CT16755 CT4279 CT27948 CT21474