GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-C4pol - C4-type zinc-finger of DNA polymerase delta
Pfam: PF14260 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Length: 73
Sequences: 409
Seq/Len: 5.6
HH_delta: 0.835 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
22_D25_Q0.355192.634
48_C51_C0.273642.030
1_C4_C0.228061.691
61_C66_C0.224981.669
63_S67_P0.21811.618
39_R43_E0.212611.577
25_Q29_N0.209211.552
15_L47_I0.208961.550
45_W49_Q0.202921.505
48_C66_C0.200031.484
20_R23_P0.196821.460
63_S66_C0.192341.427
40_R71_E0.189721.407
41_F49_Q0.187231.389
10_E33_R0.182631.355
51_C66_C0.180451.338
15_L35_R0.175221.300
33_R36_E0.174011.291
69_F72_R0.172891.282
26_T35_R0.170931.268
22_D34_L0.168141.247
6_A18_N0.163761.215
8_T15_L0.152591.132
62_D73_V0.145061.076
51_C61_C0.14341.064
66_C70_Y0.140011.038
9_Q17_S0.139811.037
58_E71_E0.139061.031
23_P26_T0.138221.025
24_Q28_Y0.138031.024
49_Q70_Y0.137751.022
2_L21_S0.137591.020
51_C65_D0.136521.013
47_I63_S0.135981.009
35_R39_R0.135121.002
6_A73_V0.135011.001
48_C63_S0.131220.973
64_L69_F0.130960.971
20_R36_E0.130720.970
36_E42_N0.130370.967
28_Y32_S0.129040.957
64_L71_E0.128970.957
22_D27_I0.128510.953
21_S25_Q0.128490.953
20_R40_R0.127910.949
43_E71_E0.127430.945
51_C63_S0.125880.934
5_G8_T0.124370.922
37_L40_R0.121980.905
48_C65_D0.121420.901
59_I70_Y0.12060.894
3_V31_L0.120450.893
54_S57_E0.120290.892
21_S27_I0.119360.885
29_N47_I0.1190.883
17_S20_R0.117210.869
61_C65_D0.116310.863
50_S65_D0.116210.862
7_K30_L0.116090.861
36_E39_R0.1160.860
31_L46_T0.114580.850
53_G59_I0.11430.848
24_Q34_L0.113630.843
21_S24_Q0.112590.835
14_P67_P0.112160.832
24_Q27_I0.11170.828
35_R53_G0.111370.826
60_E73_V0.111130.824
8_T69_F0.110310.818
21_S32_S0.110250.818
29_N36_E0.109540.812
35_R38_E0.109270.810
2_L30_L0.109160.810
24_Q33_R0.10870.806
17_S32_S0.108590.805
66_C72_R0.10790.800
23_P64_L0.107890.800
2_L10_E0.107580.798
30_L57_E0.10740.797
37_L43_E0.107160.795
37_L41_F0.106530.790
6_A39_R0.105670.784
15_L32_S0.104050.772
48_C67_P0.103880.770
17_S35_R0.103210.765
45_W59_I0.103020.764
3_V64_L0.102650.761
5_G43_E0.102540.761
10_E28_Y0.102150.758
2_L65_D0.10210.757
44_L63_S0.102080.757
45_W53_G0.102050.757
30_L40_R0.101930.756
48_C61_C0.101710.754
7_K33_R0.101480.753
41_F45_W0.10090.748
17_S38_E0.100350.744
30_L37_L0.100290.744
29_N34_L0.099770.740
17_S29_N0.09930.736
18_N31_L0.09930.736
33_R63_S0.09920.736
52_S59_I0.099120.735
19_C72_R0.099030.734
10_E21_S0.098880.733
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3d00A0.356238.50.835
3goxA0.534220.30.855
3a1bA0.835614.40.864
4hc9A0.890410.60.871
2pv0B0.86310.30.872
1a6yA0.45218.80.875
3w0fA0.36998.20.877
3mpxA0.65757.90.878
3h2yA0.75347.40.879
2ku3A0.69867.40.879
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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