GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-C4 - Zinc finger C4 type (two domains)
Pfam: PF00105 (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: 70
Sequences: 1438
Seq/Len: 20.54
HH_delta: -0.187 (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
60_F64_L0.795022.644
21_N24_K0.661292.199
55_C58_C0.641292.133
61_Q65_E0.597441.987
57_S61_Q0.588441.957
43_G57_S0.559351.860
3_C6_C0.555621.848
20_C23_C0.546921.819
47_I52_R0.545531.814
30_S60_F0.488861.626
62_K66_V0.483581.608
5_V66_V0.483471.608
63_C68_M0.464631.545
14_H24_K0.462981.540
22_A25_M0.445571.482
4_K17_V0.421221.401
15_Y24_K0.419041.394
13_Y18_L0.398251.325
55_C59_R0.395591.316
30_S37_Y0.391761.303
59_R68_M0.389511.296
55_C63_C0.385571.282
63_C67_G0.36581.217
21_N25_M0.363551.209
3_C20_C0.361081.201
6_C20_C0.344231.145
53_R56_R0.340311.132
28_R41_K0.33111.101
8_D52_R0.324821.080
58_C63_C0.314561.046
6_C23_C0.31131.035
23_C26_F0.311061.035
14_H25_M0.308661.027
14_H22_A0.305191.015
20_C26_F0.304711.013
58_C68_M0.297940.991
13_Y32_K0.294830.981
25_M28_R0.290830.967
4_K66_V0.285330.949
10_A17_V0.284310.946
10_A18_L0.284210.945
59_R67_G0.283290.942
17_V66_V0.280050.931
15_Y21_N0.278590.927
13_Y21_N0.276230.919
31_V60_F0.26970.897
58_C67_G0.268850.894
32_K37_Y0.268730.894
55_C67_G0.268430.893
43_G61_Q0.261220.869
58_C62_K0.260980.868
16_G69_K0.260750.867
21_N56_R0.256540.853
30_S33_K0.250020.832
44_N65_E0.243990.812
2_K10_A0.241710.804
41_K44_N0.240940.801
7_G18_L0.233860.778
13_Y17_V0.233360.776
12_G17_V0.232970.775
35_K56_R0.231980.772
25_M53_R0.230950.768
55_C68_M0.23040.766
46_K51_N0.230330.766
47_I53_R0.22660.754
17_V51_N0.226170.752
59_R63_C0.225120.749
14_H21_N0.22360.744
38_K43_G0.223520.743
38_K42_N0.220510.733
31_V34_K0.216470.720
10_A24_K0.214070.712
51_N54_K0.213730.711
4_K50_D0.212610.707
15_Y22_A0.211120.702
3_C16_G0.21070.701
38_K49_K0.210370.700
28_R32_K0.210070.699
6_C16_G0.210060.699
35_K50_D0.208760.694
36_P42_N0.208220.693
38_K64_L0.20770.691
56_R59_R0.20690.688
15_Y28_R0.203610.677
16_G20_C0.200590.667
35_K48_D0.199510.664
46_K49_K0.196610.654
34_K50_D0.19620.653
19_S24_K0.193090.642
30_S54_K0.192980.642
46_K62_K0.191530.637
11_S19_S0.190580.634
48_D52_R0.189790.631
22_A26_F0.187110.622
11_S21_N0.187010.622
61_Q64_L0.186880.622
2_K46_K0.186120.619
12_G15_Y0.184750.614
29_R39_C0.182560.607
35_K43_G0.179350.597
8_D49_K0.177070.589
2_K50_D0.176810.588
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
4iqrA199.9-0.187
3dzyA199.9-0.135
2hanB199.8-0.085
2a66A199.8-0.085
1kb2A199.8-0.084
1ynwB199.8-0.083
1r4iA199.8-0.081
1lo1A199.8-0.079
2hanA199.8-0.078
1citA199.8-0.078

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