GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
dCMP_cyt_deam_1 - Cytidine and deoxycytidylate deaminase zinc-binding region
Pfam: PF00383 (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. )
Clan: CL0109
Length: 102
Sequences: 7326
Seq/Len: 71.82
HH_delta: 0.001 (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
10_I40_T2.284593.439
75_T97_R1.581982.381
76_L90_I1.469582.212
75_T99_V1.446022.176
10_I13_E1.424252.144
7_F31_V1.406012.116
44_G58_N1.405432.115
51_P85_M1.330542.003
30_I59_A1.319371.986
73_G96_K1.222591.840
88_M92_H1.181581.778
57_M89_A1.175871.770
44_G48_G1.170151.761
7_F37_I1.16441.753
14_L40_T1.101891.659
14_L42_Y1.07011.611
90_I98_V1.056021.589
17_R42_Y1.045831.574
50_N61_R1.037291.561
62_K66_N1.027131.546
53_I61_R1.020121.535
14_L17_R0.924221.391
18_S42_Y0.92311.389
39_A59_A0.89921.353
26_V80_L0.894581.346
32_D36_K0.89311.344
45_E52_T0.8711.311
28_A76_L0.858341.292
53_I58_N0.84051.265
62_K65_R0.833961.255
31_V77_Y0.83311.254
58_N62_K0.810531.220
83_C86_C0.797051.200
84_G87_A0.778761.172
13_E16_K0.777971.171
10_I14_L0.771581.161
41_G59_A0.763111.149
60_I90_I0.761721.147
5_E9_R0.760791.145
48_G51_P0.752521.133
10_I37_I0.738711.112
41_G58_N0.736171.108
12_I16_K0.726051.093
12_I101_G0.721451.086
32_D38_I0.705151.061
39_A62_K0.703471.059
32_D74_C0.697961.051
11_A27_G0.691161.040
32_D73_G0.673561.014
6_E10_I0.657330.989
75_T96_K0.64880.977
21_C42_Y0.63670.958
34_D70_S0.623710.939
9_R13_E0.623240.938
11_A79_T0.61770.930
45_E92_H0.617380.929
28_A55_A0.607520.914
57_M61_R0.603550.908
36_K66_N0.59470.895
16_K19_R0.59180.891
63_A71_L0.586250.882
8_M12_I0.584690.880
39_A66_N0.584270.879
76_L95_I0.579010.872
87_A91_V0.573150.863
72_K94_G0.559820.843
24_F80_L0.55920.842
32_D35_G0.557360.839
61_R89_A0.553620.833
89_A93_A0.546830.823
19_R25_P0.544350.819
29_V38_I0.531330.800
58_N61_R0.531080.799
64_A93_A0.530030.798
27_G42_Y0.519490.782
60_I93_A0.5170.778
13_E17_R0.510240.768
16_K20_P0.509640.767
51_P64_A0.508540.765
60_I64_A0.506570.762
12_I15_A0.501880.755
54_H83_C0.493750.743
60_I89_A0.491540.740
34_D73_G0.485280.730
84_G88_M0.482540.726
50_N85_M0.480250.723
90_I95_I0.479890.722
15_A27_G0.478560.720
32_D39_A0.477190.718
53_I57_M0.471440.710
72_K96_K0.46910.706
26_V92_H0.466390.702
30_I63_A0.46520.700
14_L27_G0.45920.691
29_V37_I0.453060.682
17_R21_C0.452580.681
60_I71_L0.450690.678
18_S25_P0.448760.675
7_F77_Y0.448360.675
7_F11_A0.447180.673
14_L29_V0.444670.669
37_I40_T0.443420.667
15_A25_P0.442650.666
29_V40_T0.438080.659
30_I74_C0.435650.656
43_N56_E0.434140.653
20_P46_P0.433840.653
26_V78_V0.432020.650
7_F29_V0.431780.650
54_H86_C0.426520.642
21_C44_G0.425710.641
8_M101_G0.422080.635
18_S43_N0.419290.631
31_V37_I0.41790.629
6_E17_R0.417760.629
31_V34_D0.416120.626
28_A59_A0.415180.625
11_A29_V0.413830.623
57_M85_M0.413260.622
31_V73_G0.411740.620
38_I74_C0.402430.606
30_I76_L0.399630.602
85_M89_A0.39890.600
48_G58_N0.397470.598
25_P43_N0.394370.594
44_G62_K0.394240.593
9_R12_I0.391010.589
43_N88_M0.387380.583
17_R20_P0.382570.576
41_G44_G0.381140.574
15_A77_Y0.380910.573
24_F45_E0.380640.573
77_Y99_V0.379440.571
24_F43_N0.379370.571
21_C25_P0.378360.569
8_M11_A0.375850.566
15_A18_S0.375840.566
40_T62_K0.372310.560
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
3dh1A0.990299.90.001
2nx8A0.990299.90.004
2b3jA0.990299.90.007
2a8nA0.990299.90.009
1p6oA199.90.021
2g84A199.90.022
1wwrA0.980499.90.028
1z3aA0.990299.90.032
1wkqA0.980499.90.04
2w4lA0.960899.90.054

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