GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
KH_dom-like - KH-domain-like of EngA bacterial GTPase enzymes C-terminal
Pfam: PF14714 (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: 80
Sequences: 1373
Seq/Len: 17.16
HH_delta: 0.077 (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
41_T78_I0.762652.915
57_K79_F0.666482.548
41_T76_R0.661232.527
63_Q66_E0.602082.301
52_L79_F0.596042.278
11_L32_A0.549662.101
4_T8_N0.539852.063
32_A44_L0.491981.881
4_T31_Y0.458991.754
35_V43_V0.426671.631
27_L52_L0.420811.608
14_A60_L0.416871.593
10_F67_A0.390291.492
33_T45_F0.374941.433
54_E57_K0.359761.375
46_V49_P0.3521.345
39_P76_R0.351711.344
68_F72_G0.349541.336
32_A42_F0.343921.315
3_S6_E0.340951.303
6_E9_R0.340761.303
2_I70_F0.337021.288
48_D51_L0.336411.286
29_I44_L0.329351.259
7_L32_A0.328561.256
10_F14_A0.317641.214
14_A63_Q0.313861.200
19_P56_Y0.312071.193
29_I52_L0.310451.187
1_R37_T0.300921.150
21_P53_P0.299251.144
20_P56_Y0.287711.100
27_L48_D0.282911.081
10_F68_F0.282281.079
9_R12_Q0.281421.076
61_E65_R0.279531.068
64_L68_F0.275031.051
27_L46_V0.269681.031
25_K48_D0.269611.031
42_F64_L0.264821.012
12_Q16_E0.261621.000
40_P65_R0.261480.999
11_L64_L0.257420.984
53_P62_N0.253550.969
46_V79_F0.253380.969
8_N31_Y0.252450.965
40_P73_V0.249320.953
17_R63_Q0.24580.940
10_F76_R0.245740.939
43_V78_I0.243680.931
1_R39_P0.241380.923
17_R66_E0.240850.921
28_K36_G0.239470.915
23_K51_L0.237950.910
1_R33_T0.237010.906
39_P73_V0.231190.884
20_P59_Y0.229840.879
15_L20_P0.219730.840
6_E11_L0.219680.840
38_R76_R0.218250.834
5_S9_R0.216840.829
44_L79_F0.214860.821
9_R16_E0.214160.819
2_I68_F0.212890.814
13_K67_A0.212870.814
21_P24_G0.206230.788
14_A59_Y0.205540.786
16_E54_E0.204440.781
58_R61_E0.204430.781
43_V80_R0.203260.777
26_R43_V0.203170.777
19_P49_P0.203110.776
56_Y59_Y0.202910.776
54_E58_R0.202540.774
34_Q80_R0.201950.772
65_R74_P0.199740.763
13_K16_E0.199640.763
21_P56_Y0.1990.761
54_E62_N0.198230.758
19_P58_R0.19790.756
11_L29_I0.194430.743
34_Q69_G0.194120.742
26_R60_L0.192930.737
24_G27_L0.192740.737
6_E67_A0.191610.732
4_T20_P0.190230.727
13_K17_R0.189990.726
35_V45_F0.184070.704
21_P55_S0.184020.703
44_L61_E0.183290.701
62_N66_E0.183170.700
22_S26_R0.182910.699
22_S25_K0.178520.682
40_P58_R0.177660.679
15_L29_I0.176750.676
1_R5_S0.176570.675
25_K51_L0.176440.674
44_L52_L0.17580.672
14_A67_A0.175760.672
17_R59_Y0.173650.664
18_H22_S0.171080.654
34_Q37_T0.171070.654
36_G41_T0.169990.650
40_P72_G0.168340.643
3_S23_K0.167990.642
8_N45_F0.167440.640
8_N33_T0.167380.640
64_L71_E0.1670.638
23_K48_D0.166360.636
7_L42_F0.165230.632
53_P58_R0.16510.631
61_E73_V0.163460.625
2_I34_Q0.163320.624
30_Y47_N0.162250.620
12_Q20_P0.162070.619
12_Q66_E0.161460.617
20_P79_F0.161420.617
26_R55_S0.160890.615
47_N51_L0.159920.611
1_R35_V0.158710.607
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
2hjgA199.90.077
4dcuA199.90.093
1mkyA0.962599.90.156
4djtA0.597.10.757
2qm8A0.687593.90.818
4hvtA0.8520.20.904
4g6cA0.87516.30.908
3iujA0.887515.70.908
1t8sA0.95140.91
2bidA0.862511.20.914

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