GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HipA_C - HipA-like C-terminal domain
Pfam: PF07804 (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: 79
Sequences: 1315
Seq/Len: 16.65
HH_delta: 0.105 (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
49_F53_I0.802653.241
66_L75_A0.778263.143
4_Q64_S0.694352.804
4_Q78_Y0.594322.400
42_E46_R0.546452.207
46_R77_A0.527182.129
7_L25_L0.509732.058
30_R40_V0.496512.005
64_S78_Y0.483661.953
50_N58_R0.45321.830
33_S39_D0.434031.753
5_E9_Q0.382991.547
39_D73_R0.371761.501
22_Y47_L0.366251.479
3_H67_Y0.355781.437
41_R45_R0.353251.426
4_Q66_L0.345241.394
11_L28_A0.34521.394
42_E45_R0.317981.284
68_D73_R0.310781.255
8_C60_L0.309071.248
18_K61_K0.308491.246
46_R63_F0.306461.237
6_S18_K0.303991.228
26_A43_L0.29781.203
25_L43_L0.284431.149
58_R63_F0.280251.132
67_Y70_G0.272661.101
22_Y44_F0.269261.087
20_P60_L0.269031.086
6_S78_Y0.267991.082
67_Y72_W0.254861.029
59_H62_N0.254151.026
6_S9_Q0.251271.015
22_Y63_F0.250011.010
8_C15_P0.24981.009
9_Q18_K0.247861.001
62_N79_D0.246140.994
5_E67_Y0.241740.976
7_L11_L0.239870.969
22_Y55_N0.235730.952
59_H79_D0.232010.937
68_D71_G0.231210.934
27_Q31_Q0.22970.928
2_L68_D0.22620.913
15_P61_K0.226110.913
3_H9_Q0.225550.911
22_Y58_R0.224810.908
2_L66_L0.224610.907
26_A40_V0.22360.903
10_L65_F0.222540.899
6_S61_K0.221540.895
58_R72_W0.218480.882
22_Y26_A0.216150.873
29_L43_L0.210020.848
50_N77_A0.209150.845
15_P18_K0.204180.824
7_L63_F0.199820.807
8_C61_K0.199810.807
37_A41_R0.196450.793
57_D62_N0.190310.768
12_G28_A0.189480.765
6_S58_R0.189210.764
76_P79_D0.188290.760
65_F72_W0.187640.758
38_A73_R0.187580.757
22_Y50_N0.186050.751
21_S27_Q0.185230.748
35_D70_G0.183610.741
21_S25_L0.183470.741
5_E65_F0.182050.735
66_L72_W0.181890.734
44_F63_F0.180890.730
17_D40_V0.179770.726
57_D79_D0.178910.722
37_A71_G0.17880.722
42_E74_L0.178420.720
69_G73_R0.178270.720
47_L58_R0.176760.714
46_R75_A0.176680.713
37_A75_A0.176330.712
4_Q10_L0.175820.710
44_F60_L0.175330.708
5_E10_L0.174660.705
38_A41_R0.172320.696
44_F48_V0.1720.695
48_V77_A0.171140.691
43_L63_F0.169940.686
4_Q20_P0.169250.683
7_L43_L0.168540.681
35_D38_A0.167620.677
67_Y75_A0.167140.675
37_A73_R0.16690.674
63_F77_A0.166730.673
39_D42_E0.165870.670
35_D73_R0.165580.669
9_Q61_K0.165090.667
29_L40_V0.163980.662
47_L52_L0.162980.658
62_N78_Y0.162710.657
28_A52_L0.16250.656
10_L28_A0.161590.652
46_R50_N0.16120.651
11_L71_G0.160930.650
8_C18_K0.160580.648
15_P64_S0.159370.644
3_H50_N0.157430.636
23_E71_G0.157130.634
17_D38_A0.156970.634
34_S53_I0.156760.633
57_D78_Y0.156370.631
13_L17_D0.156340.631
27_Q30_R0.155620.628
46_R55_N0.154460.624
28_A31_Q0.154440.624
55_N58_R0.154150.622
31_Q70_G0.153490.620
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
3tpdA0.987399.80.105
3akjA199.70.201
4kqaA0.974790.30.809
1cjaA124.40.884
2zxxC122.40.886
1wlqC115.50.893
1uf2A0.860815.20.894
2wvrC113.40.896
3dn7A0.341811.10.9
3la8A0.59499.30.903

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