GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GHMP_kinases_N - GHMP kinases N terminal domain
Pfam: PF00288 (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: CL0329
Length: 67
Sequences: 4853
Seq/Len: 72.43
HH_delta: 0.056 (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
37_S40_E1.397932.818
29_N35_P1.129582.277
25_A41_L1.093752.205
29_N34_L1.059822.136
42_A65_Y0.929671.874
22_V64_A0.856891.727
39_E43_K0.795681.604
24_L28_L0.776791.566
29_N36_L0.772361.557
40_E43_K0.768721.550
18_A56_S0.711991.435
23_A27_A0.699221.410
2_I24_L0.647011.304
26_A41_L0.646631.304
32_F35_P0.643881.298
56_S59_D0.63691.284
28_L32_F0.60921.228
29_N41_L0.608541.227
26_A30_K0.595461.200
39_E65_Y0.577391.164
4_I20_L0.561131.131
19_A63_S0.546651.102
25_A44_L0.539391.087
57_G60_D0.528091.065
8_I14_L0.525011.058
42_A64_A0.513971.036
6_S20_L0.513591.035
26_A38_K0.511951.032
46_Q61_A0.511681.031
26_A66_G0.511141.030
38_K65_Y0.504111.016
15_G60_D0.499981.008
30_K33_G0.493250.994
46_Q57_G0.489310.986
43_K47_E0.482870.973
44_L47_E0.460360.928
30_K34_L0.456190.920
15_G56_S0.455280.918
23_A63_S0.450860.909
29_N38_K0.443180.893
24_L27_A0.441690.890
36_L44_L0.437620.882
19_A23_A0.4310.869
25_A45_A0.426930.861
20_L24_L0.420480.848
29_N37_S0.416340.839
15_G21_A0.413070.833
46_Q58_I0.408060.823
38_K41_L0.405830.818
27_A31_L0.401970.810
11_G18_A0.401620.810
22_V45_A0.401360.809
16_S56_S0.39450.795
15_G63_S0.390030.786
12_S15_G0.378110.762
35_P39_E0.377640.761
61_A65_Y0.375790.758
36_L40_E0.373590.753
9_P14_L0.373470.753
15_G59_D0.368550.743
16_S57_G0.368330.743
8_I19_A0.363690.733
34_L47_E0.36250.731
61_A64_A0.361930.730
46_Q56_S0.360930.728
2_I27_A0.358440.723
33_G40_E0.353830.713
41_L64_A0.348710.703
4_I24_L0.346240.698
62_A66_G0.3460.697
35_P40_E0.341520.688
4_I10_P0.338630.683
1_D5_D0.33690.679
29_N40_E0.336760.679
3_E30_K0.334850.675
23_A26_A0.334750.675
40_E44_L0.332930.671
38_K42_A0.327050.659
26_A64_A0.326920.659
56_S62_A0.325710.657
18_A58_I0.325220.656
46_Q60_D0.324520.654
33_G37_S0.323260.652
56_S60_D0.322480.650
42_A61_A0.321970.649
29_N32_F0.320740.647
42_A60_D0.31920.643
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
1pieA199.30.056
1wuuA199.30.061
3k85A199.30.066
1kkhA199.30.085
2hfsA199.30.087
2a2cA199.30.09
2oi2A199.30.098
2x7iA199.30.1
1kvkA199.20.105
1h72C199.20.105

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