GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HATPase_c_5 - GHKL domain
Pfam: PF14501 (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: CL0025
Length: 100
Sequences: 71449
Seq/Len: 714.49
HH_delta: 0.022 (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
40_F98_V3.642462.885
46_E94_T3.328032.636
74_K78_E3.082872.442
33_S44_I2.974612.356
44_I94_T2.959672.344
85_S96_K2.905612.301
29_F48_S2.738082.169
42_V96_K2.718062.153
44_I96_K2.620422.075
21_C48_S2.581172.044
42_V98_V2.559242.027
35_R42_V2.530452.004
31_S46_E2.385681.890
73_V84_L2.254511.786
15_D19_E2.243061.777
47_N51_K2.14121.696
83_S98_V2.099541.663
77_L82_G1.994291.580
37_E42_V1.993021.579
9_I77_L1.905871.510
87_E94_T1.895981.502
87_E96_K1.880311.489
35_R44_I1.857631.471
86_I95_V1.783451.413
13_L95_V1.773661.405
52_E55_K1.751391.387
10_L43_I1.735131.374
9_I73_V1.721221.363
33_S46_E1.702071.348
53_I57_E1.693111.341
13_L73_V1.670351.323
9_I76_I1.655861.312
17_A30_I1.646471.304
85_S98_V1.600771.268
8_R11_G1.600041.267
72_N76_I1.565181.240
88_S93_F1.545631.224
7_C11_G1.540261.220
53_I88_S1.530171.212
52_E57_E1.479011.171
58_S61_S1.442321.142
12_N15_D1.418331.123
71_K75_K1.410871.117
12_N73_V1.387051.099
76_I80_Y1.361661.078
78_E83_S1.324311.049
77_L84_L1.291511.023
75_K79_K1.289761.022
53_I56_L1.272791.008
49_C52_E1.268751.005
11_G15_D1.252220.992
31_S48_S1.250730.991
86_I93_F1.247720.988
77_L97_I1.23780.980
16_N69_G1.193270.945
37_E40_F1.193250.945
40_F83_S1.190040.943
75_K78_E1.179620.934
21_C30_I1.141680.904
52_E56_L1.122580.889
9_I97_I1.105080.875
22_K50_E1.094180.867
46_E92_I1.073920.851
37_E98_V1.073110.850
68_I72_N1.071920.849
10_L14_L1.069130.847
6_L80_Y1.035520.820
54_E57_E1.007190.798
82_G99_I1.003160.795
8_R72_N0.998130.791
17_A45_I0.997070.790
59_S63_K0.977560.774
60_S63_K0.950470.753
34_I41_L0.940720.745
61_S64_K0.938780.744
74_K83_S0.934450.740
53_I86_I0.924780.732
8_R76_I0.922660.731
59_S64_K0.916630.726
47_N92_I0.904360.716
13_L45_I0.900470.713
59_S62_K0.89690.710
21_C24_Y0.896620.710
43_I97_I0.896240.710
16_N20_A0.890980.706
82_G97_I0.864550.685
88_S91_G0.860410.681
51_K93_F0.857940.680
17_A21_C0.856330.678
9_I80_Y0.84020.665
47_N93_F0.838390.664
32_I45_I0.820960.650
36_E40_F0.804040.637
20_A50_E0.784590.621
57_E84_L0.783230.620
46_E89_E0.78110.619
10_L45_I0.77530.614
11_G76_I0.762250.604
85_S94_T0.757590.600
6_L10_L0.750490.594
73_V77_L0.745520.590
42_V85_S0.732450.580
13_L84_L0.73210.580
36_E41_L0.728150.577
58_S62_K0.723060.573
13_L97_I0.719550.570
76_I79_K0.719550.570
77_L80_Y0.714880.566
15_D18_I0.685550.543
9_I12_N0.685450.543
31_S34_I0.683460.541
14_L32_I0.680290.539
8_R12_N0.67760.537
14_L45_I0.67250.533
14_L30_I0.671790.532
7_C79_K0.664780.527
58_S63_K0.65480.519
71_K74_K0.652380.517
89_E92_I0.648520.514
12_N76_I0.643670.510
77_L99_I0.642360.509
16_N67_G0.640980.508
20_A24_Y0.637710.505
34_I43_I0.635120.503
22_K48_S0.634780.503
47_N50_E0.628650.498
19_E65_G0.627590.497
92_I98_V0.622860.493
30_I34_I0.618560.490
24_Y48_S0.615860.488
6_L43_I0.611160.484
13_L77_L0.606450.480
14_L17_A0.605860.480
84_L95_V0.581390.460
72_N75_K0.581080.460
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
4fppA0.9799.40.022
2c2aA199.40.033
3a0rA0.9799.40.043
1y8oA199.40.044
1gkzA199.40.044
4i5sA0.9799.40.047
2e0aA199.40.049
4e01A199.40.051
2btzA199.30.059
2q8gA199.30.061

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