GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_22 - AAA domain
Pfam: PF13401 (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: CL0023
Length: 131
Sequences: 47369
Seq/Len: 361.6
HH_delta: 0.268 (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
21_I122_V2.326993.096
21_I92_V1.491321.984
91_L119_V1.395231.857
101_S104_F1.370971.824
11_G15_S1.325151.763
25_A92_V1.308951.742
93_I119_V1.266241.685
71_T74_E1.226351.632
6_I112_L1.213831.615
77_S81_D1.207881.607
40_V47_S1.179981.570
78_L81_D1.176581.566
23_R26_R1.110931.478
6_I121_L1.11.464
57_E89_V1.07081.425
81_D85_R1.060391.411
60_E63_G1.056461.406
76_R80_I1.051981.400
110_S114_E1.04851.395
51_P55_A1.009171.343
70_Q73_D0.997051.327
38_P41_I0.993461.322
39_D42_Y0.992521.321
93_I108_L0.988541.315
42_Y45_C0.975321.298
38_P42_Y0.972051.293
9_I122_V0.938931.249
9_I20_L0.936531.246
107_F110_S0.930341.238
40_V43_V0.929891.237
73_D77_S0.925841.232
39_D45_C0.919411.223
90_L118_K0.917981.222
82_A85_R0.912061.214
53_D56_Q0.91051.212
50_T53_D0.909191.210
23_R27_Q0.904041.203
109_R112_L0.897891.195
57_E61_A0.888861.183
112_L119_V0.883461.176
57_E60_E0.870691.159
19_T23_R0.869361.157
23_R28_L0.864681.151
70_Q74_E0.863771.149
64_L67_K0.856491.140
80_I84_D0.84811.129
56_Q60_E0.841691.120
6_I119_V0.841.118
109_R113_N0.838781.116
13_P124_T0.837131.114
97_D105_L0.828421.102
70_Q75_L0.825881.099
69_R72_S0.8231.095
38_P43_V0.820351.092
23_R30_A0.817411.088
59_L66_L0.815511.085
82_A86_R0.803321.069
52_R56_Q0.800021.065
65_P68_S0.793531.056
54_F58_I0.788571.049
106_E109_R0.77881.036
85_R115_S0.776791.034
26_R30_A0.776181.033
6_I109_R0.775591.032
97_D123_G0.772161.028
53_D57_E0.771561.027
74_E77_S0.764741.018
24_L120_V0.761981.014
91_L117_I0.756961.007
96_A121_L0.752041.001
12_P15_S0.747630.995
102_D106_E0.747470.995
8_V123_G0.744110.990
26_R29_N0.728560.969
78_L82_A0.72360.963
106_E110_S0.72190.961
41_I45_C0.717320.955
18_T94_D0.716840.954
78_L88_V0.712520.948
89_V117_I0.712060.948
108_L119_V0.708470.943
73_D76_R0.706510.940
51_P54_F0.705460.939
45_C48_S0.697870.929
77_S80_I0.696530.927
84_D88_V0.68680.914
42_Y46_P0.679680.904
40_V45_C0.670720.893
44_N48_S0.669750.891
101_S105_L0.665940.886
60_E64_L0.662780.882
111_L117_I0.66150.880
81_D84_D0.660210.879
74_E78_L0.657410.875
97_D124_T0.65450.871
5_R118_K0.653750.870
82_A87_R0.653130.869
79_L86_R0.64660.860
95_E124_T0.644250.857
72_S75_L0.643820.857
104_F112_L0.64080.853
59_L63_G0.640210.852
13_P95_E0.636910.848
54_F57_E0.634170.844
9_I21_I0.631230.840
42_Y47_S0.628670.837
17_K95_E0.626910.834
71_T75_L0.624820.831
43_V47_S0.624640.831
85_R88_V0.624220.831
118_K124_T0.618750.823
55_A59_L0.618410.823
61_A64_L0.607480.808
44_N47_S0.607150.808
22_K28_L0.604380.804
72_S76_R0.603470.803
105_L123_G0.597780.795
69_R75_L0.597430.795
39_D43_V0.596270.793
9_I120_V0.592350.788
75_L79_L0.592230.788
38_P44_N0.589340.784
79_L83_L0.588640.783
72_S78_L0.58440.778
69_R73_D0.580430.772
78_L85_R0.579890.772
40_V48_S0.577940.769
59_L64_L0.577370.768
71_T76_R0.577330.768
118_K122_V0.577160.768
103_E106_E0.572080.761
93_I96_A0.5710.760
90_L120_V0.567730.755
58_I61_A0.564960.752
97_D104_F0.562870.749
81_D87_R0.559780.745
72_S84_D0.559070.744
96_A123_G0.558370.743
64_L68_S0.556260.740
96_A99_L0.555890.740
70_Q78_L0.553760.737
61_A65_P0.546660.727
25_A60_E0.546280.727
61_A93_I0.544280.724
27_Q30_A0.543780.724
76_R79_L0.539710.718
39_D44_N0.535680.713
60_E65_P0.535340.712
95_E123_G0.529760.705
22_K25_A0.529740.705
13_P98_H0.526570.701
103_E107_F0.52420.698
79_L82_A0.523390.696
14_G124_T0.519360.691
39_D46_P0.518970.691
37_H40_V0.512780.682
77_S88_V0.509950.679
30_A37_H0.504370.671
78_L87_R0.50190.668
99_L104_F0.500890.667
85_R114_E0.499760.665
95_E98_H0.49650.661
59_L62_L0.493950.657
84_D87_R0.493430.657
83_L86_R0.492190.655
80_I88_V0.489540.651
43_V46_P0.489270.651
80_I87_R0.488120.650
104_F107_F0.486380.647
93_I121_L0.485850.647
76_R82_A0.481390.641
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
3te6A199.20.268
2v1uA199.10.291
1fnnA0.961899.10.293
2qbyA0.984799.10.3
1w5sA199.10.321
2b8tA0.9237990.327
2qbyB0.9924990.331
1sxjA0.9008990.338
2qenA0.923798.90.356
1r6bX0.885598.90.36

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