GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CbiA - CobQCobBMinDParA nucleotide binding domain
Pfam: PF01656 (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: 195
Sequences: 17076
Seq/Len: 87.57
HH_delta: 0.202 (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
16_A99_I1.950093.569
125_E157_R1.889223.457
23_L97_Y1.886253.452
28_K97_Y1.691623.096
31_L95_Y1.545632.829
2_A117_A1.478692.706
29_K96_D1.47162.693
3_V19_L1.200432.197
20_A32_L1.156092.116
2_A102_T1.096032.006
28_K96_D1.073931.965
15_I154_V1.065581.950
20_A99_I1.023181.872
68_S72_Y1.004841.839
15_I156_N0.943851.727
16_A32_L0.934961.711
18_N21_Q0.899141.645
23_L99_I0.889141.627
11_G156_N0.886311.622
126_P155_I0.854351.564
119_Y151_I0.853791.562
35_L100_I0.845111.547
22_A26_K0.841961.541
119_Y152_G0.837431.533
59_A62_I0.834841.528
54_E58_N0.820841.502
138_I142_K0.820621.502
55_G58_N0.802631.469
29_K95_Y0.790941.447
21_Q25_R0.77711.422
7_K10_V0.773351.415
74_G77_Y0.771471.412
5_S10_V0.759981.391
3_V121_I0.75961.390
123_P156_N0.749891.372
69_Q72_Y0.749451.372
63_L69_Q0.747941.369
121_I154_V0.740391.355
32_L41_N0.738441.351
17_A41_N0.729591.335
65_N69_Q0.717181.312
68_S73_Q0.710591.300
22_A25_R0.709151.298
122_V137_L0.70161.284
57_E60_N0.697531.277
67_E70_D0.690671.264
84_R88_E0.686271.256
43_S132_E0.682511.249
127_D130_S0.66881.224
65_N70_D0.666751.220
65_N68_S0.661921.211
81_E85_E0.646851.184
139_E143_R0.646211.183
12_K36_D0.641671.174
69_Q73_Q0.640951.173
57_E62_I0.636991.166
33_I100_I0.626021.146
88_E91_I0.615781.127
3_V16_A0.606151.109
85_E89_S0.604411.106
52_L55_G0.600741.099
30_V97_Y0.599081.096
70_D73_Q0.592691.085
33_I98_I0.588631.077
81_E84_R0.586881.074
31_L98_I0.580711.063
17_A46_F0.578111.058
95_Y98_I0.577661.057
23_L30_V0.573061.049
56_L59_A0.565751.035
139_E142_K0.562961.030
30_V96_D0.56191.028
120_V141_L0.561531.028
63_L70_D0.556941.019
125_E130_S0.555581.017
66_F69_Q0.550181.007
52_L57_E0.547881.003
78_L81_E0.544390.996
84_R116_A0.543950.995
66_F72_Y0.535880.981
124_I153_V0.53420.978
44_I129_S0.531540.973
35_L113_A0.526060.963
56_L60_N0.525570.962
89_S92_K0.522810.957
53_R57_E0.51860.949
57_E61_A0.517730.947
52_L56_L0.517380.947
15_I19_L0.513780.940
64_K95_Y0.512380.938
91_I98_I0.511530.936
24_A30_V0.511060.935
58_N62_I0.510910.935
68_S71_I0.508840.931
110_V114_L0.508690.931
17_A42_L0.505840.926
58_N61_A0.497410.910
52_L60_N0.495270.906
31_L90_L0.494840.906
82_L86_I0.493070.902
54_E60_N0.491360.899
33_I87_L0.491020.899
82_L85_E0.490790.898
55_G60_N0.490660.898
15_I123_P0.490390.897
1_I97_Y0.479690.878
54_E57_E0.476210.871
63_L68_S0.471890.864
132_E136_R0.470820.862
64_K67_E0.469410.859
126_P158_V0.468570.858
64_K69_Q0.46820.857
134_A138_I0.468090.857
155_I158_V0.466420.854
12_K104_P0.465220.851
91_I118_D0.462510.846
5_S12_K0.461730.845
63_L66_F0.459950.842
87_L100_I0.459410.841
85_E88_E0.458730.840
66_F70_D0.457530.837
3_V15_I0.457330.837
63_L72_Y0.452920.829
136_R139_E0.452640.828
65_N72_Y0.447380.819
67_E73_Q0.447270.819
34_D101_D0.444210.813
79_D82_L0.443110.811
30_V99_I0.442580.810
121_I152_G0.441920.809
87_L91_I0.44060.806
4_T102_T0.438750.803
110_V113_A0.437070.800
65_N73_Q0.435520.797
35_L103_P0.43430.795
145_G149_K0.432770.792
53_R60_N0.431180.789
40_P43_S0.423280.775
40_P129_S0.423120.774
86_I89_S0.423010.774
132_E135_E0.422390.773
64_K72_Y0.420830.770
52_L62_I0.420210.769
86_I90_L0.415590.761
38_Q107_S0.414310.758
6_G10_V0.414310.758
55_G59_A0.41370.757
2_A113_A0.411130.752
20_A30_V0.410260.751
54_E59_A0.409130.749
29_K93_S0.406440.744
135_E139_E0.405850.743
89_S93_S0.404430.740
67_E72_Y0.403810.739
5_S123_P0.402520.737
111_R140_L0.40060.733
13_T41_N0.395850.724
37_P109_P0.395660.724
52_L59_A0.395160.723
17_A44_I0.392060.717
54_E62_I0.385420.705
137_L141_L0.38220.699
9_G101_D0.380510.696
63_L67_E0.376970.690
42_L45_L0.376240.689
17_A45_L0.374240.685
19_L22_A0.373880.684
124_I134_A0.372490.682
18_N22_A0.370870.679
131_I134_A0.368950.675
13_T101_D0.366880.671
140_L144_L0.36550.669
78_L82_L0.365320.669
113_A117_A0.363210.665
136_R140_L0.363110.665
112_N115_A0.361720.662
115_A145_G0.358970.657
32_L99_I0.35890.657
119_Y149_K0.35690.653
70_D95_Y0.356440.652
48_V65_N0.354420.649
4_T137_L0.351890.644
80_P84_R0.35020.641
64_K68_S0.349730.640
13_T42_L0.34910.639
112_N145_G0.348650.638
6_G105_G0.347440.636
35_L83_L0.346830.635
53_R58_N0.346630.634
36_D104_P0.342310.626
7_K133_G0.341660.625
102_T113_A0.340940.624
142_K145_G0.340790.624
21_Q24_A0.340080.622
39_A42_L0.339640.622
42_L46_F0.337410.617
32_L42_L0.335720.614
119_Y150_I0.334760.613
38_Q104_P0.331580.607
54_E61_A0.330450.605
122_V138_I0.329460.603
131_I135_E0.328610.601
20_A24_A0.328560.601
10_V40_P0.327110.599
7_K101_D0.32480.594
39_A104_P0.323090.591
133_G141_L0.321840.589
56_L61_A0.321640.589
1_I119_Y0.319850.585
16_A20_A0.319070.584
10_V130_S0.31890.584
19_L23_L0.316570.579
20_A41_N0.316560.579
56_L62_I0.316510.579
44_I132_E0.315390.577
41_N45_L0.313850.574
28_K31_L0.313360.573
111_R115_A0.313180.573
122_V150_I0.310660.569
66_F73_Q0.309190.566
144_L148_L0.308280.564
1_I99_I0.308040.564
130_S134_A0.307850.563
83_L87_L0.307720.563
3_V12_K0.307670.563
66_F71_I0.307430.563
52_L58_N0.307170.562
23_L26_K0.306350.561
135_E138_I0.302180.553
64_K70_D0.300920.551
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
3vx3A0.979599.90.202
3k9gA0.943699.90.204
3ea0A0.95999.90.211
3q9lA0.984699.90.212
1wcv10.95999.90.218
4dzzA0.866799.90.219
2xj4A0.969299.90.22
3kjhA0.938599.90.223
1hyqA0.953899.90.227
1g3qA0.948799.90.229

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