GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CbiX - CbiX
Pfam: PF01903 (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: CL0043
Length: 105
Sequences: 4009
Seq/Len: 38.18
HH_delta: 0.067 (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
53_R86_E1.189683.443
28_E45_R1.023642.963
28_E49_Q0.875462.534
38_S41_E0.785262.273
44_E48_A0.746792.161
66_H70_D0.680051.968
36_E41_E0.653281.891
18_R21_E0.635421.839
16_A20_R0.625821.811
16_A29_V0.590211.708
60_F67_V0.576031.667
28_E46_L0.574271.662
26_P49_Q0.563861.632
53_R88_R0.544771.577
57_V90_A0.540361.564
70_D73_E0.533511.544
46_L51_A0.519671.504
33_E66_H0.515911.493
30_A42_A0.510731.478
17_D21_E0.506931.467
17_D20_R0.50521.462
28_E42_A0.492631.426
26_P51_A0.489861.418
14_D17_D0.485571.405
18_R22_R0.471641.365
55_V90_A0.452921.311
13_E17_D0.434181.257
15_L23_L0.433171.254
99_L103_L0.414871.201
55_V88_R0.407971.181
72_P89_V0.405081.172
65_Y69_R0.40461.171
13_E31_F0.39341.139
56_V75_L0.393231.138
14_D18_R0.38781.122
56_V71_I0.386471.119
76_A79_R0.383831.111
11_E14_D0.383741.111
73_E76_A0.383311.109
44_E81_R0.372371.078
12_L29_V0.371711.076
45_R49_Q0.370681.073
44_E78_A0.36881.067
43_L54_I0.366231.060
98_L101_E0.361811.047
43_L78_A0.357841.036
42_A45_R0.347861.007
74_A78_A0.345841.001
42_A46_L0.336380.974
44_E47_V0.331390.959
43_L47_V0.330390.956
51_A54_I0.326160.944
89_V92_P0.325330.942
100_A104_A0.323760.937
78_A81_R0.314760.911
56_V89_V0.314470.910
61_L93_L0.311210.901
19_L23_L0.310890.900
60_F66_H0.308450.893
40_E77_E0.307860.891
97_P101_E0.304260.881
98_L102_L0.304150.880
15_L59_Y0.302970.877
31_F35_A0.300450.870
40_E74_A0.294590.853
33_E70_D0.293410.849
37_P45_R0.292440.846
62_F66_H0.291640.844
72_P75_L0.29120.843
101_E104_A0.287860.833
73_E77_E0.282080.816
37_P41_E0.281610.815
46_L54_I0.27840.806
41_E45_R0.2740.793
63_P66_H0.269170.779
52_R86_E0.267510.774
94_G99_L0.266710.772
37_P42_A0.266060.770
13_E29_V0.265220.768
95_P99_L0.26320.762
47_V85_I0.260450.754
30_A60_F0.257840.746
60_F64_G0.256930.744
66_H72_P0.256430.742
25_V55_V0.255520.740
76_A80_E0.254580.737
12_L15_L0.251630.728
34_F66_H0.251290.727
13_E21_E0.249630.723
13_E16_A0.247440.716
40_E81_R0.246390.713
50_G85_I0.245960.712
11_E15_L0.245740.711
43_L87_V0.243790.706
86_E91_P0.242940.703
68_K72_P0.240570.696
66_H69_R0.239030.692
31_F37_P0.238320.690
12_L31_F0.23690.686
60_F69_R0.236530.685
63_P67_V0.235690.682
12_L16_A0.233410.676
67_V92_P0.232380.673
46_L49_Q0.231820.671
14_D21_E0.225590.653
12_L30_A0.224940.651
39_L71_I0.224480.650
30_A89_V0.222720.645
74_A77_E0.221960.642
92_P95_P0.221130.640
80_E91_P0.221070.640
66_H94_G0.220810.639
63_P68_K0.220330.638
11_E35_A0.219840.636
34_F64_G0.218780.633
28_E51_A0.218340.632
58_P67_V0.218110.631
75_L79_R0.216860.628
64_G67_V0.215760.624
39_L73_E0.215620.624
90_A98_L0.214520.621
33_E67_V0.214030.619
31_F61_L0.21360.618
54_I85_I0.211910.613
33_E102_L0.210810.610
47_V78_A0.210440.609
59_Y103_L0.210040.608
33_E60_F0.209850.607
95_P104_A0.209460.606
38_S42_A0.208170.603
21_E24_P0.207860.602
64_G68_K0.206880.599
67_V89_V0.205730.595
77_E80_E0.205380.594
26_P46_L0.204360.591
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
3lyhA0.98199.70.067
1tjnA0.971499.70.091
2xwsA0.971499.60.111
2jh3A0.961999.60.177
2xvyA0.971499.60.177
2xwpA0.971499.50.2
2h1vA0.990599.40.234
2xwpA0.971499.40.236
2xvyA0.971499.40.269
1lbqA0.98199.40.275

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