GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CbbQ_C - CbbQNirQNorQ C-terminal
Pfam: PF08406 (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. )
Length: 86
Sequences: 685
Seq/Len: 7.97
HH_delta: 0.8 (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
29_L81_L0.36822.551
11_L16_A0.313542.172
10_G51_A0.290172.010
6_A13_P0.274641.903
61_R79_R0.270881.877
29_L72_P0.264341.831
12_D15_I0.233491.618
19_L46_A0.228221.581
26_I38_V0.223231.547
9_S44_I0.221361.534
50_I56_P0.2151.490
17_E21_K0.211771.467
26_I81_L0.206781.433
57_R83_D0.195191.352
55_D58_Q0.191931.330
21_K25_A0.188851.308
49_L63_A0.183321.270
2_A17_E0.183141.269
18_K28_N0.181981.261
6_A16_A0.18081.253
22_L82_I0.180221.249
46_A63_A0.177281.228
80_E83_D0.17611.220
14_E18_K0.173791.204
37_T45_Y0.173761.204
60_C82_I0.171171.186
2_A13_P0.170561.182
32_G35_E0.168291.166
4_I59_A0.166261.152
21_K48_R0.1641.136
66_E79_R0.161131.116
11_L15_I0.160091.109
38_V66_E0.157751.093
13_P17_E0.156261.083
11_L50_I0.155441.077
7_R24_N0.154511.070
15_I18_K0.151491.050
29_L40_T0.149521.036
18_K51_A0.149161.033
17_E55_D0.148441.028
6_A14_E0.147661.023
21_K85_V0.146461.015
14_E17_E0.145691.009
3_E13_P0.144861.004
44_I48_R0.143940.997
44_I47_A0.141820.983
65_V82_I0.141140.978
25_A85_V0.140990.977
3_E17_E0.138530.960
22_L56_P0.137790.955
13_P50_I0.137750.954
80_E84_A0.135820.941
8_E36_E0.135750.940
19_L23_A0.135680.940
59_A70_D0.135170.936
32_G60_C0.133940.928
32_G64_I0.133840.927
7_R17_E0.133720.926
14_E77_A0.129680.898
22_L26_I0.129010.894
15_I56_P0.128460.890
65_V79_R0.12790.886
27_R47_A0.127770.885
2_A21_K0.127510.883
5_V14_E0.127190.881
22_L81_L0.126750.878
5_V16_A0.126550.877
34_L72_P0.126530.877
31_G37_T0.126520.877
46_A65_V0.125710.871
6_A17_E0.125470.869
9_S47_A0.125340.868
72_P81_L0.124650.864
72_P80_E0.124590.863
19_L40_T0.122480.849
19_L43_L0.122210.847
40_T77_A0.120970.838
18_K76_E0.120620.836
35_E66_E0.120610.836
31_G75_R0.120250.833
18_K21_K0.119330.827
22_L70_D0.118710.822
36_E67_P0.117920.817
10_G16_A0.116680.808
2_A6_A0.116040.804
20_V65_V0.115670.801
68_L82_I0.115650.801
18_K85_V0.115350.799
32_G85_V0.114860.796
17_E76_E0.114280.792
30_K37_T0.114110.791
36_E68_L0.113720.788
32_G84_A0.11360.787
26_I30_K0.113150.784
64_I71_D0.112420.779
4_I20_V0.111950.776
21_K54_M0.111050.769
15_I39_S0.110550.766
22_L57_R0.110180.763
1_E27_R0.109540.759
20_V47_A0.109290.757
34_L70_D0.107550.745
33_G66_E0.10720.743
8_E20_V0.106910.741
21_K76_E0.106840.740
28_N54_M0.106790.740
9_S24_N0.106490.738
58_Q76_E0.106410.737
46_A69_T0.106320.737
14_E51_A0.106240.736
6_A9_S0.106130.735
50_I54_M0.105860.733
34_L48_R0.105790.733
38_V46_A0.105710.732
43_L64_I0.105640.732
33_G69_T0.105620.732
55_D76_E0.105520.731
26_I66_E0.105320.730
31_G35_E0.105050.728
48_R52_A0.104910.727
44_I69_T0.104260.722
16_A20_V0.103770.719
22_L85_V0.10350.717
27_R39_S0.102740.712
69_T75_R0.101820.705
22_L38_V0.101210.701
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
4akgA0.976789.60.8
3nbxX0.941973.80.833
3f9vA0.907640.843
3f8tA0.90761.20.846
2r44A146.20.858
3vkgA0.976745.40.859
3vf0A0.953541.20.862
2hz7A0.965133.40.869
1qkrA0.953523.10.878
1agxA0.953521.80.879
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