GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Coat_F - Coat F domain
Pfam: PF07875 (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: CL0044
Length: 64
Sequences: 787
Seq/Len: 12.3
HH_delta: 0.018 (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
17_A25_L0.446552.572
48_Y52_N0.35042.018
14_K26_E0.319951.843
35_I39_I0.281511.622
41_N45_Q0.267651.542
37_Q41_N0.266351.534
33_R48_Y0.257011.480
23_A26_E0.252481.454
17_A21_A0.235781.358
47_Q51_F0.230791.329
10_L50_L0.229311.321
15_A19_N0.22631.304
39_I42_E0.214931.238
3_K32_L0.214831.237
10_L26_E0.212631.225
20_Y43_C0.21221.222
24_A40_L0.210921.215
32_L35_I0.199641.150
13_E44_Q0.199611.150
30_P33_R0.19951.149
52_N55_N0.195651.127
22_T26_E0.192681.110
34_Q52_N0.19141.103
18_R21_A0.190161.095
37_Q45_Q0.189161.090
36_L39_I0.185831.070
13_E46_M0.1851.066
53_Y59_W0.184061.060
4_D56_Q0.183531.057
8_D13_E0.183411.057
43_C46_M0.181341.045
51_F55_N0.180321.039
21_A25_L0.179321.033
9_L50_L0.178961.031
5_I12_S0.175541.011
26_E60_Y0.172540.994
38_Q41_N0.170940.985
36_L48_Y0.170890.984
15_A48_Y0.170770.984
45_Q49_E0.169310.975
40_L44_Q0.167450.965
21_A31_E0.164850.950
2_D16_A0.162060.934
6_A53_Y0.16150.930
16_A57_K0.161170.928
54_M60_Y0.160390.924
10_L60_Y0.158650.914
30_P55_N0.157750.909
10_L47_Q0.156580.902
21_A40_L0.156390.901
4_D8_D0.156370.901
53_Y57_K0.151770.874
14_K51_F0.15010.865
34_Q60_Y0.145190.836
12_S31_E0.143890.829
45_Q56_Q0.142130.819
9_L13_E0.139960.806
2_D59_W0.139570.804
34_Q38_Q0.139450.803
3_K59_W0.137810.794
12_S15_A0.137680.793
8_D36_L0.136090.784
28_A51_F0.135820.782
19_N23_A0.135520.781
11_N51_F0.135270.779
11_N19_N0.134660.776
39_I51_F0.134010.772
36_L40_L0.132760.765
10_L14_K0.132560.764
38_Q42_E0.132260.762
15_A18_R0.131970.760
7_N23_A0.131420.757
4_D29_N0.130980.754
4_D57_K0.13020.750
3_K7_N0.129480.746
24_A37_Q0.127830.736
39_I46_M0.127050.732
13_E20_Y0.126110.726
43_C49_E0.124940.720
46_M49_E0.124730.718
21_A43_C0.124370.716
24_A49_E0.123640.712
46_M50_L0.123420.711
16_A46_M0.123220.710
30_P34_Q0.123120.709
17_A47_Q0.12260.706
13_E43_C0.122560.706
21_A44_Q0.122150.704
39_I43_C0.121910.702
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
2rbdA199.30.018
1vjxA0.906293.30.656
4etrA191.70.673
2rbdA190.80.68
2fzfA190.80.68
1vjxA0.984489.60.688
2e0zA188.20.696
2oh3A187.30.7
2oh3A187.20.7
4etrA0.9062830.717

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