GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ArfGap - Putative GTPase activating protein for Arf
Pfam: PF01412 (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: 116
Sequences: 1160
Seq/Len: 10
HH_delta: 0.006 (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
77_A81_W0.402512.388
16_C19_C0.377022.237
12_G75_K0.360682.140
101_E105_R0.359572.133
33_I77_A0.342312.031
61_W69_M0.319251.894
62_S65_E0.31391.862
27_A61_W0.310311.841
105_R109_V0.294861.749
36_C39_C0.281411.670
37_L41_G0.275051.632
39_C43_H0.262351.557
27_A69_M0.259721.541
17_A35_L0.253741.506
96_D99_K0.248961.477
5_R9_K0.246811.464
95_S99_K0.242531.439
85_S103_F0.242181.437
4_L7_L0.240571.427
3_I70_R0.237841.411
72_G77_A0.233351.385
106_A112_A0.228291.355
103_F107_K0.22781.352
85_S88_P0.226341.343
55_S59_D0.221821.316
104_I107_K0.219521.302
37_L40_A0.218431.296
106_A110_E0.214621.273
68_R72_G0.21171.256
6_E9_K0.209291.242
111_K114_I0.208641.238
41_G44_R0.207911.234
26_W55_S0.20661.226
25_T57_T0.202041.199
13_N16_C0.201361.195
6_E10_K0.201341.195
36_C43_H0.199971.186
31_Y81_W0.194581.155
75_K79_S0.193731.149
89_K96_D0.192651.143
100_R113_F0.192441.142
48_V57_T0.191961.139
28_S33_I0.191791.138
37_L58_M0.190811.132
15_V20_G0.189961.127
63_P67_Q0.189441.124
14_K22_P0.187661.113
13_N19_C0.185311.100
17_A78_N0.182411.082
34_F56_I0.182381.082
25_T58_M0.180781.073
47_G59_D0.179821.067
37_L48_V0.17791.056
66_V69_M0.177491.053
91_P95_S0.177241.052
24_P27_A0.176721.049
10_K75_K0.175391.041
30_N52_R0.174961.038
78_N90_K0.174911.038
26_W59_D0.17331.028
55_S58_M0.172851.026
45_S101_E0.172741.025
26_W51_S0.171481.017
15_V22_P0.170741.013
82_E90_K0.17061.012
68_R71_E0.166760.989
13_N74_N0.164680.977
29_L65_E0.163070.968
76_R79_S0.160450.952
92_P95_S0.160440.952
29_L54_K0.158820.942
67_Q71_E0.158430.940
47_G51_S0.15820.939
4_L24_P0.156770.930
38_E97_Q0.155430.922
78_N107_K0.154860.919
61_W65_E0.152520.905
61_W101_E0.150660.894
11_P87_P0.15060.894
43_H51_S0.150510.893
95_S100_R0.149890.889
51_S59_D0.14970.888
82_E103_F0.148990.884
86_P89_K0.148890.883
26_W37_L0.148610.882
17_A77_A0.147680.876
34_F66_V0.147060.873
70_R100_R0.146830.871
99_K113_F0.146080.867
32_G73_G0.146020.866
80_I114_I0.14510.861
56_I69_M0.14480.859
28_S31_Y0.144760.859
3_I6_E0.14370.853
16_C36_C0.143290.850
88_P92_P0.142340.845
9_K93_P0.141990.842
33_I70_R0.141740.841
106_A113_F0.141130.837
11_P15_V0.1410.837
21_A24_P0.140510.834
30_N104_I0.13980.829
3_I7_L0.139060.825
8_L25_T0.139040.825
63_P106_A0.138780.823
91_P104_I0.138180.820
13_N18_D0.135950.807
6_E96_D0.135730.805
7_L34_F0.135410.803
28_S51_S0.135310.803
44_R59_D0.135220.802
40_A53_V0.134480.798
17_A20_G0.133190.790
11_P71_E0.132350.785
41_G59_D0.132020.783
76_R111_K0.131580.781
28_S59_D0.131130.778
81_W114_I0.129940.771
18_D21_A0.129930.771
45_S52_R0.12930.767
8_L56_I0.129190.767
16_C39_C0.128280.761
62_S68_R0.128220.761
96_D102_Q0.128160.760
41_G58_M0.126370.750
5_R15_V0.126150.748
72_G109_V0.125820.747
48_V72_G0.124880.741
16_C20_G0.124880.741
38_E101_E0.124590.739
90_K106_A0.124090.736
22_P58_M0.12380.735
19_C36_C0.123260.731
52_R55_S0.122680.728
28_S35_L0.122060.724
5_R76_R0.121680.722
40_A55_S0.121170.719
78_N81_W0.120610.716
24_P41_G0.120370.714
7_L70_R0.120320.714
71_E80_I0.120050.712
51_S55_S0.120030.712
42_I48_V0.118980.706
18_D107_K0.11860.704
91_P100_R0.118510.703
34_F65_E0.11820.701
38_E79_S0.117790.699
24_P44_R0.117720.698
14_K50_I0.117650.698
16_C21_A0.117370.696
56_I72_G0.117140.695
40_A58_M0.116960.694
87_P91_P0.116630.692
4_L23_N0.116490.691
70_R93_P0.116250.690
88_P105_R0.115950.688
52_R57_T0.115790.687
10_K101_E0.115420.685
81_W111_K0.115270.684
50_I109_V0.115080.683
93_P98_E0.114270.678
37_L59_D0.114160.677
21_A79_S0.114130.677
4_L75_K0.113780.675
14_K60_N0.113710.675
18_D28_S0.113640.674
61_W67_Q0.113630.674
35_L111_K0.113610.674
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
3jueA11000.006
2iqjA0.98281000.016
3ljuX0.99141000.017
2crrA0.98281000.018
2olmA0.99141000.041
3lvqE11000.105
2owaA0.97411000.122
2b0oE11000.148
2crwA0.88791000.15
3dwdA0.97411000.155

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