GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
POTRA_1 - POTRA domain FtsQ-type
Pfam: PF08478 (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: CL0191
Length: 69
Sequences: 3643
Seq/Len: 52.8
HH_delta: 0.027 (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
9_S65_K1.069942.622
8_V19_I0.998182.446
9_S63_E0.975462.391
16_K20_L0.923432.263
7_E63_E0.916052.245
5_K61_T0.902672.212
23_L64_I0.757461.856
40_E44_E0.747641.832
57_R63_E0.710441.741
15_S18_E0.702951.723
50_K67_K0.681481.670
22_A46_L0.679331.665
55_S65_K0.614451.506
53_S65_K0.605221.483
11_N16_K0.569081.395
51_S67_K0.541441.327
4_K60_N0.527181.292
13_Y48_W0.521131.277
35_D38_K0.50641.241
11_N19_I0.504571.237
18_E22_A0.499551.224
37_K40_E0.498411.221
8_V20_L0.486591.193
11_N68_E0.482321.182
7_E61_T0.479481.175
46_L49_V0.477891.171
50_K69_R0.476381.167
12_S68_E0.457491.121
44_E52_V0.454721.114
44_E51_S0.452741.110
38_K42_R0.452291.108
30_N33_S0.446751.095
56_R62_L0.439151.076
38_K41_Q0.434511.065
18_E21_Q0.425391.043
36_L54_V0.419441.028
13_Y68_E0.417791.024
31_L36_L0.413821.014
54_V64_I0.413571.014
36_L56_R0.401510.984
43_L66_V0.400070.980
31_L58_F0.392740.963
25_I39_I0.379060.929
7_E57_R0.378940.929
3_V6_I0.369330.905
34_L49_V0.364580.894
41_Q44_E0.363220.890
4_K61_T0.360810.884
14_L46_L0.354190.868
49_V52_V0.353660.867
32_F35_D0.350060.858
49_V66_V0.349840.857
2_R30_N0.344090.843
17_E21_Q0.342370.839
43_L49_V0.336910.826
14_L48_W0.330240.809
26_Q29_K0.329090.807
39_I54_V0.326330.800
23_L29_K0.326040.799
25_I29_K0.325380.797
37_K41_Q0.312470.766
23_L39_I0.309080.757
55_S63_E0.307630.754
36_L40_E0.300730.737
3_V31_L0.300620.737
11_N14_L0.300340.736
24_G39_I0.298410.731
40_E51_S0.289450.709
32_F49_V0.288660.707
56_R59_P0.288590.707
25_I62_L0.287260.704
29_K35_D0.286980.703
17_E20_L0.28390.696
18_E48_W0.279680.685
23_L26_Q0.279030.684
31_L56_R0.276990.679
5_K27_K0.274210.672
32_F36_L0.272450.668
30_N58_F0.272240.667
3_V62_L0.269550.661
2_R29_K0.268130.657
10_G68_E0.264640.649
39_I64_I0.263310.645
57_R61_T0.259720.637
43_L52_V0.255280.626
25_I28_G0.252550.619
40_E50_K0.248760.610
31_L69_R0.248270.608
8_V23_L0.244250.599
14_L45_K0.243120.596
4_K34_L0.237840.583
56_R60_N0.235380.577
32_F56_R0.233070.571
11_N66_V0.232450.570
20_L23_L0.23090.566
22_A42_R0.22930.562
40_E54_V0.227510.558
39_I42_R0.22670.556
61_T65_K0.225390.552
19_I43_L0.220460.540
41_Q45_K0.219190.537
24_G29_K0.213880.524
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
2vh2A1990.027
2vh1A0.97198.90.062
3efcA0.985598.40.218
3q6bA0.985598.10.296
2qdfA0.985597.90.325
3mc9A197.70.368
3mc9A197.70.37
3efcA0.94297.60.381
2x8xX197.60.387
2x8xX197.40.407

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