GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MFS_1_like - MFS_1 like family
Pfam: PF12832 (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: CL0015
Length: 77
Sequences: 49200
Seq/Len: 638.96
HH_delta: -0.013 (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
65_R69_L1.971492.214
33_S36_Q1.850812.078
32_L36_Q1.82142.045
54_L57_F1.807312.029
58_L62_F1.750221.965
63_G66_K1.652041.855
57_F61_K1.585461.780
25_L29_Q1.560531.752
47_I51_A1.490491.673
25_L28_K1.428981.604
66_K69_L1.384951.555
66_K70_L1.37161.540
51_A54_L1.347141.513
62_F66_K1.343221.508
35_S39_I1.29381.453
56_G60_D1.282141.440
16_L48_R1.27931.436
39_I43_I1.277511.434
67_V70_L1.192061.338
50_L53_P1.152721.294
50_L54_L1.148161.289
27_L32_L1.134691.274
11_F15_A1.127921.266
13_F16_L1.123161.261
70_L74_F1.116421.253
15_A18_C1.065771.197
36_Q39_I1.058371.188
46_L49_F1.005711.129
39_I42_A0.99131.113
28_K34_P0.989281.111
36_Q40_L0.965211.084
58_L68_I0.958091.076
62_F67_V0.957821.075
54_L58_L0.943671.060
43_I47_I0.927691.042
24_P28_K0.908291.020
69_L73_L0.905931.017
63_G67_V0.902791.014
9_Y13_F0.885120.994
35_S38_G0.876360.984
20_Y44_R0.86980.977
53_P57_F0.851180.956
27_L34_P0.830750.933
17_G21_P0.829670.932
17_G22_F0.825430.927
28_K37_I0.81440.914
17_G20_Y0.813050.913
27_L37_I0.800320.899
67_V71_G0.79930.897
70_L73_L0.789090.886
13_F52_P0.778310.874
23_L37_I0.770030.865
26_Y30_L0.751570.844
58_L67_V0.747870.840
64_K68_I0.741390.832
55_W58_L0.721830.810
22_F25_L0.714330.802
59_A64_K0.696910.782
42_A46_L0.694740.780
64_K67_V0.684680.769
46_L50_L0.683780.768
47_I50_L0.679640.763
45_P49_F0.678510.762
51_A55_W0.676710.760
69_L72_S0.671570.754
9_Y12_Y0.669750.752
15_A19_L0.658430.739
32_L40_L0.653750.734
21_P25_L0.644720.724
17_G48_R0.626520.703
9_Y16_L0.622350.699
48_R52_P0.620030.696
55_W59_A0.616410.692
26_Y29_Q0.616280.692
44_R48_R0.611930.687
57_F60_D0.61150.687
27_L30_L0.588080.660
14_A18_C0.579470.651
60_D64_K0.576060.647
56_G59_A0.575640.646
44_R47_I0.572170.642
38_G42_A0.571510.642
16_L20_Y0.566720.636
13_F17_G0.560130.629
42_A53_P0.557340.626
38_G41_S0.549310.617
16_L44_R0.544580.611
12_Y15_A0.544280.611
19_L41_S0.54270.609
40_L44_R0.541360.608
34_P37_I0.541020.607
19_L23_L0.534250.600
14_A17_G0.526820.592
48_R71_G0.503870.566
22_F26_Y0.503620.565
62_F68_I0.503350.565
12_Y17_G0.501130.563
15_A21_P0.494980.556
15_A22_F0.4940.555
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
2cfqA198.3-0.013
3o7qA198.10.04
2gfpA198.10.056
4j05A198.10.057
4apsA1980.084
4jr9A1980.084
1pw4A0.98797.90.097
4iu9B197.90.104
2xutA197.80.122
3o7qA197.70.15

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