GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Na_H_antiport_2 - Na-H antiporter family
Pfam: PF13726 (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: CL0182
Length: 88
Sequences: 3513
Seq/Len: 39.92
HH_delta: 0.664 (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
12_V16_L0.798292.682
82_K85_K0.741422.491
38_G41_E0.72262.427
9_V30_V0.703172.362
68_V72_K0.696632.340
82_K86_K0.601832.022
6_A31_G0.580771.951
78_I82_K0.573841.928
8_L12_V0.567421.906
77_D81_K0.554051.861
48_D52_G0.551511.853
41_E44_S0.514921.730
12_V15_L0.512781.723
19_N22_L0.466661.568
10_M27_A0.453191.522
58_L61_I0.443671.490
7_V10_M0.441941.485
40_G44_S0.393411.322
59_S63_L0.380381.278
71_S77_D0.369791.242
13_L18_V0.369561.241
30_V34_V0.361641.215
81_K85_K0.36141.214
37_L45_A0.35731.200
14_S20_V0.356641.198
41_E45_A0.348841.172
51_G55_E0.34451.157
44_S48_D0.344281.157
70_I75_L0.343021.152
56_T60_Y0.338411.137
18_V23_A0.33721.133
9_V13_L0.336821.131
45_A48_D0.336141.129
13_L23_A0.3341.122
50_M54_A0.322551.084
14_S23_A0.312791.051
13_L26_I0.311441.046
70_I73_S0.307651.033
61_I64_G0.307291.032
21_V24_L0.306471.030
48_D51_G0.299271.005
49_G52_G0.292190.982
68_V71_S0.291450.979
73_S76_T0.290930.977
32_G37_L0.28650.962
78_I81_K0.284020.954
63_L67_A0.283270.952
66_F75_L0.278680.936
49_G53_N0.276010.927
20_V53_N0.274590.922
32_G42_T0.271870.913
57_A60_Y0.269240.904
24_L66_F0.269130.904
55_E60_Y0.26660.896
46_F51_G0.26010.874
11_I31_G0.259670.872
25_L46_F0.25940.871
69_A73_S0.259270.871
18_V26_I0.255790.859
27_A30_V0.253770.852
84_I87_L0.251460.845
22_L26_I0.248270.834
6_A30_V0.246250.827
13_L77_D0.246050.827
68_V79_L0.243740.819
7_V11_I0.241810.812
83_I87_L0.238880.802
12_V81_K0.238150.800
61_I66_F0.236840.796
27_A31_G0.235730.792
34_V62_L0.232810.782
54_A57_A0.230250.773
76_T80_A0.227140.763
20_V64_G0.225170.756
71_S76_T0.225020.756
25_L28_A0.224920.756
11_I14_S0.222030.746
75_L78_I0.221390.744
19_N23_A0.220460.741
74_G77_D0.219650.738
15_L26_I0.217960.732
68_V77_D0.217830.732
58_L62_L0.217230.730
64_G67_A0.217090.729
56_T76_T0.215820.725
67_A73_S0.214940.722
35_G49_G0.213980.719
28_A32_G0.211750.711
19_N72_K0.21070.708
14_S28_A0.209970.705
55_E64_G0.209870.705
65_A68_V0.20980.705
46_F63_L0.209560.704
10_M13_L0.209210.703
64_G76_T0.208930.702
78_I85_K0.20810.699
28_A62_L0.207320.696
50_M58_L0.207240.696
32_G56_T0.205870.692
50_M57_A0.204420.687
11_I15_L0.203810.685
22_L27_A0.202930.682
9_V27_A0.201580.677
46_F53_N0.199180.669
18_V49_G0.197940.665
59_S67_A0.19670.661
32_G45_A0.194580.654
45_A49_G0.193990.652
6_A32_G0.19340.650
62_L65_A0.192950.648
62_L73_S0.192090.645
24_L75_L0.192070.645
35_G77_D0.190520.640
20_V70_I0.19020.639
7_V31_G0.189620.637
29_L39_L0.188760.634
19_N35_G0.188510.633
46_F49_G0.188210.632
60_Y71_S0.18810.632
38_G42_T0.186970.628
33_L44_S0.184370.619
57_A61_I0.183850.618
14_S67_A0.183730.617
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
4f35D0.931894.60.664
3qe7A14.90.868
2vv5A0.97732.80.882
2nwlA0.897720.89
3bz1y0.22731.80.893
3suiB0.14771.70.894
3b60A0.96591.60.896
3udcA0.97731.50.897
4i5sA0.52271.50.897
2zy9A0.79551.50.898
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