GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MgtE_N - MgtE intracellular N domain
Pfam: PF03448 (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: CL0436
Length: 102
Sequences: 3330
Seq/Len: 32.65
HH_delta: 0.128 (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
74_P77_Q0.574582.541
66_A93_I0.558172.468
18_R45_I0.515912.281
90_R94_K0.452352.000
67_A93_I0.395391.748
26_P29_K0.390181.725
14_P17_E0.366951.623
7_A36_E0.353371.562
67_A96_L0.345481.528
6_I33_V0.342611.515
30_A53_E0.342581.515
22_F30_A0.338671.497
46_L54_A0.331871.467
18_R41_T0.329391.456
50_S53_E0.32591.441
22_F45_I0.325731.440
63_S89_E0.324231.434
88_E91_E0.320051.415
7_A33_V0.318241.407
19_A48_A0.302411.337
15_P19_A0.302121.336
68_D71_E0.299781.326
73_L78_R0.293551.298
76_E79_E0.283721.255
80_K83_A0.281271.244
63_S67_A0.280921.242
63_S66_A0.27821.230
13_L17_E0.274231.213
31_A35_E0.266621.179
34_L42_Q0.260021.150
30_A57_I0.258721.144
55_A66_A0.257791.140
92_E95_Q0.256851.136
19_A45_I0.251541.112
10_L18_R0.250991.110
82_L90_R0.250741.109
87_E91_E0.244321.080
6_I29_K0.240941.065
19_A43_A0.240421.063
46_L69_L0.239471.059
39_P72_E0.23741.050
59_A86_D0.237381.050
75_E86_D0.233691.033
64_D67_A0.232871.030
85_L90_R0.227371.005
20_Q87_E0.227231.005
8_E11_E0.226251.000
15_P69_L0.225820.999
33_V37_L0.22430.992
11_E38_D0.223180.987
27_P31_A0.220030.973
46_L79_E0.218420.966
86_D89_E0.218260.965
25_L33_V0.217650.962
79_E94_K0.215450.953
91_E95_Q0.21410.947
11_E41_T0.213430.944
42_Q65_D0.2130.942
78_R82_L0.212610.940
62_D65_D0.211510.935
71_E97_L0.211290.934
66_A69_L0.209320.926
63_S96_L0.208970.924
70_L81_I0.206270.912
34_L57_I0.205050.907
81_I84_A0.204060.902
20_Q23_R0.203880.901
61_M65_D0.203160.898
34_L37_L0.202940.897
21_L98_S0.202460.895
36_E73_L0.201970.893
82_L97_L0.20060.887
51_P76_E0.200150.885
92_E96_L0.199430.882
38_D41_T0.198320.877
31_A39_P0.198080.876
5_D61_M0.194510.860
85_L89_E0.193710.857
39_P68_D0.193060.854
58_L66_A0.192730.852
31_A68_D0.192640.852
25_L47_E0.191190.845
13_L16_E0.190310.841
64_D68_D0.189940.840
7_A32_E0.188680.834
52_E56_E0.188010.831
5_D64_D0.186650.825
35_E65_D0.186210.823
44_E52_E0.185250.819
15_P44_E0.185070.818
45_I48_A0.184160.814
73_L81_I0.180780.799
54_A84_A0.180750.799
20_Q24_L0.180140.797
51_P80_K0.179140.792
17_E20_Q0.17850.789
79_E98_S0.178090.787
23_R26_P0.177940.787
52_E96_L0.177930.787
73_L77_Q0.177550.785
32_E35_E0.176960.782
25_L81_I0.176650.781
16_E20_Q0.176480.780
16_E48_A0.176440.780
28_E60_E0.176110.779
89_E96_L0.1760.778
70_L79_E0.175980.778
71_E89_E0.175560.776
13_L21_L0.174550.772
43_A47_E0.173690.768
19_A23_R0.172860.764
37_L45_I0.17230.762
13_L30_A0.172070.761
48_A76_E0.172070.761
54_A65_D0.171620.759
25_L29_K0.170790.755
31_A57_I0.170170.752
62_D89_E0.169620.750
13_L44_E0.169120.748
54_A57_I0.169020.747
5_D65_D0.167360.740
20_Q27_P0.166590.737
55_A64_D0.16620.735
18_R22_F0.166130.735
28_E40_D0.165650.732
82_L94_K0.16530.731
9_L12_E0.16210.717
7_A37_L0.161950.716
7_A63_S0.161770.715
76_E83_A0.16140.714
70_L97_L0.160910.711
66_A89_E0.160690.711
12_E16_E0.160570.710
43_A70_L0.160230.708
22_F49_L0.159820.707
61_M90_R0.15840.700
65_D96_L0.158340.700
29_K33_V0.158250.700
12_E40_D0.158150.699
7_A31_A0.158050.699
42_Q54_A0.157410.696
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
2ouxA199.40.128
2zy9A199.30.185
2zy9A199.30.188
2ouxA199.30.19
2yvyA199.30.196
2yvyA199.20.233
3pkrA1980.521
3kxrA0.529497.90.529
3hjlA197.60.572
4fhrB197.40.59

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