GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EamA - EamA-like transporter family
Pfam: PF00892 (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: CL0184
Length: 126
Sequences: 33861
Seq/Len: 268.74
HH_delta: 0.404 (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
73_Y77_Y2.384183.151
98_G104_E1.970732.605
10_S72_F1.898382.509
107_S110_Q1.8132.396
49_S52_Q1.662332.197
73_Y76_K1.630262.155
18_S21_S1.547462.045
89_L93_F1.523682.014
35_I38_L1.497071.979
79_S82_I1.480921.957
50_P54_L1.324891.751
75_L83_V1.301251.720
32_I35_I1.201381.588
108_W112_I1.19611.581
98_G102_L1.190281.573
50_P53_W1.185551.567
36_L40_L1.170241.547
51_R54_L1.116271.475
7_S71_Y1.081511.429
99_W106_P1.070821.415
115_I119_I1.058441.399
78_I82_I1.023481.353
97_L101_F1.017291.344
24_F28_L0.992261.311
78_I83_V0.985321.302
111_I115_I0.977741.292
35_I39_I0.970581.283
71_Y75_L0.960591.270
108_W111_I0.954011.261
64_T68_Y0.949481.255
49_S53_W0.946541.251
69_L73_Y0.945751.250
12_K16_K0.935491.236
21_S25_W0.926741.225
95_A114_I0.923741.221
54_L58_F0.91971.215
55_W58_F0.912541.206
107_S111_I0.91191.205
11_K15_K0.886241.171
51_R55_W0.880521.164
38_L41_G0.869651.149
99_W105_R0.866241.145
93_F97_L0.851591.125
60_G65_A0.840471.111
11_K80_A0.839591.110
12_K15_K0.839141.109
106_P111_I0.835641.104
13_L22_I0.834541.103
74_A78_I0.83091.098
104_E110_Q0.819971.084
20_L69_L0.818111.081
17_I22_I0.797791.054
56_L60_G0.797041.053
74_A83_V0.795281.051
95_A99_W0.786961.040
109_R112_I0.77881.029
34_L38_L0.777041.027
100_L103_G0.761961.007
95_A110_Q0.761331.006
31_G34_L0.756291.000
6_Y72_F0.755480.998
89_L92_V0.753810.996
23_T72_F0.746630.987
10_S14_L0.738550.976
10_S75_L0.732750.968
97_L100_L0.7320.967
29_I32_I0.728890.963
7_S84_S0.720960.953
38_L43_K0.713230.943
92_V117_I0.708540.936
25_W29_I0.707740.935
53_W57_L0.704480.931
70_L73_Y0.7040.930
21_S24_F0.70310.929
79_S83_V0.70210.928
67_A71_Y0.69890.924
110_Q114_I0.694840.918
6_Y10_S0.689860.912
106_P110_Q0.6880.909
49_S54_L0.686720.908
114_I118_I0.685890.906
66_L70_L0.683850.904
65_A69_L0.682140.902
72_F76_K0.679210.898
58_F61_L0.675580.893
54_L57_L0.669980.885
71_Y83_V0.66620.880
75_L79_S0.665560.880
30_A33_L0.662880.876
52_Q55_W0.662170.875
57_L60_G0.660660.873
92_V114_I0.658780.871
87_Q90_S0.658380.870
37_L41_G0.657310.869
6_Y26_R0.655220.866
112_I116_L0.654370.865
95_A106_P0.65040.860
3_W7_S0.64430.852
24_F31_G0.640880.847
96_I100_L0.640140.846
4_A8_V0.629730.832
23_T26_R0.624280.825
82_I85_I0.616840.815
6_Y68_Y0.615410.813
28_L32_I0.611350.808
111_I114_I0.60890.805
11_K79_S0.606780.802
5_I9_F0.606590.802
55_W59_L0.602110.796
7_S87_Q0.599430.792
99_W102_L0.599280.792
46_K49_S0.598880.791
17_I21_S0.598320.791
94_A98_G0.596280.788
6_Y71_Y0.58930.779
47_N50_P0.589040.778
112_I115_I0.588180.777
88_Y91_P0.58570.774
105_R109_R0.584940.773
27_F68_Y0.582920.770
10_S23_T0.581020.768
23_T27_F0.580510.767
80_A84_S0.577990.764
95_A98_G0.57790.764
36_L39_I0.573980.759
40_L43_K0.572420.757
7_S80_A0.57230.756
88_Y121_V0.571020.755
64_T67_A0.570510.754
48_L53_W0.570460.754
5_I8_V0.565520.747
11_K75_L0.565330.747
119_I123_L0.564460.746
58_F62_L0.563770.745
6_Y87_Q0.561490.742
74_A77_Y0.560640.741
107_S112_I0.55920.739
46_K50_P0.556960.736
3_W87_Q0.555660.734
19_P23_T0.555640.734
38_L42_R0.552270.730
78_I81_S0.55220.730
62_L66_L0.54980.727
37_L40_L0.548190.724
105_R108_W0.547880.724
47_N53_W0.539690.713
53_W56_L0.536530.709
14_L22_I0.536150.709
66_L69_L0.534680.707
112_I119_I0.534480.706
23_T68_Y0.534460.706
70_L74_A0.528740.699
48_L52_Q0.528050.698
82_I86_L0.527440.697
67_A90_S0.527160.697
8_V80_A0.525870.695
48_L51_R0.525190.694
39_I42_R0.525120.694
14_L76_K0.520440.688
67_A88_Y0.512790.678
85_I124_I0.512670.678
7_S88_Y0.510940.675
23_T69_L0.509810.674
87_Q91_P0.50720.670
98_G101_F0.504020.666
52_Q56_L0.503280.665
43_K46_K0.502270.664
6_Y9_F0.499460.660
90_S94_A0.498650.659
90_S93_F0.498010.658
113_G116_L0.497780.658
96_I99_W0.497250.657
20_L73_Y0.496790.657
8_V11_K0.49530.655
67_A84_S0.49250.651
25_W28_L0.49020.648
10_S13_L0.489770.647
27_F64_T0.488690.646
68_Y71_Y0.488570.646
67_A87_Q0.487660.645
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
2i68A0.801698.40.404
3b5dA0.801698.20.452
4he8J0.96034.40.876
3rkoM0.357140.878
4ev6A0.59523.90.879
4i0uA0.58733.20.884
4j05A12.80.886
2iubA0.59522.60.889
4gx0A0.72221.60.9
3j01B0.38891.20.907

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