GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MotA_ExbB - MotATolQExbB proton channel family
Pfam: PF01618 (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. )
Length: 139
Sequences: 3195
Seq/Len: 22.99
HH_delta: 0.907 (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
79_E101_V0.739263.149
48_E131_I0.613682.614
60_T118_P0.540332.302
62_A117_L0.4411.879
55_L127_V0.405571.728
57_I61_I0.400341.705
110_L114_I0.393841.678
74_V106_T0.384191.637
51_L127_V0.374131.594
122_Y126_R0.366361.561
59_R120_Y0.356131.517
126_R130_I0.356051.517
71_L107_A0.335321.428
20_R47_E0.335241.428
32_S35_E0.322761.375
112_V117_L0.316251.347
47_E51_L0.315721.345
21_I43_A0.315531.344
82_Q100_S0.313981.338
60_T121_N0.309541.319
44_L48_E0.30941.318
120_Y124_K0.300671.281
42_E46_R0.293441.250
91_D94_Q0.291661.242
38_E41_E0.290561.238
44_L131_I0.288951.231
32_S36_I0.286571.221
102_A106_T0.285931.218
79_E82_Q0.282891.205
47_E50_R0.282321.203
74_V99_I0.281.193
33_P37_R0.279651.191
65_A112_V0.27521.172
58_L119_F0.274991.171
43_A47_E0.274961.171
67_L99_I0.270191.151
61_I116_A0.269421.148
15_D19_L0.266171.134
67_L113_A0.265291.130
71_L111_V0.264811.128
44_L134_M0.262221.117
16_N134_M0.260291.109
21_I24_A0.260131.108
94_Q97_G0.258921.103
97_G100_S0.258551.101
76_G98_G0.258421.101
58_L116_A0.257861.098
44_L135_E0.25761.097
48_E127_V0.257451.097
37_R41_E0.252851.077
62_A95_L0.25071.068
80_A98_G0.249431.063
131_I135_E0.247921.056
70_L99_I0.247261.053
95_L99_I0.245751.047
16_N19_L0.245421.045
75_I101_V0.24491.043
19_L22_G0.244551.042
67_L103_L0.244541.042
97_G101_V0.243891.039
17_P20_R0.243861.039
64_I68_L0.242831.034
46_R136_E0.242751.034
71_L114_I0.241881.030
73_T81_F0.241631.029
51_L130_I0.235721.004
59_R121_N0.234210.998
128_E131_I0.233460.995
54_N57_I0.23150.986
63_S103_L0.231290.985
19_L24_A0.229120.976
59_R62_A0.228680.974
75_I107_A0.228420.973
70_L113_A0.227930.971
70_L105_T0.227610.970
129_R133_R0.226780.966
28_V31_K0.22580.962
126_R129_R0.225460.960
73_T107_A0.225030.959
112_V116_A0.224420.956
116_A120_Y0.222680.949
64_I118_P0.220490.939
83_A94_Q0.21970.936
81_F98_G0.218810.932
59_R124_K0.216110.921
80_A103_L0.2160.920
71_L75_I0.215660.919
49_E132_H0.21450.914
79_E98_G0.214380.913
23_L27_L0.213970.911
39_A43_A0.211890.903
45_E48_E0.209250.891
36_I40_M0.208950.890
125_R129_R0.207420.884
77_M97_G0.20710.882
20_R24_A0.206660.880
111_V115_P0.20650.880
130_I133_R0.206370.879
31_K35_E0.205590.876
79_E83_A0.204850.873
56_S125_R0.204850.873
66_P113_A0.204420.871
15_D20_R0.202570.863
34_E38_E0.202430.862
17_P21_I0.202320.862
58_L117_L0.201490.858
101_V104_I0.201340.858
78_I104_I0.198790.847
50_R129_R0.198560.846
19_L23_L0.198310.845
81_F100_S0.197850.843
77_M103_L0.196360.836
15_D21_I0.195360.832
49_E133_R0.194060.827
67_L77_M0.192460.820
99_I105_T0.192340.819
85_A95_L0.189960.809
90_G100_S0.189680.808
24_A29_S0.189260.806
35_E39_A0.189190.806
26_L53_R0.189140.806
74_V80_A0.188120.801
53_R129_R0.187650.799
18_F134_M0.187320.798
52_E135_E0.186770.796
18_F22_G0.186750.796
64_I114_I0.186630.795
48_E52_E0.186380.794
52_E131_I0.185680.791
74_V110_L0.184150.784
78_I99_I0.184140.784
27_L31_K0.18390.783
65_A109_G0.183510.782
128_E135_E0.183440.781
49_E136_E0.183160.780
104_I108_Y0.182570.778
72_G105_T0.182440.777
62_A115_P0.181880.775
78_I105_T0.180870.770
92_P97_G0.180230.768
26_L30_G0.179890.766
96_A100_S0.179880.766
67_L92_P0.178690.761
70_L110_L0.178270.759
105_T110_L0.178030.758
74_V102_A0.176020.750
35_E91_D0.175670.748
84_L91_D0.175250.747
80_A95_L0.17480.745
39_A42_E0.174610.744
68_L79_E0.173260.738
85_A90_G0.173220.738
15_D18_F0.172860.736
82_Q85_A0.172520.735
77_M99_I0.172320.734
17_P23_L0.171640.731
77_M107_A0.171410.730
45_E135_E0.171350.730
49_E129_R0.1710.728
64_I70_L0.170930.728
62_A105_T0.170650.727
78_I98_G0.169020.720
19_L26_L0.168730.719
23_L26_L0.168520.718
22_G29_S0.167820.715
80_A99_I0.167680.714
62_A82_Q0.167430.713
53_R56_S0.167140.712
70_L117_L0.16690.711
84_L90_G0.166780.710
35_E119_F0.16660.710
35_E38_E0.166080.707
84_L98_G0.166040.707
107_A111_V0.165810.706
60_T117_L0.165510.705
128_E132_H0.165230.704
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
4i0uA0.827334.70.907
4ev6A0.827328.90.91
3zk1A0.589924.40.913
2x2vA0.438819.70.917
2iubA0.820119.40.917
2xndJ0.467619.40.917
2xquA0.532417.50.918
4f4sA0.496415.90.92
1wu0A0.460414.60.921
4il3A0.992812.70.923
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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