GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ABC_membrane_3 - ABC transporter transmembrane region
Pfam: PF13748 (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: CL0241
Length: 237
Sequences: 16153
Seq/Len: 68.16
HH_delta: 0.279 (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
131_V135_V1.149243.274
83_P87_S1.080493.079
134_L141_G0.842912.402
94_S97_T0.842672.401
34_G38_N0.818432.332
6_R9_R0.777432.215
77_Y81_A0.773612.204
134_L138_F0.766772.185
153_L157_R0.76632.183
93_L97_T0.73742.101
8_H75_R0.730252.081
49_L53_A0.725132.066
188_L192_Y0.700991.997
161_R164_R0.689741.965
172_R191_H0.684441.950
78_A82_V0.646341.842
186_A190_R0.642541.831
81_A85_I0.625381.782
142_L146_L0.610151.738
89_R93_L0.59811.704
138_F142_L0.597511.702
53_A57_L0.588241.676
9_R13_A0.587361.674
184_K187_S0.585151.667
196_S200_I0.579251.650
97_T101_R0.573061.633
215_I219_L0.572731.632
10_K14_L0.56881.621
147_I220_L0.56241.602
13_A17_L0.549541.566
95_V99_A0.549441.565
194_R198_L0.534831.524
176_E184_K0.534061.522
31_L35_F0.532541.517
182_R186_A0.527721.504
19_V121_T0.523811.492
101_R104_L0.522881.490
75_R79_E0.521361.485
130_A141_G0.518811.478
193_R197_R0.518741.478
152_L156_P0.517291.474
127_V131_V0.516251.471
133_L141_G0.510741.455
74_S78_A0.504171.436
189_R193_R0.499471.423
7_R75_R0.493711.407
137_E140_L0.492721.404
200_I204_D0.489791.396
165_L201_R0.482141.374
201_R204_D0.47981.367
96_S100_A0.474111.351
190_R194_R0.469731.338
187_S191_H0.4691.336
185_P189_R0.46631.329
50_M54_L0.460721.313
132_M136_F0.458851.307
134_L145_L0.456951.302
24_V28_L0.454231.294
35_F38_N0.447991.276
172_R176_E0.447391.275
183_R187_S0.446891.273
50_M53_A0.446791.273
168_R198_L0.445051.268
132_M135_V0.437331.246
34_G37_I0.436271.243
54_L58_M0.435041.240
90_Q93_L0.433441.235
137_E141_G0.433081.234
104_L108_F0.427451.218
55_V59_W0.42581.213
79_E83_P0.424671.210
88_Q92_G0.424571.210
27_L128_G0.423461.207
153_L156_P0.421741.202
63_A67_I0.420361.198
146_L149_A0.418491.192
198_L201_R0.416141.186
31_L132_M0.410651.170
8_H11_K0.40961.167
135_V138_F0.408641.164
191_H194_R0.407531.161
154_I212_L0.40721.160
73_F109_V0.401931.145
207_A211_L0.400741.142
82_V86_L0.40061.141
90_Q101_R0.396121.129
195_L199_R0.396061.128
183_R186_A0.395771.128
197_R201_R0.39531.126
47_Q50_M0.394131.123
35_F39_A0.393261.120
218_A222_V0.392951.120
182_R185_P0.392441.118
51_Y54_L0.392031.117
165_L198_L0.392011.117
100_A103_A0.390541.113
175_K179_I0.389541.110
157_R161_R0.387671.105
70_T73_F0.387661.105
10_K13_A0.38591.100
71_R75_R0.384851.097
58_M62_G0.383661.093
164_R168_R0.380771.085
186_A189_R0.380731.085
162_N166_Y0.378091.077
172_R187_S0.378041.077
52_A56_L0.377041.074
161_R205_R0.37681.074
90_Q98_I0.376641.073
110_D114_Q0.374651.067
19_V23_N0.371681.059
161_R165_L0.369821.054
190_R193_R0.369611.053
17_L21_A0.368441.050
149_A153_L0.356851.017
134_L142_L0.355561.013
90_Q94_S0.354491.010
46_W50_M0.353271.007
139_W142_L0.348320.992
192_Y196_S0.34680.988
65_R69_D0.344980.983
133_L144_C0.342940.977
193_R196_S0.342320.975
13_A16_F0.341690.974
106_R110_D0.341570.973
38_N41_L0.341030.972
18_L22_E0.340610.970
174_E178_D0.339540.967
31_L34_G0.336970.960
71_R74_S0.336620.959
187_S190_R0.336240.958
77_Y83_P0.334280.952
219_L223_F0.332620.948
135_V139_W0.332070.946
51_Y55_V0.331860.946
197_R200_I0.331090.943
39_A42_N0.330760.942
100_A104_L0.330360.941
131_V134_L0.330060.940
23_N27_L0.328970.937
81_A87_S0.328590.936
114_Q118_T0.326810.931
201_R205_R0.326570.930
90_Q96_S0.326020.929
221_F224_T0.324720.925
104_L107_E0.324520.925
149_A152_L0.321630.916
181_E184_K0.318460.907
31_L136_F0.317690.905
168_R201_R0.317630.905
203_S207_A0.317040.903
55_V58_M0.315460.899
96_S101_R0.313130.892
35_F51_Y0.312970.892
165_L205_R0.312750.891
53_A56_L0.312490.890
28_L31_L0.312220.890
146_L150_L0.312160.889
96_S174_E0.312110.889
170_N174_E0.312020.889
22_E26_L0.309380.881
34_G136_F0.308780.880
82_V185_P0.308770.880
69_D73_F0.308560.879
78_A81_A0.30790.877
61_I65_R0.30680.874
91_Q94_S0.306640.874
67_I71_R0.303860.866
169_L195_L0.303770.866
56_L60_A0.302760.863
199_R203_S0.302710.862
210_Y214_G0.298770.851
94_S101_R0.296650.845
73_F77_Y0.295820.843
117_P120_I0.295660.842
49_L52_A0.29410.838
14_L18_L0.29360.837
106_R109_V0.293590.837
11_K14_L0.292370.833
81_A176_E0.29160.831
192_Y195_L0.28860.822
23_N26_L0.288390.822
214_G218_A0.28680.817
58_M63_A0.284460.810
103_A106_R0.284420.810
171_N174_E0.28430.810
52_A55_V0.284090.809
29_Y33_I0.283720.808
27_L30_P0.282650.805
23_N125_S0.282410.805
171_N175_K0.279990.798
32_F51_Y0.277310.790
165_L202_L0.277260.790
77_Y85_I0.276920.789
220_L223_F0.276890.789
177_V180_I0.276340.787
125_S129_A0.275820.786
44_D47_Q0.275690.786
165_L168_R0.274490.782
107_E111_F0.274250.781
137_E142_L0.274170.781
46_W49_L0.274060.781
208_L211_L0.273330.779
79_E82_V0.273240.779
162_N165_L0.273030.778
74_S192_Y0.272180.775
109_V112_F0.272170.775
125_S128_G0.271570.774
48_A52_A0.271120.772
9_R12_L0.270080.770
38_N42_N0.269840.769
56_L59_W0.2690.766
145_L149_A0.268450.765
176_E180_I0.268060.764
170_N177_V0.267970.764
51_Y58_M0.267760.763
156_P160_R0.266150.758
172_R175_K0.26560.757
119_L123_V0.265220.756
169_L173_L0.26460.754
173_L178_D0.26390.752
93_L101_R0.263490.751
123_V127_V0.263250.750
75_R78_A0.262380.748
121_T124_V0.262260.747
198_L202_L0.262230.747
130_A134_L0.26210.747
118_T121_T0.26080.743
126_I130_A0.260360.742
83_P86_L0.259920.741
122_S125_S0.259540.739
158_F209_G0.259040.738
58_M61_I0.258760.737
173_L176_E0.257960.735
18_L21_A0.257770.734
94_S99_A0.25590.729
87_S90_Q0.255310.727
76_I79_E0.25470.726
77_Y104_L0.253160.721
154_I216_V0.251670.717
204_D208_L0.250960.715
142_L145_L0.250670.714
89_R98_I0.250510.714
60_A63_A0.250080.713
211_L215_I0.249270.710
107_E110_D0.248640.708
215_I218_A0.248610.708
128_G131_V0.247930.706
121_T125_S0.247480.705
32_F54_L0.247470.705
6_R10_K0.247130.704
150_L154_I0.246470.702
7_R79_E0.246430.702
160_R164_R0.244770.697
130_A145_L0.244130.696
23_N121_T0.243680.694
98_I101_R0.242970.692
66_R70_T0.242520.691
122_S126_I0.241590.688
160_R163_Y0.240040.684
18_L64_A0.239270.682
191_H195_L0.239120.681
69_D72_V0.239090.681
30_P33_I0.238620.680
112_F115_H0.238510.680
84_V90_Q0.238390.679
184_K188_L0.238260.679
77_Y84_V0.237970.678
163_Y167_R0.236070.673
64_A68_Y0.235670.671
84_V87_S0.235280.670
23_N124_V0.234860.669
7_R12_L0.234740.669
93_L98_I0.233410.665
76_I81_A0.232430.662
57_L60_A0.232310.662
80_L105_S0.231870.661
168_R194_R0.231490.660
176_E179_I0.231170.659
91_Q101_R0.230820.658
23_N129_A0.23070.657
152_L155_L0.230520.657
77_Y87_S0.230090.656
15_T19_V0.229820.655
65_R70_T0.229630.654
97_T100_A0.228870.652
60_A64_A0.228280.650
196_S199_R0.228060.650
88_Q91_Q0.227970.650
70_T74_S0.227730.649
63_A66_R0.227610.649
12_L15_T0.227420.648
118_T122_S0.227410.648
16_F19_V0.227170.647
190_R197_R0.226190.644
138_F141_G0.226160.644
55_V62_G0.225870.644
57_L61_I0.225570.643
32_F35_F0.225460.642
80_L83_P0.224140.639
30_P34_G0.223810.638
204_D207_A0.223010.635
28_L35_F0.222390.634
194_R197_R0.221950.632
48_A51_Y0.220330.628
50_M58_M0.219580.626
189_R192_Y0.219430.625
25_L28_L0.219270.625
86_L90_Q0.219010.624
195_L198_L0.218690.623
170_N176_E0.218620.623
72_V75_R0.21770.620
173_L188_L0.217690.620
183_R190_R0.217470.620
199_R202_L0.217190.619
214_G221_F0.216470.617
157_R164_R0.216250.616
74_S189_R0.215830.615
209_G213_I0.214760.612
87_S91_Q0.214630.612
94_S171_N0.214190.610
105_S109_V0.213770.609
80_L102_V0.213640.609
36_A47_Q0.21240.605
151_F213_I0.212330.605
99_A103_A0.212290.605
65_R68_Y0.21120.602
16_F117_P0.211090.601
70_T203_S0.210560.600
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
3b60A199.80.279
3qf4B199.80.279
4f4cA199.80.281
3b5xA199.80.281
3qf4A199.70.292
4a82A199.70.295
2yl4A199.70.298
3g5uA199.70.325
4f4cA199.50.412
3g5uA199.40.444

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