GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ABC_membrane - ABC transporter transmembrane region
Pfam: PF00664 (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: 275
Sequences: 24635
Seq/Len: 89.58
HH_delta: -0.025 (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
134_I138_F1.372623.119
175_A212_K1.202312.732
27_D259_G1.183952.690
198_A201_Y1.162682.642
83_K87_L1.06292.415
248_Y253_N1.055912.399
244_I248_Y1.018062.313
27_D257_S1.00452.283
182_F209_A0.993222.257
140_S249_L0.981272.230
137_F144_A0.961882.186
156_L160_I0.894942.034
175_A216_A0.890152.023
178_E212_K0.889792.022
175_A178_E0.841641.912
171_K216_A0.840131.909
41_I45_F0.835961.900
186_S202_F0.832421.892
249_L255_Q0.827461.880
164_K167_K0.823121.870
257_S260_T0.821321.866
23_G27_D0.815651.853
137_F141_W0.800011.818
23_G263_A0.791681.799
204_E208_K0.778431.769
45_F49_A0.768021.745
42_S46_L0.767461.744
96_S99_E0.7671.743
78_K82_E0.751161.707
178_E209_A0.748441.701
168_L219_K0.747351.698
95_N99_E0.744411.692
198_A202_F0.729591.658
182_F205_R0.720111.636
194_K199_E0.715941.627
141_W145_L0.710821.615
143_L264_F0.704591.601
206_F210_L0.70041.592
202_F205_R0.698521.587
245_F249_L0.679341.544
193_I202_F0.677471.539
75_D79_R0.672791.529
91_Y95_N0.670161.523
82_E86_R0.663281.507
212_K216_A0.659491.499
172_Y217_S0.65861.497
142_K255_Q0.655181.489
205_R209_A0.65471.488
200_D204_E0.642711.460
171_K175_A0.642281.459
10_L57_F0.639641.453
201_Y204_E0.639321.453
150_I238_S0.638971.452
145_L149_I0.637211.448
214_R218_F0.634881.443
99_E177_S0.633521.440
40_L44_A0.631791.436
74_K78_K0.630171.432
67_R71_R0.625971.422
38_S42_S0.620351.410
20_L24_Q0.615871.399
7_L57_F0.605771.376
203_L207_N0.597891.359
201_Y205_R0.595811.354
164_K223_I0.589471.339
42_S45_F0.587431.335
19_P267_L0.58351.326
4_A65_S0.581951.322
211_E215_K0.581531.321
80_L104_I0.580861.320
218_F222_K0.577031.311
247_A252_I0.576991.311
136_L144_A0.575441.308
209_A212_K0.573051.302
7_L60_I0.570171.296
157_I230_I0.569981.295
133_L144_A0.567971.291
139_I260_T0.564351.282
155_F159_F0.563461.280
216_A219_K0.562291.278
23_G260_T0.561141.275
79_R83_K0.560911.275
7_L64_L0.56021.273
208_K212_K0.557581.267
170_K174_E0.548221.246
90_S94_K0.547111.243
192_T196_F0.546051.241
140_S256_I0.545181.239
259_G263_A0.544781.238
136_L264_F0.54451.237
142_K249_L0.542921.234
171_K219_K0.54071.229
149_I152_P0.532361.210
246_G261_L0.530691.206
27_D31_S0.528871.202
39_S42_S0.528751.201
200_D203_L0.526821.197
16_L131_F0.526681.197
140_S144_A0.526311.196
164_K168_L0.52541.194
160_I164_K0.520141.182
219_K222_K0.513251.166
135_L139_I0.513141.166
190_I194_K0.511531.162
13_L17_L0.508961.157
138_F141_W0.508211.155
233_F237_L0.50751.153
83_K86_R0.505351.148
251_V256_I0.503541.144
245_F248_Y0.498421.133
130_I134_I0.498091.132
113_N117_S0.495081.125
24_Q28_S0.494111.123
137_F148_L0.492051.118
211_E214_R0.491011.116
142_K145_L0.487641.108
24_Q27_D0.485781.104
59_Y63_Y0.484671.101
89_Y93_D0.484461.101
189_G192_T0.478541.087
146_I245_F0.478541.087
45_F48_I0.47511.080
168_L216_A0.474021.077
246_G251_V0.468961.066
135_L138_F0.46791.063
204_E207_N0.467431.062
84_L92_F0.466891.061
167_K171_K0.463611.053
175_A209_A0.461791.049
207_N211_E0.460451.046
6_L10_L0.458321.041
179_L213_Y0.456191.037
99_E103_R0.45271.029
102_S176_N0.452271.028
205_R208_K0.452051.027
79_R82_E0.451011.025
212_K215_K0.448931.020
47_L51_F0.447381.017
143_L249_L0.447251.016
215_K219_K0.446891.015
249_L253_N0.446151.014
219_K223_I0.446071.014
92_F95_N0.445451.012
152_P156_L0.444641.010
132_S270_Q0.441831.004
91_Y100_L0.440811.002
225_A229_S0.438460.996
168_L223_I0.43790.995
183_L206_F0.436610.992
56_L60_I0.435880.990
171_K174_E0.435040.989
173_Q176_N0.433410.985
20_L23_G0.431070.980
133_L137_F0.429850.977
182_F186_S0.429480.976
107_D173_Q0.428850.974
82_E203_L0.428620.974
53_L57_F0.426490.969
26_I262_V0.426310.969
71_R74_K0.423870.963
96_S181_S0.422910.961
103_R107_D0.420730.956
73_R112_E0.420040.954
8_S124_S0.419560.953
14_L57_F0.417730.949
20_L139_I0.416690.947
44_A48_I0.416590.947
168_L220_Y0.415710.945
16_L19_P0.412460.937
81_F85_L0.411910.936
43_L46_L0.409940.932
4_A68_I0.408210.928
23_G26_I0.408120.927
60_I64_L0.405630.922
102_S107_D0.404510.919
182_F202_F0.401790.913
156_L159_F0.401170.912
172_Y220_Y0.401030.911
175_A213_Y0.397070.902
215_K218_F0.396410.901
169_S220_Y0.394030.895
73_R77_R0.393910.895
119_L122_I0.392520.892
159_F163_K0.389960.886
43_L47_L0.386830.879
131_F134_I0.38450.874
39_S43_L0.384280.873
102_S106_N0.383670.872
168_L171_K0.383650.872
12_G16_L0.383230.871
80_L108_I0.382860.870
76_L108_I0.382240.869
213_Y217_S0.382120.868
241_L245_F0.380670.865
8_S61_Y0.380390.864
256_I261_L0.378280.860
55_F59_Y0.376460.855
73_R108_I0.376230.855
135_L267_L0.374690.851
97_S101_L0.373690.849
161_F227_L0.371070.843
71_R75_D0.369780.840
52_L56_L0.368990.838
208_K211_E0.367790.836
192_T195_A0.366920.834
260_T263_A0.366270.832
140_S143_L0.364970.829
66_S70_Q0.364960.829
88_P91_Y0.364670.829
169_S173_Q0.364330.828
147_L268_S0.36330.826
98_G177_S0.362740.824
69_S116_S0.360940.820
11_S58_S0.360560.819
139_I263_A0.359880.818
20_L135_L0.359770.818
163_K167_K0.359070.816
98_G181_S0.359010.816
160_I163_K0.358840.815
256_I260_T0.358750.815
70_Q73_R0.358530.815
14_L53_L0.357270.812
236_Y240_V0.356940.811
109_E113_N0.35690.811
185_E189_G0.356640.810
129_I133_L0.353730.804
239_I269_S0.353390.803
179_L206_F0.353360.803
76_L111_I0.353040.802
144_A148_L0.35230.801
46_L49_A0.351670.799
107_D111_I0.35150.799
232_Q236_Y0.351490.799
61_Y65_S0.351410.799
249_L254_G0.35110.798
21_L43_L0.349930.795
63_Y66_S0.34940.794
174_E178_E0.34940.794
41_I44_A0.348580.792
28_S31_S0.348250.791
144_A147_L0.345660.785
221_A225_A0.345360.785
24_Q43_L0.343240.780
102_S180_N0.343080.780
226_L229_S0.343060.780
267_L270_Q0.342880.779
263_A267_L0.341630.776
134_I137_F0.341430.776
63_Y67_R0.341320.776
126_I130_I0.341220.775
141_W144_A0.34080.774
137_F145_L0.340640.774
138_F142_K0.340590.774
109_E112_E0.338740.770
49_A53_L0.338480.769
7_L11_S0.338030.768
240_V244_I0.337470.767
186_S193_I0.337270.766
12_G15_S0.336130.764
14_L17_L0.33470.761
74_K210_L0.334650.760
136_L140_S0.333950.759
84_L87_L0.333740.758
17_L50_I0.332890.756
98_G184_S0.33250.756
216_A220_Y0.330040.750
251_V261_L0.329570.749
93_D191_R0.328670.747
178_E181_S0.328540.747
176_N180_N0.328360.746
218_F221_A0.327710.745
110_Q113_N0.327160.743
106_N109_E0.326750.742
125_S128_S0.326560.742
18_F22_L0.326260.741
62_F66_S0.325990.741
48_I52_L0.324630.738
85_L88_P0.324350.737
166_R170_K0.323720.736
7_L10_L0.32340.735
107_D110_Q0.323210.734
144_A264_F0.321650.731
191_R195_A0.321150.730
172_Y176_N0.320470.728
155_F158_S0.320340.728
238_S241_L0.319710.726
84_L100_L0.319490.726
4_A64_L0.318920.725
87_L91_Y0.318270.723
17_L20_L0.318020.723
14_L50_I0.317460.721
75_D78_K0.316490.719
128_S131_F0.316160.718
26_I29_L0.31590.718
44_A47_L0.314960.716
20_L263_A0.314780.715
171_K212_K0.313780.713
54_I59_Y0.313120.712
153_L157_I0.313020.711
102_S177_S0.312750.711
30_S33_N0.312460.710
21_L50_I0.310770.706
193_I199_E0.309280.703
133_L136_L0.309150.702
131_F135_L0.308160.700
220_Y224_Q0.308120.700
38_S41_I0.307680.699
252_I255_Q0.307370.698
124_S128_S0.307260.698
228_S232_Q0.305830.695
68_I72_I0.30540.694
266_S270_Q0.304980.693
132_S267_L0.304840.693
8_S12_G0.304630.692
258_I262_V0.303720.690
179_L183_L0.301870.686
54_I58_S0.301260.685
81_F186_S0.300690.683
98_G102_S0.30.682
5_I8_S0.299990.682
70_Q112_E0.29850.678
117_S121_Q0.298350.678
23_G139_I0.297210.675
20_L267_L0.296920.675
89_Y92_F0.296430.674
64_L67_R0.296290.673
95_N103_R0.295320.671
114_F118_S0.295260.671
248_Y252_I0.295020.670
104_I108_I0.294940.670
176_N213_Y0.293610.667
11_S15_S0.291760.663
157_I234_I0.29140.662
21_L46_L0.290750.661
207_N210_L0.289960.659
10_L53_L0.289110.657
263_A266_S0.288780.656
65_S120_F0.287650.654
21_L24_Q0.287080.652
158_S162_S0.286720.652
241_L244_I0.286580.651
130_I133_L0.286530.651
102_S173_Q0.286450.651
106_N110_Q0.286070.650
87_L92_F0.28480.647
103_R177_S0.283850.645
184_S188_S0.28290.643
237_L241_L0.280880.638
136_L147_L0.280630.638
28_S39_S0.279730.636
210_L214_R0.279120.634
47_L50_I0.278670.633
10_L14_L0.278480.633
183_L186_S0.277730.631
265_L268_S0.277670.631
148_L152_P0.277610.631
210_L213_Y0.277450.630
172_Y216_A0.27740.630
51_F55_F0.277150.630
68_I71_R0.277010.629
57_F60_I0.276870.629
107_D177_S0.276760.629
12_G127_I0.27540.626
40_L43_L0.275250.625
51_F54_I0.275090.625
215_K222_K0.274320.623
143_L246_G0.274140.623
115_L118_S0.273970.623
132_S136_L0.273960.623
230_I234_I0.273410.621
84_L104_I0.273080.621
153_L156_L0.272760.620
28_S32_G0.272440.619
146_I149_I0.272130.618
81_F206_F0.272020.618
69_S112_E0.271820.618
142_K245_F0.27150.617
217_S220_Y0.270840.615
266_S269_S0.270760.615
264_F267_L0.270520.615
145_L148_L0.269590.613
106_N173_Q0.269430.612
85_L89_Y0.269070.611
22_L26_I0.26840.610
140_S145_L0.268360.610
247_A251_V0.268360.610
85_L186_S0.268320.610
23_G29_L0.268250.610
158_S227_L0.267780.608
179_L209_A0.267250.607
142_K146_I0.266930.607
46_L50_I0.266350.605
101_L184_S0.265640.604
193_I198_A0.265420.603
152_P155_F0.264290.601
172_Y213_Y0.263730.599
66_S117_S0.262970.598
64_L68_I0.262590.597
238_S272_I0.262110.596
31_S34_S0.261750.595
22_L266_S0.261640.595
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
4f4cA0.9964100-0.025
3qf4B0.98911000.009
3b60A0.98911000.017
3b5xA0.98911000.018
4a82A0.99641000.02
3qf4A0.98911000.028
2yl4A0.99641000.031
3g5uA0.99641000.033
4f4cA0.996499.90.131
3g5uA0.996499.90.182

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