GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ABC_sub_bind - ABC transporter substrate binding protein
Pfam: PF04392 (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: CL0144
Length: 294
Sequences: 17263
Seq/Len: 58.72
HH_delta: 0.07 (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_A186_D2.226393.395
62_L245_A2.012013.068
114_R154_K1.977233.015
149_I153_R1.840142.806
120_Q215_F1.740322.654
219_D231_S1.678322.560
23_G26_E1.543182.353
19_G238_G1.504152.294
23_G239_R1.494632.279
23_G243_E1.484812.264
240_Q243_E1.428042.178
122_E126_K1.420022.166
24_L242_A1.385342.113
22_D235_Y1.382722.109
118_E158_K1.377752.101
131_A213_P1.357232.070
247_R252_E1.340062.044
175_E205_Q1.321542.015
117_I121_L1.280721.953
124_I187_A1.234311.882
118_E154_K1.220231.861
122_E155_A1.20521.838
203_I212_I1.191221.817
109_T112_S1.189271.814
125_K159_L1.185261.808
118_E155_A1.166661.779
179_E206_L1.154361.760
233_D236_E1.133771.729
87_C241_A1.130491.724
236_E239_R1.123941.714
115_P119_K1.118231.705
118_E122_E1.111151.695
122_E159_L1.101711.680
121_L125_K1.098731.676
27_L246_V1.085851.656
123_L127_L1.074741.639
23_G242_A1.061381.619
116_P217_S1.057771.613
135_G185_V1.057531.613
19_G235_Y1.05681.612
3_G60_P1.049221.600
136_V191_L1.047471.597
150_E154_K1.041851.589
246_V250_K1.041381.588
210_A213_P1.041151.588
179_E202_A1.024981.563
121_L152_L1.001161.527
178_L188_L0.995711.519
123_L126_K0.994831.517
190_L199_N0.992061.513
133_R162_E0.990621.511
115_P118_E0.982521.498
23_G27_L0.977951.491
151_Q155_A0.965571.473
174_L198_S0.961621.467
236_E240_Q0.959971.464
125_K155_A0.953541.454
114_R150_E0.935561.427
175_E202_A0.934061.425
155_A158_K0.933151.423
153_R157_K0.927581.415
243_E247_R0.926561.413
2_V24_L0.917451.399
3_G55_L0.915511.396
24_L31_E0.907491.384
202_A206_L0.906021.382
215_F228_G0.90111.374
178_L199_N0.899361.372
133_R186_D0.895261.365
39_K51_I0.887611.354
202_A205_Q0.886351.352
147_A150_E0.878581.340
133_R184_K0.867921.324
39_K55_L0.860751.313
119_K122_E0.860231.312
137_L199_N0.855221.304
20_F64_I0.854621.303
208_N211_K0.851571.299
4_I20_F0.845591.290
164_V167_P0.841341.283
122_E158_K0.83391.272
133_R164_V0.822631.255
21_K25_K0.821091.252
117_I189_Y0.807491.231
131_A187_A0.800611.221
47_K50_Q0.79721.216
114_R118_E0.795431.213
193_D229_G0.788281.202
64_I241_A0.786081.199
17_V21_K0.783441.195
20_F242_A0.780071.190
190_L196_V0.767851.171
238_G242_A0.764591.166
150_E153_R0.764391.166
136_V149_I0.763921.165
27_L243_E0.759331.158
53_R77_H0.757931.156
152_L156_A0.757631.155
175_E179_E0.757231.155
235_Y239_R0.753041.148
239_R243_E0.752851.148
198_S202_A0.743161.133
117_I151_Q0.741351.131
121_L151_Q0.740551.129
76_K80_D0.738341.126
22_D26_E0.736481.123
200_F214_V0.733381.118
132_K186_D0.728841.112
125_K161_I0.725441.106
29_Y246_V0.724091.104
146_V150_E0.72231.102
134_I156_A0.721251.100
175_E201_E0.720281.098
121_L155_A0.719311.097
240_Q244_M0.706011.077
27_L250_K0.704621.075
178_L203_I0.70111.069
26_E239_R0.698781.066
4_I31_E0.696221.062
112_S115_P0.694121.059
182_A185_V0.689581.052
179_E205_Q0.686091.046
172_E176_Q0.684391.044
154_K158_K0.679391.036
18_R22_D0.677531.033
107_N248_I0.672451.026
190_L195_L0.67241.025
152_L189_Y0.672271.025
188_L199_N0.66771.018
176_Q180_A0.666211.016
123_L228_G0.661441.009
174_L178_L0.660291.007
22_D239_R0.657771.003
203_I208_N0.657521.003
155_A159_L0.6571.002
156_A161_I0.655210.999
12_A234_Y0.650520.992
209_E213_P0.649590.991
64_I245_A0.647680.988
18_R21_K0.643890.982
173_D176_Q0.633430.966
216_G229_G0.624070.952
85_V248_I0.621940.949
193_D216_G0.619840.945
20_F238_G0.618850.944
245_A249_L0.614840.938
121_L156_A0.614560.937
153_R163_L0.613020.935
49_R53_R0.611690.933
114_R151_Q0.608620.928
127_L213_P0.607620.927
134_I187_A0.605850.924
171_S174_L0.60360.921
193_D196_V0.601670.918
204_L226_A0.598960.913
170_S173_D0.595940.909
62_L249_L0.589530.899
4_I17_V0.588670.898
163_L166_I0.587680.896
165_E168_V0.587230.896
218_S232_V0.583660.890
154_K157_K0.582420.888
47_K51_I0.579730.884
176_Q179_E0.572930.874
42_E47_K0.56910.868
53_R57_A0.564640.861
126_K159_L0.563910.860
177_A180_A0.561630.857
19_G239_R0.556250.848
119_K230_Y0.552370.842
120_Q189_Y0.551710.841
147_A151_Q0.549580.838
37_E60_P0.546840.834
124_I215_F0.54450.830
135_G188_L0.543530.829
127_L131_A0.542360.827
56_K82_I0.539780.823
76_K79_K0.53890.822
193_D219_D0.537760.820
173_D177_A0.536060.818
114_R147_A0.535280.816
116_P119_K0.535110.816
18_R235_Y0.534430.815
203_I214_V0.534250.815
175_E178_L0.531520.811
44_D47_K0.531360.810
120_Q230_Y0.530240.809
136_V189_Y0.528890.807
219_D223_K0.528810.806
16_I87_C0.528520.806
232_V237_Q0.524250.800
25_K47_K0.523050.798
16_I234_Y0.518270.790
192_P195_L0.50970.777
178_L202_A0.508140.775
135_G181_L0.507250.774
171_S201_E0.504330.769
50_Q53_R0.503210.767
62_L85_V0.502950.767
122_E125_K0.500950.764
114_R117_I0.496780.758
189_Y215_F0.495260.755
132_K161_I0.493410.752
235_Y238_G0.492450.751
46_E50_Q0.492230.751
203_I206_L0.491930.750
247_R251_G0.485140.740
21_K31_E0.481920.735
3_G63_I0.480050.732
134_I152_L0.479930.732
15_D235_Y0.476640.727
133_R183_E0.473480.722
174_L177_A0.473410.722
111_V232_V0.471080.718
138_Y149_I0.47050.718
153_R165_E0.469970.717
244_M247_R0.469480.716
170_S174_L0.468030.714
41_A51_I0.467250.713
41_A48_L0.467220.713
207_A210_A0.467070.712
125_K132_K0.466540.712
20_F31_E0.466220.711
201_E205_Q0.466140.711
187_A215_F0.464510.708
29_Y249_L0.462860.706
55_L60_P0.462620.706
62_L83_P0.459150.700
56_K81_D0.458480.699
137_L190_L0.45640.696
118_E151_Q0.454730.693
10_H194_N0.454560.693
88_G237_Q0.452510.690
85_V245_A0.451930.689
72_Q76_K0.447460.682
242_A246_V0.447050.682
136_V152_L0.446820.681
77_H80_D0.44570.680
65_A86_F0.445280.679
178_L181_L0.444860.678
2_V64_I0.44380.677
19_G23_G0.439270.670
10_H13_L0.437310.667
60_P63_I0.435970.665
17_V38_Y0.435310.664
201_E204_L0.432960.660
37_E58_Q0.432730.660
145_S191_L0.431270.658
172_E175_E0.430980.657
196_V216_G0.429160.654
52_A63_I0.427460.652
78_L84_V0.426260.650
54_K58_Q0.426210.650
12_A16_I0.425340.649
207_A211_K0.424720.648
156_A163_L0.424630.648
178_L198_S0.41880.639
71_A74_L0.414460.632
196_V214_V0.414410.632
188_L212_I0.414310.632
15_D18_R0.413250.630
29_Y61_D0.4130.630
39_K54_K0.412460.629
24_L29_Y0.408720.623
22_D25_K0.408320.623
164_V168_V0.408060.622
134_I186_D0.407530.622
189_Y217_S0.407410.621
124_I189_Y0.406510.620
85_V241_A0.406070.619
195_L198_S0.403880.616
64_I87_C0.403860.616
190_L216_G0.40070.611
197_D201_E0.399970.610
3_G39_K0.398850.608
23_G246_V0.397550.606
46_E49_R0.393710.600
62_L241_A0.393310.600
135_G178_L0.392990.599
217_S232_V0.392710.599
148_Q218_S0.391160.597
119_K126_K0.39040.595
107_N112_S0.389910.595
16_I20_F0.389460.594
11_P194_N0.389290.594
21_K40_N0.388380.592
5_L51_I0.387040.590
2_V249_L0.386610.590
248_I251_G0.385240.588
173_D195_L0.384440.586
2_V29_Y0.380670.581
19_G22_D0.380270.580
192_P218_S0.379870.579
53_R56_K0.377690.576
74_L77_H0.376250.574
148_Q232_V0.375880.573
191_L195_L0.375740.573
127_L186_D0.375710.573
233_D237_Q0.375460.573
208_N212_I0.373540.570
74_L78_L0.373440.570
119_K123_L0.372290.568
5_L41_A0.366850.559
20_F241_A0.366560.559
54_K57_A0.36650.559
15_D234_Y0.36620.558
20_F24_L0.365020.557
169_P173_D0.363710.555
27_L247_R0.363480.554
133_R185_V0.363360.554
177_A181_L0.363290.554
30_D37_E0.363040.554
87_C237_Q0.362950.554
196_V227_L0.362880.553
139_D145_S0.362270.552
63_I78_L0.361290.551
148_Q151_Q0.361040.551
88_G144_N0.360480.550
137_L178_L0.358610.547
200_F204_L0.357420.545
2_V242_A0.357330.545
196_V229_G0.357280.545
186_D213_P0.355550.542
83_P249_L0.3550.541
52_A56_K0.354810.541
19_G234_Y0.354620.541
120_Q187_A0.354590.541
244_M248_I0.354430.541
123_L215_F0.354260.540
131_A134_I0.35060.535
162_E165_E0.349950.534
88_G113_E0.349440.533
113_E116_P0.349160.532
19_G242_A0.349030.532
152_L163_L0.34860.532
219_D229_G0.348190.531
56_K59_K0.347130.529
45_P49_R0.346980.529
16_I238_G0.344260.525
201_E226_A0.341480.521
175_E198_S0.340520.519
197_D222_V0.340420.519
48_L51_I0.340120.519
171_S175_E0.33970.518
151_Q154_K0.339170.517
59_K82_I0.338350.516
120_Q124_I0.336270.513
18_R42_E0.335260.511
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
2qh8A0.9831000.07
3lftA0.9831000.086
3lkvA0.99321000.186
3kkeA0.90481000.253
3huuA0.90141000.258
3dbiA0.87761000.259
3k9cA0.90141000.259
2hsgA0.86731000.26
3h5oA0.88781000.266
3qk7A0.90821000.267

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