GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BcrAD_BadFG - BadFBadGBcrABcrD ATPase family
Pfam: PF01869 (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: CL0108
Length: 271
Sequences: 8320
Seq/Len: 30.7
HH_delta: 0.201 (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
16_D20_N1.29334.176
13_V264_A0.784712.534
24_R261_Y0.781972.525
93_V130_R0.754652.437
15_V268_A0.732512.365
204_D243_A0.713042.302
200_A239_A0.709752.292
12_A47_A0.688022.221
93_V97_A0.679972.195
109_I213_V0.678942.192
110_V227_S0.677342.187
68_G98_I0.635042.050
2_G264_A0.633162.044
13_V21_I0.594851.921
107_D220_E0.587111.896
203_A207_A0.586351.893
25_G54_Q0.586051.892
25_G50_E0.584471.887
123_D129_I0.576881.863
207_A243_A0.575621.859
104_T108_G0.570361.842
99_A110_V0.559351.806
241_R245_K0.558521.803
93_V98_I0.545981.763
1_L48_I0.541831.749
214_L244_L0.528561.707
203_A239_A0.524111.692
186_E190_Q0.522411.687
237_V241_R0.514071.660
74_R77_D0.513221.657
12_A51_A0.496721.604
243_A246_E0.491531.587
239_A242_D0.489831.582
137_C212_A0.485881.569
235_P238_K0.483691.562
111_V210_I0.481111.553
203_A240_L0.476811.539
3_I12_A0.476161.537
23_G54_Q0.471681.523
106_E125_D0.47071.520
145_Y148_G0.467941.511
221_K254_I0.46781.510
238_K242_D0.4621.492
39_E42_E0.45891.482
80_E83_E0.457511.477
113_A206_L0.455981.472
187_A192_D0.452321.460
45_K49_E0.450411.454
144_G147_I0.44641.441
242_D246_E0.445631.439
50_E54_Q0.442721.429
210_I240_L0.441381.425
208_E212_A0.441021.424
136_H145_Y0.438391.415
25_G47_A0.437411.412
118_I121_G0.435841.407
2_G267_A0.434661.403
42_E46_E0.434431.403
107_D123_D0.434191.402
7_G115_T0.431851.394
74_R78_E0.429051.385
210_I224_V0.421991.362
189_Q235_P0.415841.343
109_I121_G0.412561.332
108_G122_R0.4111.327
243_A247_K0.409981.324
6_G229_G0.408281.318
193_E197_D0.403481.303
187_A195_A0.401441.296
4_D8_T0.398231.286
200_A243_A0.390141.260
43_N46_E0.385421.244
237_V255_I0.383511.238
106_E220_E0.38261.235
3_I48_I0.380411.228
207_A211_K0.379671.226
185_F199_L0.379571.226
180_F183_T0.377771.220
213_V216_R0.375941.214
6_G115_T0.375691.213
23_G51_A0.374191.208
196_R200_A0.373381.206
46_E50_E0.373351.205
96_A112_I0.372821.204
15_V21_I0.372551.203
111_V119_A0.372421.202
100_L120_Y0.371191.198
182_P186_E0.369561.193
147_I151_A0.365641.181
64_A89_E0.363971.175
30_A43_N0.362341.170
8_T115_T0.362311.170
188_A191_G0.362131.169
96_A120_Y0.361421.167
9_K26_K0.360451.164
153_R157_R0.357291.154
100_L122_R0.354541.145
200_A242_D0.353161.140
204_D208_E0.351491.135
183_T187_A0.351141.134
2_G66_C0.350551.132
108_G221_K0.347541.122
188_A196_R0.341551.103
188_A199_L0.34021.098
253_I256_P0.336981.088
50_E53_S0.336931.088
234_S238_K0.335151.082
203_A243_A0.334891.081
136_H147_I0.334331.079
14_L51_A0.330551.067
13_V24_R0.325291.050
214_L224_V0.322511.041
21_I24_R0.318981.030
187_A190_Q0.318451.028
109_I224_V0.316591.022
242_D245_K0.316491.022
186_E189_Q0.316431.022
147_I152_L0.31491.017
102_G258_E0.314741.016
98_I267_A0.313551.012
254_I257_V0.312791.010
27_G50_E0.312591.009
16_D22_L0.31211.008
238_K241_R0.310411.002
239_A243_A0.310271.002
183_T186_E0.309010.998
110_V114_G0.308160.995
4_D115_T0.307420.993
104_T225_V0.307060.991
244_L253_I0.306320.989
47_A50_E0.305970.988
5_G69_A0.303750.981
107_D129_I0.303610.980
100_L108_G0.303430.980
259_P262_D0.302330.976
112_I263_P0.302060.975
27_G46_E0.302060.975
154_A157_R0.30130.973
14_L62_I0.301120.972
6_G114_G0.30110.972
138_L212_A0.299950.968
49_E53_S0.299330.966
116_G133_G0.298090.962
226_L231_F0.296670.958
142_G145_Y0.296240.956
11_K26_K0.294650.951
69_A73_G0.291570.941
192_D195_A0.291160.940
211_K215_K0.290880.939
27_G43_N0.28990.936
194_V197_D0.288840.933
94_N133_G0.287970.930
15_V265_Y0.287620.929
97_A128_V0.287350.928
12_A25_G0.286770.926
208_E247_K0.286020.923
227_S231_F0.285630.922
210_I244_L0.284860.920
234_S255_I0.28430.918
193_E196_R0.283840.916
1_L14_L0.283590.916
198_I201_E0.283570.916
121_G129_I0.282840.913
148_G152_L0.28180.910
179_V183_T0.281340.908
83_E86_V0.280380.905
123_D127_R0.279980.904
95_D115_T0.279430.902
151_A155_V0.279250.902
121_G217_L0.278920.901
47_A51_A0.278360.899
75_A78_E0.278040.898
234_S237_V0.277450.896
4_D7_G0.277190.895
108_G225_V0.276250.892
207_A247_K0.275220.889
145_Y152_L0.27490.888
96_A118_I0.274180.885
12_A27_G0.273730.884
27_G47_A0.27130.876
82_Q86_V0.271010.875
261_Y264_A0.270930.875
197_D201_E0.270790.874
133_G136_H0.269080.869
11_K24_R0.268710.868
11_K264_A0.266830.862
207_A244_L0.266670.861
46_E49_E0.266440.860
15_V19_G0.266320.860
43_N47_A0.265080.856
25_G51_A0.265070.856
131_F134_W0.265040.856
66_C98_I0.26470.855
99_A112_I0.264010.852
68_G263_P0.263080.849
209_L213_V0.261520.844
258_E265_Y0.261510.844
143_S147_I0.260310.840
119_A134_W0.260130.840
10_T29_G0.258660.835
3_I44_I0.258240.834
42_E45_K0.257860.833
5_G10_T0.257810.832
155_V158_E0.257290.831
152_L155_V0.256920.830
184_V188_A0.256620.829
230_V233_N0.256410.828
144_G149_R0.255240.824
7_G114_G0.254950.823
150_R153_R0.253820.820
4_D229_G0.252860.816
185_F189_Q0.252850.816
4_D11_K0.252720.816
132_G218_G0.252060.814
39_E43_N0.251310.811
123_D126_G0.25110.811
256_P259_P0.251080.811
51_A55_A0.250580.809
188_A195_A0.248270.802
1_L62_I0.248030.801
109_I210_I0.246310.795
237_V240_L0.245750.793
258_E262_D0.245490.793
95_D116_G0.244420.789
227_S230_V0.243080.785
7_G95_D0.24220.782
8_T229_G0.241990.781
95_D99_A0.24180.781
6_G9_K0.241290.779
139_G205_E0.241060.778
147_I150_R0.23960.774
143_S146_W0.239390.773
197_D200_A0.238980.772
146_W149_R0.238570.770
5_G40_A0.238020.768
146_W150_R0.237570.767
38_E42_E0.237490.767
200_A203_A0.237420.767
121_G132_G0.237010.765
155_V159_L0.235760.761
151_A154_A0.235320.760
116_G135_G0.234250.756
114_G229_G0.233630.754
73_G78_E0.233330.753
209_L216_R0.232380.750
210_I226_L0.232010.749
234_S239_A0.231940.749
185_F203_A0.2310.746
145_Y149_R0.230980.746
113_A117_S0.228250.737
261_Y265_Y0.228010.736
113_A231_F0.227280.734
146_W152_L0.226020.730
115_T263_P0.225160.727
37_F40_A0.224390.724
17_E63_A0.222540.719
188_A203_A0.222280.718
131_F137_C0.222270.718
10_T27_G0.221750.716
201_E205_E0.220830.713
45_K48_I0.220760.713
185_F233_N0.220620.712
8_T114_G0.220230.711
204_D239_A0.219420.708
181_A184_V0.215590.696
144_G148_G0.21530.695
5_G44_I0.215250.695
137_C140_D0.214740.693
80_E86_V0.214260.692
133_G139_G0.213810.690
148_G151_A0.213380.689
152_L156_L0.212770.687
232_K260_Q0.21250.686
41_M45_K0.211610.683
21_I265_Y0.211610.683
7_G112_I0.211390.683
99_A263_P0.208950.675
146_W151_A0.208940.675
265_Y268_A0.208710.674
16_D19_G0.207320.669
64_A91_I0.206530.667
235_P239_A0.206510.667
44_I48_I0.206440.667
206_L240_L0.205730.664
205_E209_L0.205170.662
3_I65_I0.204860.661
211_K214_L0.203610.657
4_D263_P0.203450.657
253_I258_E0.203120.656
107_D128_V0.203050.656
23_G55_A0.201320.650
73_G94_N0.200290.647
81_F84_E0.199750.645
209_L214_L0.199490.644
117_S202_A0.199010.643
94_N116_G0.198840.642
142_G152_L0.198830.642
98_I110_V0.198670.641
103_A225_V0.198090.640
3_I67_I0.197960.639
1_L12_A0.197310.637
94_N97_A0.197010.636
173_S176_R0.196790.635
52_L62_I0.196280.634
120_Y128_V0.196010.633
56_G61_D0.194880.629
7_G70_A0.194810.629
95_D98_I0.194760.629
100_L103_A0.19470.629
134_W137_C0.194610.628
150_R201_E0.194170.627
71_G74_R0.193830.626
211_K247_K0.193290.624
26_K182_P0.193270.624
2_G68_G0.193260.624
11_K260_Q0.193210.624
141_E148_G0.193210.624
19_G22_L0.192860.623
125_D129_I0.191790.619
8_T116_G0.19130.618
111_V134_W0.190820.616
138_L208_E0.189630.612
14_L55_A0.189370.611
83_E87_R0.189050.610
109_I119_A0.187560.606
123_D217_L0.186970.604
94_N128_V0.186690.603
139_G143_S0.184840.597
226_L237_V0.184590.596
66_C93_V0.184080.594
100_L110_V0.183980.594
4_D94_N0.183750.593
225_V254_I0.183560.593
129_I217_L0.183550.593
137_C141_E0.183270.592
204_D242_D0.182960.591
215_K249_P0.182720.590
87_R90_V0.181580.586
9_K229_G0.181560.586
112_I118_I0.181340.585
7_G116_G0.18080.584
67_I92_V0.180340.582
4_D114_G0.180160.582
136_H139_G0.180070.581
39_E46_E0.179950.581
107_D122_R0.179660.580
204_D247_K0.17850.576
4_D68_G0.178110.575
107_D125_D0.177890.574
79_Q84_E0.17770.574
258_E261_Y0.177670.574
207_A214_L0.177570.573
226_L240_L0.177410.573
111_V213_V0.177410.573
154_A158_E0.177370.573
52_L55_A0.177360.573
145_Y151_A0.177210.572
212_A215_K0.176850.571
185_F230_V0.176250.569
199_L203_A0.176240.569
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
1z05A0.96681000.201
2qm1A0.97421000.208
4db3A0.94461000.209
1z6rA0.97051000.21
2hoeA0.92621000.213
4ijaA0.94831000.218
3vglA0.94831000.22
2yhwA0.95571000.224
2ap1A0.94461000.227
3r8eA0.9521000.239

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