GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
E1-E2_ATPase - E1-E2 ATPase
Pfam: PF00122 (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: 230
Sequences: 11877
Seq/Len: 51.64
HH_delta: 0.034 (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
70_G118_G1.98684.767
71_I119_V1.542813.702
78_A116_G1.428243.427
74_E117_I1.322423.173
34_K46_K1.298783.116
78_A111_V1.241912.980
39_I117_I1.202532.885
44_W59_I1.095292.628
68_A120_V1.094012.625
57_I117_I1.076632.583
57_I73_L1.064122.553
37_T46_K1.056622.535
105_I118_G1.020592.449
82_E94_K0.997382.393
169_F188_A0.988252.371
57_I119_V0.987342.369
59_I117_I0.961452.307
70_G105_I0.891862.140
37_T44_W0.887422.129
73_L119_V0.880192.112
39_I44_W0.87972.111
37_T64_D0.877882.106
104_I121_I0.876232.102
58_I70_G0.870642.089
71_I121_I0.866942.080
79_Y93_K0.817471.961
66_V80_V0.778691.868
38_V45_Q0.776571.863
40_R45_Q0.776091.862
134_Q138_K0.772721.854
40_R56_D0.77071.849
47_I51_E0.770611.849
54_P123_T0.761911.828
72_L116_G0.761771.828
152_K156_I0.745881.790
52_L68_A0.740561.777
81_D112_V0.731521.755
37_T61_K0.727861.746
172_W184_S0.726821.744
58_I118_G0.7221.732
40_R43_R0.719481.726
95_T103_N0.712431.709
80_V111_V0.711351.707
52_L120_V0.700221.680
143_K151_N0.695321.668
36_V39_I0.684031.641
71_I104_I0.678881.629
55_G119_V0.661631.588
214_R218_N0.653141.567
80_V116_G0.639751.535
173_F181_F0.637641.530
104_I122_A0.636631.528
85_L106_F0.623971.497
95_T101_P0.623311.496
52_L58_I0.604331.450
15_W19_R0.599431.438
70_G121_I0.594371.426
77_S93_K0.591611.420
79_Y113_S0.580971.394
53_V56_D0.571811.372
58_I67_P0.568321.364
77_S95_T0.56561.357
155_K159_I0.558831.341
22_K25_K0.556681.336
170_I174_F0.553971.329
168_V187_F0.55271.326
123_T126_D0.547061.313
48_P51_E0.546611.312
38_V56_D0.545361.309
59_I115_W0.54351.304
34_K48_P0.540261.296
163_A167_L0.539141.294
124_G127_T0.536011.286
61_K64_D0.532561.278
58_I120_V0.527271.265
214_R217_K0.52641.263
11_I15_W0.521561.251
120_V123_T0.520031.248
40_R47_I0.519871.247
108_G129_L0.517961.243
122_A126_D0.51581.238
60_L66_V0.511931.228
18_Y22_K0.505411.213
169_F173_F0.504721.211
60_L111_V0.499131.198
148_R152_K0.490681.177
128_K131_R0.484151.162
39_I59_I0.483331.160
22_K26_K0.482971.159
106_F109_S0.48041.153
85_L128_K0.470751.130
131_R134_Q0.469161.126
14_I18_Y0.466961.120
38_V47_I0.462671.110
82_E109_S0.462531.110
60_L67_P0.458671.101
72_L105_I0.457211.097
224_N227_A0.455641.093
180_S183_K0.454161.090
19_R22_K0.44821.075
44_W117_I0.447011.073
150_L204_L0.4411.058
105_I116_G0.438461.052
226_S230_A0.435681.045
72_L80_V0.435521.045
65_I110_I0.430961.034
26_K29_N0.423421.016
134_Q137_S0.422491.014
84_A109_S0.41681.000
71_I102_G0.416360.999
40_R53_V0.415150.996
162_L166_I0.41220.989
82_E92_V0.409790.983
66_V105_I0.404780.971
33_Q50_S0.401120.962
72_L118_G0.39740.954
56_D68_A0.391610.940
170_I173_F0.388340.932
36_V52_L0.3870.929
53_V123_T0.384920.924
118_G121_I0.384260.922
54_P126_D0.382720.918
184_S188_A0.38240.918
156_I159_I0.381750.916
73_L117_I0.380180.912
86_T92_V0.378890.909
208_L229_E0.376350.903
167_L171_I0.375760.902
60_L118_G0.373090.895
60_L64_D0.371350.891
222_V228_L0.36860.884
80_V94_K0.363460.872
67_P118_G0.361460.867
61_K115_W0.35930.862
127_T130_G0.357220.857
80_V105_I0.356520.855
125_S130_G0.353320.848
128_K132_I0.352520.846
196_I199_A0.34820.835
107_A127_T0.347570.834
47_I56_D0.346260.831
20_S213_R0.345210.828
54_P122_A0.345110.828
49_S52_L0.344490.827
168_V188_A0.340310.817
44_W61_K0.338620.812
39_I57_I0.338080.811
34_K37_T0.335540.805
184_S187_F0.332210.797
18_Y21_K0.331050.794
37_T59_I0.328760.789
161_I164_I0.327140.785
66_V111_V0.325670.781
36_V40_R0.325440.781
156_I160_I0.323320.776
62_A111_V0.321470.771
29_N33_Q0.320780.770
165_A192_L0.320590.769
159_I163_A0.320310.769
94_K103_N0.319890.768
3_L7_L0.319330.766
82_E86_T0.318730.765
143_K147_E0.318330.764
58_I68_A0.318040.763
91_P112_V0.318020.763
6_I10_N0.317680.762
132_I135_L0.316820.760
39_I42_G0.316430.759
21_K25_K0.316390.759
111_V116_G0.31520.756
25_K29_N0.314990.756
179_I183_K0.314670.755
36_V67_P0.314020.753
157_L198_C0.313040.751
68_A127_T0.310680.745
165_A169_F0.310320.745
169_F184_S0.310.744
187_F190_S0.308770.741
157_L161_I0.308560.740
17_E20_S0.307450.738
56_D120_V0.307240.737
45_Q51_E0.307050.737
161_I195_L0.306070.734
183_K187_F0.30410.730
62_A78_A0.302030.725
135_L139_S0.301110.722
142_K226_S0.2980.715
143_K148_R0.295670.709
189_I193_I0.29460.707
85_L88_E0.293130.703
79_Y90_E0.292270.701
45_Q56_D0.292010.701
68_A124_G0.289830.695
72_L94_K0.289070.694
144_S224_N0.288970.693
46_K64_D0.288360.692
74_E101_P0.287960.691
4_F8_L0.287240.689
124_G130_G0.285610.685
150_L157_L0.284990.684
79_Y112_V0.284610.683
160_I164_I0.283430.680
213_R217_K0.281820.676
94_K109_S0.281690.676
88_E94_K0.28140.675
52_L56_D0.281020.674
20_S221_I0.280840.674
106_F128_K0.279330.670
5_L10_N0.278160.667
71_I103_N0.27750.666
168_V192_L0.277350.665
171_I174_F0.276430.663
26_K217_K0.276360.663
39_I43_R0.27610.662
36_V58_I0.275460.661
146_L230_A0.27540.661
101_P104_I0.273990.657
122_A131_R0.273030.655
123_T127_T0.271080.650
81_D110_I0.270810.650
39_I45_Q0.266010.638
196_I200_L0.265010.636
33_Q65_I0.264090.634
185_F189_I0.263690.633
215_L222_V0.262370.630
188_A192_L0.260420.625
10_N17_E0.260110.624
8_L12_I0.259730.623
72_L78_A0.25950.623
146_L204_L0.257240.617
122_A128_K0.257150.617
66_V109_S0.257010.617
153_I157_L0.256880.616
166_I170_I0.255240.612
73_L101_P0.254360.610
144_S208_L0.251990.605
51_E54_P0.250840.602
33_Q48_P0.250710.602
200_L225_L0.249910.600
80_V109_S0.248730.597
168_V191_L0.248150.595
5_L9_S0.247850.595
150_L155_K0.247180.593
6_I186_L0.24710.593
152_K155_K0.246470.591
83_S88_E0.24640.591
7_L11_I0.246180.591
144_S229_E0.246150.591
6_I17_E0.24610.591
65_I81_D0.24590.590
72_L95_T0.244380.586
30_L129_L0.243410.584
101_P106_F0.243220.584
84_A107_A0.240690.578
133_L136_V0.240340.577
38_V53_V0.239970.576
36_V47_I0.238830.573
125_S134_Q0.237030.569
129_L133_L0.236980.569
136_V139_S0.236820.568
177_S180_S0.236310.567
74_E115_W0.235850.566
197_P200_L0.235830.566
173_F184_S0.235350.565
55_G71_I0.235180.564
21_K223_K0.235060.564
147_E226_S0.2350.564
196_I201_P0.234430.563
215_L218_N0.234090.562
33_Q49_S0.233390.560
82_E106_F0.230770.554
79_Y91_P0.230750.554
60_L70_G0.230510.553
139_S142_K0.230360.553
19_R213_R0.230250.552
147_E204_L0.22910.550
66_V116_G0.228930.549
179_I184_S0.227960.547
212_A222_V0.227690.546
186_L190_S0.227310.545
66_V118_G0.226640.544
101_P119_V0.22640.543
105_I111_V0.225510.541
71_I101_P0.225230.540
5_L199_A0.224830.539
9_S196_I0.224070.538
38_V52_L0.224030.538
49_S68_A0.223930.537
149_K152_K0.223510.536
90_E93_K0.223170.535
181_F184_S0.221560.532
77_S101_P0.221530.532
154_A229_E0.220770.530
158_I165_A0.220110.528
32_P36_V0.220020.528
94_K106_F0.219420.526
166_I169_F0.218580.524
158_I162_L0.217450.522
142_K224_N0.217010.521
181_F185_F0.215950.518
46_K61_K0.215850.518
171_I177_S0.215340.517
198_C205_P0.215130.516
38_V58_I0.215010.516
60_L116_G0.214410.514
190_S194_V0.214010.514
25_K28_N0.2140.513
9_S12_I0.213610.513
187_F193_I0.212680.510
72_L76_G0.212260.509
120_V124_G0.212080.509
195_L201_P0.211880.508
2_I159_I0.211540.508
104_I119_V0.211480.507
153_I161_I0.211180.507
210_I214_R0.211090.506
29_N32_P0.210350.505
154_A196_I0.209690.503
9_S13_E0.20920.502
194_V198_C0.208440.500
204_L207_S0.208260.500
195_L199_A0.208150.499
89_S92_V0.208110.499
149_K153_I0.208070.499
34_K49_S0.207390.498
81_D84_A0.207020.497
158_I201_P0.207020.497
72_L103_N0.206960.497
16_Q210_I0.206310.495
142_K147_E0.206110.495
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
3ixzA0.9871000.034
2zxeA0.9871000.034
1mhsA0.96521000.061
3b8cA0.96091000.068
3ar4A0.99571000.077
3rfuA0.96961000.086
3j08A0.96521000.095
3j09A0.96521000.096
2hc8A0.491399.90.442
2kijA0.51399.90.452

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