GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATPgrasp_TupA - TupA-like ATPgrasp
Pfam: PF14305 (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: CL0179
Length: 239
Sequences: 7794
Seq/Len: 32.61
HH_delta: 0.353 (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
39_P116_E1.181323.167
53_D78_K1.086272.912
77_S80_D1.076782.887
186_E190_K1.071382.872
205_V208_K1.042862.796
30_E194_G1.028622.758
177_K180_N1.013672.718
25_R115_E0.990412.655
36_Y208_K0.91382.450
28_V211_F0.912122.445
57_D78_K0.853172.287
189_E193_K0.799932.145
178_P182_E0.782732.099
22_Y26_E0.774152.076
46_N49_D0.77312.073
204_N209_I0.760272.038
41_L54_S0.750572.012
78_K82_E0.735621.972
183_E186_E0.683431.832
16_T23_A0.675281.810
24_V28_V0.674671.809
17_K23_A0.655771.758
20_D64_N0.631581.693
82_E86_K0.604661.621
203_Y212_G0.587081.574
182_E185_I0.585531.570
200_V214_L0.571971.534
50_I85_K0.569951.528
60_V74_R0.557841.496
138_P189_E0.549241.473
26_E30_E0.545471.462
76_K80_D0.542011.453
36_Y187_I0.52961.420
188_A202_L0.518621.390
129_Y143_V0.518281.390
26_E29_E0.505911.356
39_P54_S0.503111.349
55_L59_F0.501921.346
182_E186_E0.501911.346
59_F114_V0.500561.342
205_V210_Y0.51.341
118_L210_Y0.493311.323
116_E210_Y0.487711.308
23_A26_E0.483181.295
80_D83_E0.481341.291
181_L185_I0.480541.288
83_E87_K0.477281.280
131_F188_A0.47631.277
186_E189_E0.473521.270
185_I189_E0.472071.266
197_F217_T0.471661.265
179_K207_G0.470221.261
61_I114_V0.468141.255
57_D77_S0.462541.240
60_V72_I0.460291.234
28_V191_L0.457661.227
17_K27_Y0.456551.224
180_N204_N0.451491.210
29_E37_L0.444591.192
51_D54_S0.436991.172
180_N183_E0.42531.140
37_L40_L0.420381.127
21_K62_K0.419631.125
192_S198_V0.415251.113
183_E187_I0.414261.111
61_I84_A0.414231.111
64_N111_R0.413921.110
45_D49_D0.412591.106
38_P210_Y0.412261.105
79_L82_E0.408241.095
17_K30_E0.403841.083
25_R37_L0.402451.079
183_E208_K0.402041.078
79_L83_E0.394541.058
52_F59_F0.394181.057
202_L209_I0.392181.051
45_D111_R0.390081.046
85_K112_I0.387381.039
157_D161_N0.380471.020
35_E190_K0.377471.012
136_G193_K0.37661.010
27_Y194_G0.376391.009
141_I144_D0.375361.006
52_F57_D0.372220.998
60_V117_L0.371410.996
35_E187_I0.370180.992
85_K88_L0.369330.990
142_Q145_S0.368210.987
187_I202_L0.366120.982
131_F198_V0.365570.980
170_P174_D0.362830.973
69_S199_R0.358690.962
184_M209_I0.354460.950
131_F184_M0.352170.944
59_F75_D0.35160.943
40_L115_E0.35140.942
27_Y31_K0.348480.934
27_Y30_E0.34530.926
116_E205_V0.344220.923
36_Y210_Y0.343620.921
130_K199_R0.343250.920
73_V87_K0.342860.919
57_D81_I0.340630.913
41_L44_Y0.337050.904
137_K189_E0.334080.896
17_K194_G0.331980.890
62_K115_E0.32920.883
178_P181_L0.3290.882
23_A27_Y0.328670.881
25_R29_E0.328230.880
116_E208_K0.324940.871
118_L205_V0.324820.871
120_D203_Y0.321260.861
29_E40_L0.31940.856
47_P50_I0.317720.852
15_F216_F0.317070.850
74_R117_L0.316510.849
137_K193_K0.315480.846
212_G215_T0.314830.844
44_Y50_I0.31440.843
75_D84_A0.310810.833
83_E86_K0.309750.830
22_Y43_V0.308440.827
179_K183_E0.307730.825
35_E211_F0.30760.825
129_Y188_A0.306460.822
36_Y183_E0.300620.806
190_K193_K0.300340.805
48_D51_D0.299880.804
73_V84_A0.299660.803
22_Y111_R0.298540.800
158_R162_R0.294310.789
198_V214_L0.292150.783
61_I112_I0.291380.781
200_V211_F0.288030.772
64_N113_I0.287480.771
199_R219_G0.287050.770
36_Y211_F0.285860.766
20_D65_H0.285740.766
21_K201_D0.285480.765
31_K35_E0.284540.763
24_V215_T0.284460.763
133_C138_P0.284190.762
204_N207_G0.283610.760
119_E206_D0.283230.759
71_I88_L0.283180.759
25_R40_L0.28250.757
18_L216_F0.280380.752
129_Y204_N0.280050.751
75_D112_I0.280010.751
40_L116_E0.279850.750
217_T220_A0.278330.746
24_V211_F0.277610.744
47_P86_K0.277360.744
20_D23_A0.276690.742
29_E42_G0.276090.740
65_H70_N0.274780.737
179_K182_E0.274660.736
52_F55_L0.27450.736
191_L211_F0.274410.736
197_F218_P0.274290.735
143_V181_L0.274060.735
38_P118_L0.272490.731
187_I190_K0.267540.717
180_N207_G0.264960.710
46_N50_I0.263650.707
184_M202_L0.261610.701
191_L200_V0.26160.701
132_F197_F0.261520.701
32_I36_Y0.259990.697
171_P181_L0.259660.696
191_L194_G0.259430.696
130_K201_D0.257340.690
159_D162_R0.257020.689
187_I209_I0.255170.684
133_C200_V0.254910.683
183_E209_I0.254640.683
47_P82_E0.253940.681
115_E118_L0.252310.676
134_F139_K0.251360.674
69_S215_T0.249960.670
44_Y49_D0.249670.669
58_K117_L0.249120.668
192_S200_V0.248810.667
76_K154_N0.247630.664
32_I35_E0.246660.661
174_D177_K0.24640.661
42_G54_S0.244420.655
29_E39_P0.243970.654
201_D219_G0.243820.654
42_G45_D0.243490.653
129_Y144_D0.243230.652
134_F142_Q0.242510.650
21_K72_I0.242250.649
119_E205_V0.241650.648
81_I85_K0.241470.647
187_I191_L0.24030.644
63_P72_I0.240150.644
62_K201_D0.239690.643
58_K74_R0.239020.641
21_K66_G0.238490.639
56_P59_F0.238130.638
53_D56_P0.237310.636
56_P116_E0.236040.633
130_K220_A0.235720.632
117_L120_D0.235710.632
199_R220_A0.234730.629
120_D212_G0.234520.629
84_A88_L0.234060.628
199_R218_P0.233360.626
52_F56_P0.232990.625
26_E31_K0.232420.623
121_E145_S0.230430.618
199_R215_T0.229910.616
29_E41_L0.229120.614
31_K193_K0.227890.611
24_V214_L0.22680.608
190_K194_G0.226710.608
175_I181_L0.226590.608
133_C188_A0.226350.607
55_L58_K0.225470.605
24_V199_R0.224250.601
66_G72_I0.223940.600
48_D82_E0.223930.600
154_N159_D0.223860.600
129_Y184_M0.222960.598
81_I84_A0.221720.594
36_Y41_L0.221570.594
31_K194_G0.221360.593
53_D81_I0.221120.593
17_K26_E0.221010.593
155_F158_R0.219520.589
203_Y210_Y0.217850.584
76_K119_E0.217510.583
183_E190_K0.216830.581
27_Y191_L0.215150.577
131_F140_F0.214720.576
19_A69_S0.213980.574
19_A24_V0.213320.572
19_A199_R0.21240.569
180_N209_I0.212150.569
184_M188_A0.211450.567
22_Y64_N0.211190.566
130_K217_T0.210940.566
141_I145_S0.210780.565
73_V83_E0.208750.560
118_L203_Y0.208730.560
201_D217_T0.208280.558
43_V46_N0.20820.558
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
3votA0.891299.90.353
2pvpA0.870399.90.359
4dimA0.853699.90.373
4fu0A0.878799.90.375
1e4eA0.882899.90.378
3tqtA0.878799.90.385
3se7A0.882899.90.388
1a9xA0.861999.90.388
3lwbA0.891299.90.39
4eg0A0.866199.90.391

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