GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATP-synt_ab - ATP synthase alphabeta family nucleotide-binding domain
Pfam: PF00006 (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: CL0023
Length: 215
Sequences: 2604
Seq/Len: 12.11
HH_delta: -0.033 (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
196_S209_D0.804154.323
14_R106_D0.769124.135
47_A93_A0.746944.015
115_T119_Q0.534512.873
67_G70_E0.501372.695
61_E64_K0.492992.650
97_A164_I0.486762.617
61_E65_G0.474522.551
45_V97_A0.452582.433
73_V96_I0.417182.243
12_I167_I0.404782.176
94_L164_I0.403522.169
5_A208_I0.399032.145
60_I74_V0.398542.142
170_V185_T0.394092.119
94_L168_P0.386422.077
94_L152_A0.37682.026
101_R155_V0.359711.934
57_T61_E0.355091.909
177_I194_V0.354591.906
18_I191_G0.351491.890
12_I193_I0.348061.871
23_G26_V0.346271.861
3_I6_I0.344941.854
107_V164_I0.342431.841
199_L204_I0.335531.804
53_G78_T0.327471.760
99_Y103_Q0.323451.739
3_I31_L0.314581.691
75_V96_I0.311281.673
66_E70_E0.29951.610
177_I212_K0.298051.602
98_E151_R0.294791.585
18_I167_I0.289711.557
1_T7_D0.289421.556
81_E85_A0.285021.532
64_K69_L0.277441.491
91_Y121_Y0.274881.478
70_E73_V0.274361.475
19_G189_L0.274031.473
106_D163_S0.268491.443
1_T12_I0.267391.437
182_P194_V0.266681.434
106_D154_K0.265381.427
48_L56_V0.259721.396
101_R107_V0.258041.387
198_K201_E0.257421.384
209_D212_K0.248731.337
20_I32_L0.246581.326
104_G161_G0.245831.322
86_R123_E0.24461.315
125_S133_G0.243191.307
194_V197_R0.241021.296
45_V75_V0.23911.285
10_F208_I0.237651.278
107_V123_E0.237291.276
36_A110_I0.236261.270
42_D105_K0.235331.265
45_V96_I0.229531.234
175_D197_R0.227671.224
99_Y102_D0.225921.214
194_V212_K0.225611.213
3_I38_N0.224451.207
10_F193_I0.22331.200
47_A111_I0.222331.195
52_R55_E0.221521.191
37_N42_D0.219841.182
22_G26_V0.219821.182
65_G68_A0.219621.181
42_D107_V0.219491.180
64_K70_E0.218581.175
149_Y188_I0.216991.166
49_I89_A0.209461.126
145_L184_N0.207621.116
179_D182_P0.207231.114
90_P148_L0.206181.108
141_L144_D0.205181.103
6_I193_I0.204771.101
114_L185_T0.201381.083
102_D155_V0.201181.082
6_I35_I0.201121.081
73_V100_F0.199111.070
101_R164_I0.198041.065
155_V161_G0.197031.059
119_Q173_P0.196521.056
121_Y144_D0.196241.055
36_A72_T0.19621.055
32_L110_I0.195551.051
1_T167_I0.195051.049
127_L132_P0.194851.047
94_L109_L0.193711.041
92_T96_I0.192711.036
149_Y185_T0.192481.035
51_E55_E0.192211.033
6_I10_F0.191951.032
84_A124_I0.191281.028
82_P85_A0.190561.024
6_I31_L0.190071.022
25_G201_E0.18871.014
62_E65_G0.188431.013
77_A86_R0.187061.006
60_I64_K0.186061.000
33_Q59_F0.185931.000
97_A107_V0.184440.992
86_R119_Q0.18260.982
108_L167_I0.18210.979
23_G175_D0.179110.963
103_Q107_V0.178860.962
32_L169_T0.178770.961
88_R92_T0.178640.960
82_P86_R0.178350.959
44_V105_K0.178250.958
152_A166_A0.178080.957
175_D178_T0.176780.950
65_G69_L0.176160.947
96_I100_F0.175950.946
201_E212_K0.175530.944
91_Y144_D0.175150.942
43_V100_F0.175120.941
41_A44_V0.174780.940
62_E66_E0.174640.939
123_E139_P0.172110.925
47_A109_L0.170450.916
39_Q106_D0.17030.915
7_D11_P0.169650.912
110_I169_T0.169530.911
155_V160_G0.168270.905
104_G160_G0.167320.899
56_V78_T0.166730.896
53_G58_E0.165990.892
173_P178_T0.165610.890
49_I111_I0.163950.881
119_Q184_N0.163320.878
81_E109_L0.162790.875
68_A72_T0.162070.871
12_I18_I0.162020.871
93_A109_L0.161930.871
3_I34_E0.159620.858
145_L185_T0.158810.854
85_A88_R0.158780.854
68_A71_R0.158560.852
33_Q58_E0.158310.851
23_G183_D0.158080.850
37_N71_R0.156770.843
23_G197_R0.156630.842
84_A127_L0.156450.841
130_E140_S0.155370.835
1_T39_Q0.154910.833
45_V107_V0.154360.830
137_Y176_D0.153660.826
51_E116_R0.153210.824
119_Q137_Y0.153010.823
34_E38_N0.152980.822
95_T99_Y0.152820.822
8_L11_P0.152480.820
43_V105_K0.152440.819
35_I108_L0.152350.819
9_L210_V0.152110.818
30_V33_Q0.15150.814
53_G80_D0.151030.812
70_E105_K0.150740.810
125_S138_P0.150660.810
143_S147_S0.150550.809
92_T95_T0.150420.809
14_R43_V0.150210.807
143_S146_A0.150010.806
105_K161_G0.149160.802
62_E95_T0.147810.795
14_R163_S0.147570.793
12_I165_T0.147570.793
127_L139_P0.147520.793
134_R184_N0.147080.791
104_G162_G0.146440.787
61_E197_R0.145690.783
58_E86_R0.144550.777
86_R98_E0.144350.776
33_Q72_T0.14430.776
194_V201_E0.143840.773
52_R116_R0.14360.772
87_Y121_Y0.143530.772
39_Q108_L0.142940.768
30_V34_E0.141840.763
94_L97_A0.14130.760
37_N62_E0.141180.759
59_F72_T0.140970.758
187_S192_H0.140730.757
134_R138_P0.140350.754
81_E89_A0.140090.753
204_I208_I0.139960.752
187_S190_D0.138870.747
31_L59_F0.138350.744
7_D211_L0.138160.743
42_D106_D0.13790.741
77_A81_E0.137820.741
125_S139_P0.136430.733
89_A93_A0.13640.733
82_P124_I0.135970.731
10_F214_V0.135610.729
45_V73_V0.135530.729
197_R201_E0.135220.727
100_F123_E0.133980.720
118_A145_L0.133940.720
42_D71_R0.133840.719
154_K160_G0.133070.715
172_V182_P0.132980.715
101_R153_G0.132950.715
43_V107_V0.132890.714
140_S143_S0.132640.713
183_D186_K0.131980.709
58_E62_E0.131520.707
9_L103_Q0.13150.707
1_T6_I0.131320.706
23_G176_D0.131240.706
6_I202_R0.130950.704
37_N66_E0.130940.704
181_I188_I0.130930.704
69_L72_T0.130670.702
95_T98_E0.130490.701
130_E153_G0.130180.700
20_I169_T0.130050.699
24_A186_K0.129990.699
58_E173_P0.129910.698
114_L149_Y0.129830.698
35_I38_N0.129630.697
26_V182_P0.12920.695
119_Q196_S0.129010.694
100_F105_K0.128710.692
42_D123_E0.128590.691
154_K161_G0.128260.689
55_E84_A0.128250.689
61_E161_G0.128240.689
177_I182_P0.128230.689
36_A44_V0.128140.689
122_R181_I0.127380.685
7_D38_N0.127360.685
43_V71_R0.127140.683
84_A132_P0.127090.683
1_T21_F0.12690.682
6_I164_I0.126750.681
30_V125_S0.126660.681
200_A205_F0.126460.680
30_V57_T0.126350.679
65_G105_K0.126260.679
43_V73_V0.126080.678
55_E61_E0.125910.677
87_Y124_I0.125850.677
56_V76_A0.125740.676
25_G58_E0.125560.675
126_L131_P0.125260.673
7_D21_F0.125070.672
60_I76_A0.124870.671
63_L68_A0.124780.671
81_E88_R0.124340.668
140_S144_D0.124240.668
61_E66_E0.124190.668
37_N41_A0.124040.667
154_K163_S0.124030.667
174_G179_D0.123680.665
115_T122_R0.123680.665
87_Y144_D0.123670.665
94_L153_G0.123590.664
3_I9_L0.122890.661
62_E160_G0.122810.660
45_V93_A0.122690.660
187_S214_V0.122320.658
186_K190_D0.122120.656
33_Q74_V0.121980.656
162_G195_L0.121980.656
31_L198_K0.121670.654
178_T185_T0.121520.653
145_L188_I0.121450.653
33_Q63_L0.121320.652
196_S204_I0.120980.650
31_L197_R0.12090.650
31_L195_L0.12060.648
39_Q214_V0.120590.648
172_V177_I0.120390.647
46_Y65_G0.120290.647
37_N64_K0.119920.645
94_L111_I0.119840.644
55_E58_E0.119460.642
83_P137_Y0.119370.642
98_E123_E0.118920.639
53_G66_E0.118610.638
78_T86_R0.118260.636
113_S169_T0.118240.636
196_S212_K0.117810.633
75_V89_A0.117550.632
83_P116_R0.117540.632
36_A46_Y0.117360.631
162_G165_T0.117210.630
41_A70_E0.116770.628
32_L193_I0.116750.628
25_G182_P0.116570.627
27_G112_D0.116530.626
48_L51_E0.11640.626
36_A68_A0.115740.622
4_R97_A0.11560.621
28_K51_E0.115430.621
73_V104_G0.115340.620
40_D106_D0.11510.619
25_G123_E0.114710.617
9_L211_L0.114670.616
68_A135_E0.114540.616
23_G172_V0.114460.615
15_G27_G0.114320.615
95_T201_E0.11420.614
53_G57_T0.113340.609
36_A116_R0.112890.607
184_N187_S0.112760.606
24_A184_N0.112730.606
25_G55_E0.112290.604
204_I210_V0.112240.603
55_E197_R0.112050.602
106_D161_G0.112020.602
186_K192_H0.111920.602
121_Y134_R0.111780.601
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
1fx0B0.9814100-0.033
2c61A0.9907100-0.03
3vr4D0.9907100-0.03
3oaaA1100-0.027
2r9vA1100-0.025
3gqbB0.9907100-0.024
2qe7A1100-0.024
1fx0A1100-0.024
2ck3D0.9814100-0.02
2ck3A1100-0.02

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