GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mt_ATP-synt_B - Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
Pfam: PF05405 (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: CL0255
Length: 163
Sequences: 2393
Seq/Len: 14.68
HH_delta: 0.414 (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
40_E44_E0.735092.893
50_E54_N0.636962.507
43_D47_Q0.571392.249
83_M87_A0.561872.211
47_Q51_D0.548982.161
58_N62_K0.533122.098
51_D55_Q0.525432.068
57_R61_I0.520082.047
146_T149_K0.518012.039
103_Q107_V0.515762.030
102_E106_A0.494931.948
67_R71_V0.479121.886
108_A112_K0.478891.885
65_K69_E0.474321.867
98_A102_E0.471351.855
72_K76_S0.461981.818
107_V110_E0.451561.777
119_V123_Q0.446211.756
93_A97_E0.445021.751
68_I71_V0.42681.680
97_E101_R0.425981.677
62_K65_K0.398211.567
28_I32_K0.396481.560
44_E48_K0.381831.503
96_L99_F0.381481.501
76_S80_G0.378461.489
86_E90_E0.375241.477
54_N58_N0.373181.469
48_K52_E0.371931.464
43_D46_I0.3641.433
90_E94_L0.363581.431
24_I28_I0.360611.419
95_Q98_A0.354481.395
60_H64_L0.352121.386
112_K116_D0.351091.382
82_K86_E0.348461.371
64_L68_I0.347881.369
61_I65_K0.34581.361
122_E126_R0.345281.359
80_G83_M0.343811.353
96_L100_Y0.34131.343
105_A109_Q0.336371.324
109_Q113_R0.332481.309
54_N57_R0.331961.306
86_E89_K0.328151.291
70_Q73_K0.324041.275
148_P152_K0.319351.257
93_A96_L0.318871.255
77_L81_T0.316711.246
128_R132_H0.314421.237
46_I50_E0.313341.233
55_Q59_D0.312211.229
68_I72_K0.311841.227
101_R105_A0.303751.195
28_I31_Y0.302661.191
104_Q108_A0.298031.173
95_Q100_Y0.296691.168
27_I31_Y0.29561.163
100_Y104_Q0.293891.157
34_F37_S0.292961.153
133_L137_V0.288981.137
153_Q157_Q0.286281.127
111_V115_L0.282741.113
63_A67_R0.282591.112
88_S92_V0.280071.102
73_K76_S0.279851.101
79_E82_K0.278831.097
76_S79_E0.276611.089
56_S63_A0.276261.087
69_E72_K0.272321.072
32_K36_P0.26931.060
143_K149_K0.268091.055
105_A108_A0.265331.044
137_V140_K0.264341.040
87_A91_N0.264181.040
110_E118_W0.262991.035
121_Y124_S0.262671.034
72_K75_Q0.257371.013
52_E60_H0.256651.010
101_R104_Q0.256511.010
120_E124_S0.256111.008
31_Y36_P0.250240.985
65_K68_I0.248210.977
69_E73_K0.247080.972
106_A110_E0.245960.968
119_V122_E0.245610.967
30_I35_G0.242070.953
71_V75_Q0.241570.951
94_L98_A0.24090.948
141_V144_S0.237880.936
99_F103_Q0.23770.936
44_E47_Q0.237110.933
114_R118_W0.235550.927
144_S151_Q0.23490.924
113_R116_D0.233310.918
18_L21_L0.232230.914
23_F27_I0.230630.908
102_E105_A0.229120.902
118_W125_V0.227970.897
149_K153_Q0.226320.891
85_F88_S0.226180.890
19_V22_C0.224020.882
58_N61_I0.223570.880
152_K156_Q0.222650.876
21_L25_I0.221240.871
55_Q58_N0.220580.868
30_I34_F0.219290.863
124_S128_R0.218780.861
19_V37_S0.218720.861
95_Q99_F0.218210.859
123_Q127_R0.218020.858
107_V111_V0.217780.857
61_I64_L0.216740.853
151_Q154_I0.214990.846
116_D119_V0.214780.845
112_K115_L0.213580.841
81_T85_F0.213330.840
41_W44_E0.211940.834
31_Y35_G0.210160.827
99_F107_V0.209750.826
22_C35_G0.207610.817
62_K66_E0.206080.811
79_E83_M0.205790.810
22_C25_I0.204180.804
85_F89_K0.203590.801
91_N94_L0.201460.793
118_W129_E0.199120.784
64_L67_R0.195480.769
74_E78_V0.195160.768
155_L159_I0.194590.766
19_V27_I0.19270.758
47_Q50_E0.19260.758
59_D63_A0.191180.752
148_P153_Q0.191130.752
66_E69_E0.186660.735
91_N117_Y0.185230.729
124_S127_R0.184410.726
23_F35_G0.183280.721
18_L22_C0.182630.719
139_S142_L0.182460.718
74_E77_L0.182270.717
39_A42_L0.181110.713
151_Q155_L0.178710.703
22_C36_P0.178660.703
92_V96_L0.178410.702
37_S40_E0.177620.699
23_F26_F0.176550.695
67_R70_Q0.175360.690
133_L136_W0.175260.690
49_I53_L0.175150.689
49_I56_S0.174580.687
111_V117_Y0.174260.686
127_R131_K0.173790.684
98_A101_R0.173640.683
154_I157_Q0.172860.680
90_E93_A0.171960.677
106_A109_Q0.171750.676
63_A73_K0.17150.675
87_A90_E0.170540.671
26_F29_F0.170160.670
80_G84_L0.169530.667
45_R49_I0.166890.657
143_K153_Q0.166290.654
41_W138_I0.166140.654
48_K51_D0.165570.652
75_Q79_E0.165450.651
22_C46_I0.165220.650
61_I68_I0.165150.650
81_T84_L0.165030.650
154_I158_C0.164980.649
108_A111_V0.163970.645
31_Y34_F0.163960.645
40_E152_K0.162980.641
84_L88_S0.161960.637
57_R60_H0.160760.633
132_H135_K0.160730.633
126_R129_E0.160020.630
127_R130_Q0.159980.630
38_I42_L0.159240.627
145_I155_L0.158840.625
153_Q156_Q0.158120.622
66_E71_V0.157920.622
52_E59_D0.157460.620
22_C34_F0.156840.617
87_A94_L0.156570.616
62_K67_R0.156320.615
27_I35_G0.15540.612
129_E133_L0.15530.611
135_K152_K0.154410.608
38_I153_Q0.15390.606
82_K85_F0.153210.603
35_G39_A0.152550.600
86_E93_A0.152040.598
23_F41_W0.152010.598
83_M102_E0.151910.598
33_K136_W0.150660.593
25_I28_I0.150430.592
66_E70_Q0.149320.588
99_F102_E0.148240.583
23_F137_V0.147220.579
31_Y39_A0.147130.579
138_I141_V0.14690.578
140_K158_C0.146670.577
110_E114_R0.145560.573
129_E135_K0.145490.573
47_Q55_Q0.145450.572
145_I149_K0.144830.570
128_R131_K0.143920.566
19_V141_V0.143220.564
139_S143_K0.143070.563
19_V23_F0.14270.562
40_E47_Q0.142680.562
91_N95_Q0.142650.561
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
2clyA0.993999.60.414
2khkA0.325297.40.763
1b9uA0.202597.10.773
1l2pA0.374296.80.787
2dm9A0.674896.20.802
2dm9A0.558394.60.824
3v6iA0.662693.70.831
4efaE0.699485.90.858
3v6iB0.644277.60.87
3v6iA0.527674.10.873

Page generated in 0.0126 seconds.