GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATP-synt_B - ATP synthase BB CF(0)
Pfam: PF00430 (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: 132
Sequences: 2457
Seq/Len: 18.61
HH_delta: 0.702 (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
26_K30_E0.858922.872
69_E73_E0.716782.397
36_Q40_E0.705922.361
89_A93_A0.647712.166
37_S41_E0.632662.116
44_E48_E0.615262.057
43_E47_E0.614582.055
29_D33_A0.606932.030
84_E88_E0.592521.981
51_Q55_E0.559521.871
58_E62_E0.54041.807
33_A37_S0.534911.789
94_E98_E0.530731.775
83_E87_A0.525611.758
93_A96_I0.518311.733
79_E83_E0.499011.669
53_L57_E0.488131.632
14_F18_K0.487521.630
98_E102_A0.485261.623
72_E76_E0.481361.610
105_E109_E0.480521.607
91_K95_R0.46451.553
66_E69_E0.464331.553
50_E54_A0.464171.552
82_K86_L0.463961.552
88_E92_E0.461421.543
87_A91_K0.455261.522
54_A57_E0.453061.515
30_E34_K0.452111.512
76_E80_K0.438131.465
40_E44_E0.431141.442
123_A127_A0.430681.440
47_E51_Q0.422251.412
54_A58_E0.419861.404
81_E84_E0.414571.386
62_E66_E0.414421.386
55_E59_K0.414061.385
97_I101_E0.413571.383
10_L14_F0.41261.380
63_A67_A0.407541.363
82_K85_I0.404421.352
29_D32_K0.395051.321
34_K38_E0.390821.307
108_K112_K0.385871.290
48_E51_Q0.383941.284
123_A126_I0.381841.277
107_E110_K0.380551.273
32_K36_Q0.366831.227
40_E43_E0.366361.225
56_Y59_K0.365081.221
62_E65_E0.357971.197
59_K62_E0.35791.197
14_F17_N0.35241.178
90_E94_E0.351631.176
95_R99_Q0.350421.172
68_Q72_E0.34991.170
81_E86_L0.349891.170
72_E75_K0.346741.160
96_I104_I0.342621.146
13_F17_N0.33741.128
79_E82_K0.334731.119
119_I123_A0.334631.119
71_I74_A0.330771.106
74_A78_A0.328821.100
51_Q54_A0.328491.098
88_E91_K0.328061.097
80_K84_E0.324021.084
41_E45_L0.318961.067
114_E118_E0.31341.048
98_E101_E0.305231.021
5_Q8_N0.305091.020
99_Q102_A0.304591.019
47_E50_E0.300811.006
106_Q110_K0.298720.999
46_K50_E0.297720.996
42_A49_A0.297170.994
71_I75_K0.294120.984
49_A53_L0.293870.983
41_E44_E0.291250.974
78_A82_K0.29050.971
58_E61_A0.289540.968
65_E68_Q0.287080.960
73_E77_E0.284170.950
103_E107_E0.283640.949
55_E58_E0.280620.938
109_E113_K0.278420.931
100_A104_I0.277740.929
104_I111_A0.27590.923
65_E69_E0.274610.918
91_K94_E0.271550.908
33_A36_Q0.270420.904
70_I74_A0.269020.900
102_A105_E0.268850.899
84_E87_A0.268820.899
104_I115_L0.268680.898
86_L90_E0.268390.898
5_Q23_P0.266780.892
2_L5_Q0.264490.884
23_P26_K0.264140.883
20_L23_P0.263590.881
16_L21_Y0.260590.871
9_F13_F0.260440.871
17_N21_Y0.259260.867
93_A97_I0.257020.859
110_K114_E0.254940.853
66_E70_I0.254090.850
44_E47_E0.251140.840
35_I39_L0.250910.839
105_E108_K0.249260.834
87_A90_E0.248390.831
57_E61_A0.247840.829
18_K22_K0.241830.809
61_A65_E0.240970.806
27_F30_E0.24070.805
15_L19_F0.239260.800
38_E46_K0.235730.788
81_E85_I0.234940.786
92_E96_I0.234560.784
7_I11_I0.227960.762
76_E79_E0.227060.759
60_L64_R0.226870.759
17_N22_K0.225810.755
85_I89_A0.225470.754
52_L55_E0.225090.753
118_E121_D0.22450.751
77_E80_K0.219280.733
67_A71_I0.217510.727
30_E33_A0.217150.726
8_N21_Y0.21690.725
112_K115_L0.215630.721
9_F21_Y0.215250.720
50_E53_L0.212640.711
96_I99_Q0.212190.710
110_K113_K0.209490.701
77_E81_E0.20890.699
101_E105_E0.208810.698
121_D125_D0.203840.682
73_E80_K0.202640.678
125_D129_K0.202060.676
8_N20_L0.201440.674
47_E54_A0.200220.670
5_Q13_F0.200160.669
75_K79_E0.198150.663
85_I93_A0.197360.660
111_A119_I0.195550.654
4_W13_F0.195350.653
73_E76_E0.194610.651
69_E72_E0.193740.648
125_D128_E0.193670.648
122_L129_K0.192980.645
49_A59_K0.191750.641
4_W8_N0.191450.640
113_K117_Q0.190790.638
35_I42_A0.188090.629
9_F31_R0.187310.626
34_K37_S0.186230.623
39_L82_K0.18350.614
92_E99_Q0.181760.608
69_E88_E0.181470.607
67_A70_I0.181370.607
120_V124_V0.180830.605
4_W7_I0.180570.604
49_A56_Y0.178610.597
3_F6_L0.175190.586
77_E103_E0.175050.585
21_Y25_K0.173050.579
97_I103_E0.172860.578
113_K116_R0.172830.578
120_V126_I0.17270.578
92_E95_R0.171590.574
124_V127_A0.170610.571
31_R35_I0.169590.567
43_E46_K0.168980.565
101_E107_E0.167980.562
53_L56_Y0.167390.560
37_S69_E0.167280.559
100_A111_A0.167060.559
85_I88_E0.166250.556
78_A85_I0.165290.553
52_L57_E0.164870.551
8_N32_K0.164150.549
48_E52_L0.1640.548
4_W24_I0.16390.548
38_E45_L0.163380.546
49_A52_L0.163110.545
109_E112_K0.162950.545
26_K33_A0.161810.541
8_N11_I0.160330.536
120_V127_A0.159870.535
24_I28_L0.159360.533
8_N16_L0.159290.533
99_Q103_E0.158810.531
13_F21_Y0.158340.529
3_F17_N0.157930.528
124_V128_E0.157410.526
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
1b9uA0.219797.40.702
2khkA0.401597.40.704
1l2pA0.462197.30.71
2dm9A0.712197.20.712
3v6iA0.6894960.759
2dm9A0.6364940.787
2clyA0.977393.70.79
1l2pA0.462190.20.81
4efaE0.734889.10.814
3v6iA0.606185.40.825
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