GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ATP-synt_ab_N - ATP synthase alphabeta family beta-barrel domain
Pfam: PF02874 (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: CL0275
Length: 69
Sequences: 4870
Seq/Len: 70.58
HH_delta: 0.119 (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
23_E67_F1.855114.548
11_V65_V0.945032.317
38_G50_L0.914972.243
20_G23_E0.802391.967
52_V56_T0.75851.860
28_E66_R0.74311.822
26_E66_R0.707861.736
10_E47_E0.694911.704
3_Q10_E0.665211.631
12_E47_E0.661661.622
26_E68_T0.654531.605
25_V65_V0.628761.542
39_E53_F0.588151.442
28_E64_E0.582751.429
4_V67_F0.571611.401
24_A40_V0.545621.338
36_V58_G0.538271.320
12_E46_D0.520081.275
35_G54_G0.508381.246
22_G40_V0.495171.214
60_S63_T0.470881.155
40_V50_L0.459261.126
8_V49_R0.456571.119
4_V23_E0.4541.113
27_V63_T0.43811.074
31_D34_N0.437961.074
27_V37_L0.421131.033
30_V65_V0.419331.028
40_V51_Q0.417621.024
5_V8_V0.405870.995
55_S58_G0.40390.990
10_E49_R0.402950.988
26_E36_V0.399430.979
8_V59_L0.3970.973
3_Q22_G0.394110.966
28_E31_D0.38650.948
42_G47_E0.374510.918
25_V38_G0.364460.894
12_E15_P0.360920.885
4_V9_V0.355240.871
37_L50_L0.354020.868
20_G43_L0.349970.858
24_A53_F0.348680.855
26_E35_G0.348490.854
30_V50_L0.34710.851
13_F61_R0.344930.846
9_V19_P0.340130.834
25_V50_L0.33860.830
41_V51_Q0.337140.827
19_P69_G0.335620.823
31_D66_R0.331810.814
12_E34_N0.329370.808
34_N63_T0.327150.802
11_V25_V0.324180.795
44_D49_R0.322430.791
35_G66_R0.321230.788
23_E69_G0.314840.772
11_V14_G0.314420.771
29_L36_V0.313840.769
21_I42_G0.310930.762
43_L49_R0.310170.760
42_G49_R0.305070.748
7_P41_V0.302910.743
56_T59_L0.302450.742
34_N58_G0.299580.735
7_P52_V0.296990.728
19_P40_V0.296790.728
24_A30_V0.295440.724
26_E37_L0.294150.721
13_F46_D0.290550.712
9_V37_L0.290140.711
11_V50_L0.286690.703
10_E51_Q0.286550.703
49_R61_R0.281920.691
38_G52_V0.277040.679
8_V48_V0.274730.674
42_G54_G0.271610.666
36_V54_G0.271330.665
41_V50_L0.268050.657
22_G34_N0.264640.649
48_V61_R0.26390.647
12_E45_E0.260960.640
11_V15_P0.260260.638
29_L40_V0.258130.633
10_E45_E0.255780.627
13_F38_G0.251550.617
20_G28_E0.251220.616
6_G59_L0.248490.609
44_D62_G0.246370.604
29_L46_D0.245970.603
14_G46_D0.237610.583
13_F35_G0.23760.583
28_E34_N0.236850.581
9_V50_L0.234480.575
26_E34_N0.233950.574
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
3mfyA0.91398.70.119
3gqbB0.94298.70.128
2dpyA0.94298.70.13
3vr4D0.956598.70.13
2c61A0.956598.60.135
3vr4A0.91398.60.136
3gqbA0.91398.60.139
3oaaA0.898698.40.202
2r9vA0.898698.40.219
1fx0A0.884198.30.222

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