GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PB1 - PB1 domain
Pfam: PF00564 (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: CL0072
Length: 84
Sequences: 1641
Seq/Len: 19.54
HH_delta: 0.087 (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
31_I44_L0.367691.847
47_K51_G0.34321.724
29_S32_R0.335371.684
45_K53_L0.318511.600
59_D63_Q0.317781.596
64_E68_Q0.300381.509
25_D29_S0.297781.496
13_R35_F0.297331.493
57_S61_D0.293051.472
27_L62_L0.278191.397
22_V25_D0.269771.355
54_V61_D0.264951.331
48_D54_V0.264811.330
48_D52_D0.26411.326
28_R32_R0.263811.325
52_D64_E0.261771.315
11_D14_R0.245291.232
32_R37_L0.24241.217
64_E67_E0.241551.213
37_L41_D0.240371.207
30_K60_E0.237521.193
46_Y65_A0.23441.177
16_I33_E0.233631.173
33_E36_G0.233221.171
24_F62_L0.226421.137
59_D62_L0.224841.129
45_K55_T0.222841.119
28_R36_G0.222821.119
19_P29_S0.221921.115
37_L40_E0.220021.105
61_D65_A0.213811.074
33_E67_E0.213581.073
6_V31_I0.208251.046
49_E68_Q0.207981.045
3_R14_R0.20631.036
31_I40_E0.203051.020
30_K33_E0.201311.011
20_S66_I0.201241.011
48_D65_A0.200321.006
47_K53_L0.199551.002
29_S33_E0.19780.993
17_S71_E0.192840.969
37_L42_F0.191660.963
49_E54_V0.191470.962
22_V29_S0.191050.960
25_D41_D0.189310.951
24_F28_R0.189030.949
3_R20_S0.188070.945
5_K12_I0.186390.936
50_D54_V0.18620.935
33_E38_L0.185340.931
38_L41_D0.181880.914
51_G68_Q0.179840.903
9_G31_I0.176970.889
46_Y61_D0.176440.886
45_K50_D0.176130.885
8_Y33_E0.174610.877
6_V45_K0.174530.877
13_R34_K0.174430.876
48_D64_E0.170830.858
4_V18_L0.168580.847
53_L67_E0.168240.845
48_D51_G0.167830.843
57_S71_E0.165810.833
21_D47_K0.16560.832
18_L34_K0.162010.814
21_D66_I0.159810.803
28_R43_Q0.159650.802
56_I65_A0.158690.797
54_V68_Q0.157920.793
19_P22_V0.157270.790
56_I61_D0.157180.789
14_R35_F0.157160.789
9_G41_D0.156010.784
26_D29_S0.15560.782
32_R40_E0.15550.781
32_R56_I0.155430.781
47_K64_E0.154750.777
65_A68_Q0.154540.776
24_F42_F0.153780.772
8_Y14_R0.153620.772
3_R68_Q0.15290.768
22_V30_K0.151320.760
10_G71_E0.151310.760
23_S33_E0.1510.758
28_R33_E0.150360.755
3_R7_R0.149530.751
27_L64_E0.149460.751
25_D33_E0.149230.750
13_R38_L0.148550.746
6_V10_G0.14680.737
57_S64_E0.146490.736
17_S30_K0.14470.727
3_R6_V0.14470.727
29_S40_E0.143480.721
52_D60_E0.142880.718
16_I22_V0.14280.717
20_S70_K0.142190.714
35_F45_K0.142040.713
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
1vd2A0.988199.60.087
2ktrA0.952499.50.163
1q1oA0.964399.40.178
2kkcA0.952499.40.179
1wmhB0.940599.30.23
1wj6A0.952499.30.238
2bkfA0.952499.30.238
1pqsA0.857199.30.252
1oeyA0.928699.20.272
4ic7E0.988198.70.413

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