GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_terminase - Phage terminase small subunit
Pfam: PF10668 (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: CL0123
Length: 60
Sequences: 9996
Seq/Len: 166.6
HH_delta: 0.24 (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
15_I31_K1.550892.064
36_E40_R1.294741.723
24_K27_D1.287141.713
25_L40_R1.237571.647
25_L43_K1.226291.632
45_R49_D1.197131.593
35_S38_T1.19471.590
23_I31_K1.153991.536
26_K36_E1.150191.531
41_K45_R1.104441.470
15_I23_I1.080281.438
11_K15_I1.054231.403
37_S41_K1.046171.392
37_S40_R1.042341.387
34_V38_T0.985361.311
8_N34_V0.956051.272
9_R45_R0.928761.236
8_N11_K0.918151.222
29_A36_E0.903181.202
9_R42_W0.900211.198
26_K30_E0.89191.187
44_S48_W0.876621.167
27_D31_K0.876521.167
27_D30_E0.856741.140
10_D14_E0.852571.135
32_L39_I0.838231.116
25_L36_E0.834671.111
23_I27_D0.827061.101
14_E17_K0.790691.052
47_K54_G0.781561.040
46_D52_L0.779421.037
34_V39_I0.753651.003
13_F51_K0.753521.003
26_K40_R0.721860.961
41_K44_S0.719270.957
12_A28_I0.715820.953
29_A39_I0.707650.942
7_P11_K0.697080.928
11_K14_E0.678790.903
46_D51_K0.67760.902
14_E18_E0.674270.897
15_I28_I0.660880.880
8_N12_A0.656590.874
12_A39_I0.603870.804
38_T41_K0.575590.766
28_I39_I0.551270.734
40_R44_S0.548140.730
15_I18_E0.533430.710
12_A15_I0.519210.691
37_S44_S0.516980.688
9_R13_F0.506880.675
12_A16_Y0.505830.673
46_D50_E0.500890.667
13_F46_D0.497820.663
16_Y46_D0.483390.643
25_L29_A0.479190.638
45_R48_W0.474950.632
28_I43_K0.467630.622
44_S47_K0.46030.613
43_K52_L0.455710.606
7_P10_D0.447240.595
8_N42_W0.446360.594
13_F16_Y0.445910.593
8_N38_T0.440990.587
15_I32_L0.440180.586
8_N14_E0.440090.586
29_A34_V0.437730.583
6_S10_D0.436060.580
13_F17_K0.434530.578
12_A42_W0.431680.575
25_L41_K0.431380.574
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
2k27A0.9597.60.24
2jn6A0.966797.60.242
1k78A0.9597.60.245
2lvsA0.933397.60.252
1pdnC0.9597.50.26
2elhA0.9597.50.269
1u78A0.916797.40.285
2rn7A0.966797.20.312
1tc3C0.816797.20.315
2heoA197.20.315

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