GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Phage_tail_X - Phage Tail Protein X
Pfam: PF05489 (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: CL0187
Length: 60
Sequences: 7281
Seq/Len: 121.35
HH_delta: 0.135 (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
32_A52_P1.754822.833
3_V48_V1.488282.403
5_T48_V1.468082.370
3_V50_I1.302142.102
4_Y9_D1.26622.044
10_T13_L1.258992.033
44_P47_T1.235161.994
15_A29_L1.122861.813
28_A32_A1.016861.642
4_Y18_H0.983191.587
12_D16_Y0.966841.561
11_L29_L0.874281.411
29_L51_L0.842821.361
30_L39_T0.832471.344
27_E31_E0.746271.205
28_A31_E0.717151.158
18_H51_L0.715561.155
38_D41_P0.69371.120
36_L47_T0.68251.102
29_L49_I0.681781.101
13_L17_R0.670291.082
11_L50_I0.634691.025
50_I53_D0.591270.955
11_L30_L0.56470.912
43_L47_T0.556830.899
32_A53_D0.550480.889
7_Q45_A0.538010.869
30_L38_D0.536280.866
8_G45_A0.527050.851
30_L35_G0.509220.822
9_D17_R0.505940.817
9_D13_L0.499580.807
27_E30_L0.493580.797
31_E53_D0.486560.786
11_L36_L0.482280.779
3_V6_T0.480890.776
30_L37_A0.459650.742
19_Y28_A0.448010.723
9_D45_A0.440340.711
4_Y14_I0.437640.707
12_D41_P0.427910.691
19_Y32_A0.424860.686
20_G32_A0.41980.678
15_A51_L0.40810.659
21_R27_E0.407890.659
14_I18_H0.407740.658
6_T14_I0.40010.646
45_A48_V0.39980.645
19_Y27_E0.397020.641
6_T47_T0.395560.639
32_A50_I0.37910.612
35_G50_I0.372080.601
27_E39_T0.366080.591
20_G28_A0.364910.589
14_I49_I0.363880.587
16_Y19_Y0.362010.584
15_A18_H0.361070.583
6_T43_L0.357010.576
20_G52_P0.356560.576
38_D42_V0.354810.573
5_T46_G0.353770.571
9_D14_I0.350330.566
21_R52_P0.349230.564
29_L33_N0.34890.563
37_A41_P0.348510.563
30_L41_P0.340050.549
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
2ltfA198.60.135
2l9yA0.998.30.218
4ebyA0.916798.20.259
2djpA0.998.10.263
4a1kA0.883398.10.268
4ebyA0.883397.90.31
1e0gA0.766797.70.345
2gu1A0.916797.40.398
2gu1A0.9167950.549
3sluA0.966793.80.574

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