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1sbp from pdb 103-209

ID: 1513800683 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 107 (107)
Sequences: 1085 (452.5)
Seq/Len: 10.140
Nf(neff/√len): 43.7

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 10.140).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

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] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
14_I60_L3.1361.00
22_T34_N2.2951.00
59_A63_N2.2371.00
11_N45_H2.2351.00
43_L53_A2.2161.00
55_D59_A2.1901.00
53_A57_V2.1891.00
19_S65_E2.0911.00
21_I65_E2.0491.00
41_Y56_F2.0081.00
20_V65_E1.8681.00
58_K62_K1.8521.00
43_L50_Q1.7531.00
20_V60_L1.7341.00
46_N53_A1.6771.00
71_A90_W1.6711.00
11_N41_Y1.6631.00
46_N52_K1.6361.00
30_G71_A1.6111.00
19_S63_N1.5701.00
95_L100_E1.5631.00
39_W57_V1.4901.00
77_T83_I1.4801.00
39_W43_L1.4451.00
30_G34_N1.4030.99
1_K107_E1.3880.99
30_G33_W1.3660.99
21_I83_I1.3480.99
61_F67_L1.3120.99
79_V101_L1.2980.99
75_T87_L1.2450.98
24_N32_R1.2060.98
33_W90_W1.2030.98
23_P34_N1.1800.98
31_A34_N1.1730.98
38_A60_L1.1680.97
30_G74_S1.1670.97
23_P68_D1.1620.97
30_G90_W1.1600.97
8_H16_P1.1490.97
39_W53_A1.1480.97
17_G63_N1.1240.97
52_K55_D1.1050.96
5_K85_D1.1020.96
49_D52_K1.0990.96
22_T33_W1.0830.96
15_K18_V1.0820.96
98_T104_D1.0820.96
16_P105_K1.0770.95
68_D77_T1.0490.94
21_I77_T1.0490.94
13_L64_V1.0340.94
43_L48_N1.0130.93
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
1sbpA1199.60.649Contact Map
4jb7A10.869298.70.769Contact Map
2hxwA20.925297.90.816Contact Map
3cg1A20.925296.10.861Contact Map
3cfzA10.962695.90.863Contact Map
4rxlA10.841195.30.868Contact Map
3pu5A10.97294.80.872Contact Map
4g68A10.981394.50.874Contact Map
2qryA40.915994.30.875Contact Map
3rpwA10.9252940.877Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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