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Adhiron3

ID: 1515336172 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 79 (79)
Sequences: 162 (103.7)
Seq/Len: 2.051
Nf(neff/√len): 11.7

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: 2.051).

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
16_E73_L2.6611.00
65_K70_F2.2461.00
63_W70_F2.0090.99
41_T66_P1.9240.99
29_R43_Y1.8740.98
16_E19_K1.7520.97
33_A45_L1.7150.97
3_S9_L1.6610.96
41_T73_L1.4840.91
5_E64_V1.4060.88
52_G78_P1.2990.81
61_K75_E1.2810.80
26_E55_K1.2610.79
23_A51_D1.2580.78
35_E39_A1.2420.77
35_E64_V1.2240.76
19_K43_Y1.2200.75
43_Y52_G1.2190.75
41_T65_K1.2140.75
31_V53_G1.1940.73
28_V50_K1.1820.72
57_L73_L1.1570.70
21_E54_K1.1560.69
3_S21_E1.1520.69
26_E53_G1.1450.68
27_F47_L1.1410.68
42_M61_K1.1360.68
34_K44_Y1.0890.63
67_W70_F1.0850.62
47_L62_V1.0830.62
2_N69_N1.0560.59
29_R48_E1.0470.58
8_E21_E1.0400.57
44_Y61_K1.0170.55
23_A72_E1.0120.54
1_E16_E1.0090.54
28_V42_M1.0080.54
68_E79_V1.0080.54
32_K73_L1.0070.54
16_E27_F1.0060.54
27_F49_A1.0060.54
65_K68_E1.0010.53
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  
3imaB20.974799.90.352Contact Map
2l4vA1199.90.352Contact Map
3ul5A4199.90.354Contact Map
1eqkA1199.90.362Contact Map
4n6tA1199.90.366Contact Map
2kxgA10.974799.90.372Contact Map
4lziA1199.90.376Contact Map
5a0oB2099.90.381Contact Map
2octA2199.80.466Contact Map
4n6oB1199.70.482Contact 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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