GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Adhiron4

ID: 1515350477 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 79 (79)
Sequences: 1811 (1329.4)
Seq/Len: 22.924
Nf(neff/√len): 149.6

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: 22.924).

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
29_R48_E3.1021.00
34_K44_Y2.6121.00
32_K46_T2.1811.00
16_E19_K2.1761.00
65_K70_F2.0701.00
65_K68_E2.0221.00
35_E41_T1.9941.00
42_M61_K1.9881.00
58_Y78_P1.9371.00
10_A27_F1.8371.00
28_V50_K1.6631.00
42_M63_W1.6541.00
33_A45_L1.6431.00
10_A45_L1.6221.00
5_E64_V1.5381.00
63_W70_F1.5361.00
6_I33_A1.5011.00
36_Q42_M1.4861.00
42_M74_Q1.4671.00
25_L49_A1.4511.00
31_V57_L1.4391.00
47_L60_A1.4331.00
64_V71_K1.4321.00
46_T59_E1.3660.99
17_H21_E1.3440.99
31_V48_E1.3000.99
38_V42_M1.2840.99
16_E73_L1.2240.98
25_L58_Y1.2100.98
10_A14_V1.2070.98
14_V18_N1.1970.98
17_H60_A1.1960.98
27_F47_L1.1880.98
49_A60_A1.1860.98
6_I9_L1.1190.96
39_A65_K1.0980.96
16_E20_K1.0930.96
44_Y59_E1.0850.96
3_S7_E1.0820.96
12_F73_L1.0300.94
61_K75_E1.0270.94
10_A47_L1.0260.94
28_V55_K1.0080.93
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  
2l4vA1199.6-0.045Contact Map
3ul5A4199.6-0.031Contact Map
1eqkA1199.6-0.017Contact Map
3imaB20.974799.6-0.003Contact Map
4n6tA1199.60.005Contact Map
4lziA1199.60.01Contact Map
5a0oB2099.50.024Contact Map
2kxgA10.974799.50.057Contact Map
3gaxA2199.50.071Contact Map
4n6oB1199.40.079Contact 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.

Page generated in 0.0416 seconds.