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RcnRparsed

ID: 1507627765 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 90 (90)
Sequences: 3028 (1786.8)
Seq/Len: 33.644
Nf(neff/√len): 188.3

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: 33.644).

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
19_Q23_V5.3721.00
16_S26_K3.3821.00
9_Q13_A2.8171.00
27_K31_E2.6881.00
22_V45_I2.2521.00
13_A17_K2.1661.00
46_R50_N1.9951.00
25_L45_I1.8891.00
8_K32_P1.7591.00
18_I22_V1.7171.00
33_H37_A1.7051.00
12_K26_K1.7001.00
15_A29_L1.6861.00
42_I53_M1.6311.00
18_I52_L1.6241.00
34_E37_A1.5971.00
19_Q26_K1.5661.00
7_D10_K1.5441.00
11_L29_L1.5251.00
21_Q24_A1.4611.00
79_D83_K1.4561.00
10_K13_A1.4361.00
45_I49_V1.3240.99
12_K30_D1.3010.99
15_A22_V1.2990.99
77_D80_V1.2640.99
14_R48_A1.2520.99
19_Q22_V1.2340.98
17_K21_Q1.2290.98
21_Q45_I1.1730.98
58_K86_D1.1510.97
18_I45_I1.1340.97
10_K55_E1.1070.96
18_I48_A1.0940.96
23_V27_K1.0930.96
58_K62_T1.0890.96
42_I52_L1.0840.96
35_C64_H1.0630.95
66_V70_D1.0590.95
54_R86_D1.0430.94
67_H70_D1.0210.93
24_A28_M1.0200.93
36_A80_V1.0140.93
46_R53_M1.0110.93
41_Q44_A1.0030.93
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  
4m1pA1199.9-0.013Contact Map
2hh7A10.933399.90.006Contact Map
4adzA20.966799.90.013Contact Map
3aaiA40.888999.90.054Contact Map
2fb5A30.911165.50.845Contact Map
1gaxA20.755612.80.895Contact Map
4qinA10.811112.50.895Contact Map
3frtA20.766711.40.897Contact Map
2gd5A40.83337.90.904Contact Map
2hyeC10.96674.90.913Contact 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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