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Kristian Davidsen

ID: 1500490834 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 119 (118)
Sequences: 5114 (2738.2)
Seq/Len: 43.339
Nf(neff/√len): 252.1

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: 43.339).

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
110_G113_T2.6061.00
12_V86_L2.3401.00
12_V16_G2.3171.00
48_V68_F2.1901.00
68_F83_M2.1261.00
62_D65_K2.1051.00
13_K16_G2.0891.00
38_R92_A2.0501.00
109_W112_G1.9271.00
36_W81_L1.7671.00
19_R80_Y1.7441.00
112_G115_V1.7351.00
49_T70_I1.6061.00
24_A34_M1.5941.00
39_Q45_L1.5581.00
50_Y59_Y1.5571.00
113_T117_V1.5281.00
7_S10_G1.4911.00
37_I47_W1.4631.00
38_R46_E1.4571.00
35_N47_W1.4481.00
109_W115_V1.4411.00
10_G18_L1.4241.00
108_V111_Q1.3910.99
34_M79_L1.3810.99
33_Y50_Y1.3630.99
105_G111_Q1.3350.99
90_D94_Y1.3290.99
19_R82_Q1.3090.99
33_Y52_S1.3030.99
105_G108_V1.2720.99
23_A78_S1.2480.99
24_A29_F1.2050.98
106_M109_W1.2000.98
112_G117_V1.1920.98
15_G19_R1.1910.98
107_D116_T1.1880.98
110_G115_V1.1760.98
109_W113_T1.1760.98
107_D114_T1.1660.97
35_N97_A1.1570.97
5_V8_G1.1470.97
18_L115_V1.1460.97
106_M114_T1.1440.97
110_G114_T1.1390.97
67_R83_M1.1250.97
1_Q5_V1.1250.97
109_W114_T1.1160.96
42_G45_L1.0980.96
114_T117_V1.0940.96
94_Y97_A1.0860.96
12_V18_L1.0780.95
105_G114_T1.0770.95
5_V9_G1.0670.95
6_E9_G1.0670.95
108_V114_T1.0620.95
51_I79_L1.0610.95
114_T118_S1.0500.94
108_V116_T1.0430.94
48_V64_V1.0320.94
109_W118_S1.0310.94
106_M115_V1.0230.93
50_Y57_T1.0060.93
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  
4ut7H10.991699.90.164Contact Map
4pfeA2099.90.166Contact Map
4qgyA2199.80.195Contact Map
4i13B1199.80.214Contact Map
1yc8A20.983299.80.221Contact Map
1dqtA40.949699.80.222Contact Map
3k3qA1199.80.223Contact Map
3j6971199.80.223Contact Map
3g9aB10.974899.80.224Contact Map
1zvyA10.983299.80.228Contact 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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