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Kristian Davidsen

ID: 1500493862 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 125 (122)
Sequences: 4845 (2641.5)
Seq/Len: 39.713
Nf(neff/√len): 239.2

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: 39.713).

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
116_G119_T2.7041.00
12_V86_L2.6051.00
111_Y114_V2.3061.00
13_H16_T2.2051.00
62_D65_K2.1951.00
114_V120_K2.1401.00
12_V16_T2.1051.00
68_F83_M2.0461.00
105_E109_Y1.8481.00
48_V68_F1.8311.00
115_W118_G1.7201.00
39_Q45_L1.6301.00
33_G52_W1.6231.00
19_R80_Y1.5981.00
118_G121_V1.5911.00
112_M120_K1.5471.00
38_R46_E1.5351.00
104_L110_Y1.5321.00
24_A34_M1.5291.00
36_W81_L1.4771.00
35_H47_W1.4641.00
90_D94_Y1.4481.00
19_R82_Q1.4421.00
104_L109_Y1.4421.00
105_E108_Y1.4321.00
110_Y114_V1.3960.99
34_M79_L1.3930.99
105_E110_Y1.3810.99
49_A70_V1.3600.99
6_E9_G1.3470.99
112_M115_W1.3470.99
119_T123_V1.3360.99
111_Y120_K1.3340.99
50_V59_Y1.3050.99
18_L121_V1.2820.99
115_W119_T1.2720.99
24_A29_F1.2700.99
38_R92_A1.2670.99
90_D96_C1.2640.99
114_V117_K1.2620.99
115_W120_K1.2620.99
33_G50_V1.2590.99
118_G123_V1.2090.98
102_G105_E1.2090.98
113_D120_K1.2030.98
115_W121_V1.1910.98
109_Y112_M1.1900.98
113_D122_T1.1860.98
12_V18_L1.1780.98
110_Y120_K1.1630.97
104_L108_Y1.1560.97
48_V64_V1.1390.97
60_Y64_V1.1210.97
103_R108_Y1.1060.96
67_R83_M1.1050.96
100_V103_R1.1000.96
23_A78_T1.1000.96
7_S10_G1.0980.96
116_G121_V1.0860.96
6_E10_G1.0810.95
94_Y97_A1.0540.95
37_V47_W1.0510.94
10_G18_L1.0390.94
35_H50_V1.0330.94
102_G109_Y1.0200.93
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  
4ut7H10.99299.90.171Contact Map
4pfeA2099.90.183Contact Map
4qgyA2199.80.216Contact Map
4i13B1199.80.233Contact Map
3g9aB10.97699.80.236Contact Map
3k3qA1199.80.237Contact Map
1dqtA40.9299.80.238Contact Map
1zvyA10.98499.80.244Contact Map
4qo1A10.97699.80.246Contact Map
2vyrE80.99299.80.248Contact 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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