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leafs_1ptf_fastRelax_4

ID: 1507536205 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 499 (345.8)
Seq/Len: 5.736
Nf(neff/√len): 37.1

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: 5.736).

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
36_D41_R2.3621.00
16_G19_A1.8791.00
16_G27_A1.7331.00
75_R79_A1.7061.00
32_L38_N1.6421.00
1_D86_I1.5670.99
71_V81_F1.5480.99
25_L80_L1.5290.99
29_F76_S1.5150.99
65_I69_N1.5090.99
8_T12_I1.4620.99
14_I17_A1.4240.98
22_L69_N1.3690.98
29_F80_L1.3010.97
51_R86_I1.2880.96
4_R44_V1.2830.96
55_V86_I1.2830.96
69_N75_R1.2790.96
53_L70_A1.2750.96
77_L82_V1.2720.96
33_I86_I1.2540.95
3_S62_L1.2360.95
38_N82_V1.1940.94
24_E52_M1.1910.94
49_A58_H1.1850.93
47_D51_R1.1680.93
18_A86_I1.1640.93
66_H72_L1.1520.92
44_V55_V1.1500.92
15_N64_V1.1450.92
53_L66_H1.1440.92
44_V50_I1.1330.91
21_L56_P1.1240.91
27_A44_V1.1100.90
2_D17_A1.1000.89
24_E65_I1.0890.89
19_A73_T1.0840.89
8_T37_L1.0750.88
16_G20_R1.0620.87
17_A29_F1.0600.87
42_I51_R1.0520.86
7_I60_K1.0330.85
23_A61_F1.0130.83
76_S84_Y1.0110.83
35_F60_K1.0090.83
66_H82_V1.0000.82
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  
1kklH3197.20.777Contact Map
1ka5A1197.20.777Contact Map
1pchA10.988597.20.777Contact Map
3ccdA20.977970.783Contact Map
1ptfA11970.784Contact Map
1sphA20.9885970.785Contact Map
1y51A30.988596.90.785Contact Map
3ihsA20.93196.80.789Contact Map
3le1A20.988596.40.8Contact Map
3nasA20.666780.927Contact 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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