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fastRelax_offset_4

ID: 1507196381 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 614 (288.4)
Seq/Len: 7.057
Nf(neff/√len): 30.9

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: 7.057).

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
16_G19_A2.0071.00
36_D41_R1.8641.00
1_D86_I1.8561.00
65_I69_N1.5941.00
29_F76_S1.5360.99
16_G27_A1.5310.99
14_I17_A1.4790.99
51_R86_I1.4580.99
38_N82_V1.4460.99
32_L38_N1.3770.99
4_R44_V1.3660.98
75_R79_A1.3600.98
77_L82_V1.3000.98
3_S62_L1.2940.98
53_L70_A1.2820.97
22_L69_N1.2790.97
2_D17_A1.2410.97
8_T12_I1.2320.97
71_V81_F1.2280.96
44_V50_I1.2200.96
20_R24_E1.1990.96
55_V86_I1.1740.95
53_L66_H1.1720.95
18_A80_L1.1720.95
8_T37_L1.1670.95
29_F80_L1.1650.95
47_D51_R1.1560.95
16_G20_R1.1240.93
25_L80_L1.1230.93
28_A56_P1.1070.93
19_A73_T1.1070.93
7_I28_A1.0830.92
24_E65_I1.0800.92
66_H72_L1.0800.92
52_M68_S1.0790.91
44_V55_V1.0700.91
20_R47_D1.0660.91
8_T28_A1.0620.91
76_S84_Y1.0500.90
4_R14_I1.0480.90
48_G52_M1.0400.89
21_L56_P1.0290.89
37_L70_A1.0290.89
27_A44_V1.0250.88
15_N64_V1.0240.88
18_A86_I1.0180.88
11_P47_D1.0120.88
57_R84_Y1.0110.88
6_L34_L1.0070.87
7_I33_I1.0020.87
23_A61_F1.0000.87
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
1ka5A1197.20.778Contact Map
1pchA10.988597.20.778Contact Map
1ptfA11970.784Contact Map
3ccdA20.977970.785Contact Map
1sphA20.988596.90.786Contact Map
1y51A30.988596.90.786Contact Map
3ihsA20.93196.80.79Contact Map
3le1A20.988596.30.8Contact Map
3nasA20.66675.80.931Contact 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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