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v2 19-115

ID: 1513969484 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 97 (97)
Sequences: 249 (89.5)
Seq/Len: 2.567
Nf(neff/√len): 9.1

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: 2.567).

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
30_I33_S2.5161.00
11_S30_I1.7860.98
3_S7_L1.7620.98
23_L46_F1.6330.97
83_A89_Q1.5540.95
44_R79_M1.5480.95
81_K87_E1.5110.94
44_R47_N1.4690.93
62_I67_C1.4510.93
78_G85_E1.4440.93
9_L12_Q1.4380.92
26_D73_R1.4270.92
14_Y20_G1.3990.91
10_L13_D1.3500.89
80_D87_E1.3420.88
29_C33_S1.3380.88
4_V8_Q1.2970.86
9_L19_L1.2930.86
71_C74_H1.2890.86
81_K93_D1.2850.85
70_H73_R1.2800.85
68_C71_C1.2710.84
82_Q85_E1.2700.84
17_D53_T1.2680.84
91_I96_K1.2680.84
58_L68_C1.2590.84
13_D17_D1.2170.81
15_S21_Y1.2040.80
38_E65_P1.1980.79
63_H80_D1.1970.79
34_R84_Y1.1950.79
11_S24_I1.1800.78
26_D70_H1.1780.78
76_T85_E1.1560.76
52_S91_I1.1490.75
48_A91_I1.1440.75
35_N57_E1.1370.74
42_R49_R1.1270.73
64_Q75_K1.1230.73
44_R91_I1.1100.72
45_H51_E1.1050.71
18_T26_D1.1020.71
9_L95_Q1.0910.70
44_R85_E1.0900.70
4_V85_E1.0820.69
17_D21_Y1.0630.67
29_C91_I1.0620.67
66_C69_P1.0570.66
60_Q72_P1.0430.65
21_Y34_R1.0310.63
52_S97_S1.0230.62
68_C74_H1.0150.62
53_T57_E1.0130.61
5_K94_V1.0100.61
19_L48_A1.0020.60
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  
4mbeH40.09285.90.954Contact Map
3pdeA40.32995.80.954Contact Map
4wwsA50.64955.20.955Contact Map
4w8yA20.55674.70.956Contact Map
1t0tV50.64954.60.956Contact Map
4p0gA10.55674.50.956Contact Map
3x1lA104.40.956Contact Map
4bzjA204.20.957Contact Map
3h8vA20.54644.20.957Contact Map
1vdhA50.63924.10.957Contact 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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