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v2 19-121

ID: 1513317243 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 103 (100)
Sequences: 240 (95.3)
Seq/Len: 2.400
Nf(neff/√len): 9.5

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: 2.400).

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_S2.5631.00
11_S30_I1.9360.99
23_L46_F1.7030.97
83_A89_Q1.6860.97
44_R79_M1.6650.97
9_L12_Q1.6030.96
26_D73_R1.5690.95
44_R47_N1.5370.94
9_L19_L1.5120.94
62_I67_C1.4810.93
10_L13_D1.4560.92
52_S91_I1.4210.91
17_D21_Y1.3770.89
15_S21_Y1.3680.89
71_C74_H1.3650.88
14_Y20_G1.3420.87
58_L68_C1.3340.87
81_K93_D1.3240.86
29_C91_I1.2920.84
81_K87_E1.2640.83
68_C71_C1.2600.82
70_H73_R1.2600.82
48_A54_S1.2530.82
50_V88_A1.2510.82
4_V41_C1.2410.81
26_D70_H1.2410.81
29_C33_S1.2230.80
4_V8_Q1.2100.79
78_G85_E1.2040.78
45_H51_E1.2000.78
17_D53_T1.1990.78
54_S87_E1.1970.78
3_S7_L1.1850.77
48_A91_I1.1820.76
35_N41_C1.1640.75
33_S41_C1.1600.74
91_I96_K1.1570.74
5_K94_V1.1550.74
42_R49_R1.1280.71
80_D87_E1.1260.71
9_L95_Q1.1090.70
11_S24_I1.0940.68
13_D17_D1.0940.68
47_N50_V1.0870.67
60_Q72_P1.0770.66
56_S90_N1.0730.66
24_I80_D1.0680.65
35_N57_E1.0660.65
78_G87_E1.0650.65
50_V76_T1.0520.64
76_T85_E1.0460.63
38_E65_P1.0450.63
31_L52_S1.0420.63
4_V85_E1.0380.62
19_L31_L1.0250.61
82_Q85_E1.0220.60
68_C74_H1.0220.60
8_Q20_G1.0210.60
97_S100_S1.0200.60
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  
1vdhA50.601910.60.951Contact Map
3pdeA40.31076.60.955Contact Map
4mbeH40.08746.50.955Contact Map
3nsjA10.96126.30.956Contact Map
4w8yA20.52435.40.957Contact Map
4bzjA205.10.957Contact Map
3x1lA105.10.957Contact Map
4wwsA50.61175.10.957Contact Map
4p0gA10.52434.80.958Contact Map
4g0dW40.13594.50.959Contact 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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