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V2EDI

ID: 1514006357 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 94 (90)
Sequences: 225 (80.9)
Seq/Len: 2.500
Nf(neff/√len): 8.5

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: 2.500).

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
33_V36_A2.2331.00
22_L49_F1.7120.98
11_E33_V1.7080.98
13_Y19_G1.6360.97
57_S84_E1.5520.95
80_A86_Q1.5440.95
51_A88_V1.5100.94
9_L18_L1.5000.94
47_N77_M1.4740.93
4_V8_Q1.4630.93
16_D20_Y1.4160.91
47_N50_H1.4060.91
88_V93_K1.3820.90
11_E23_I1.3680.89
79_Q82_V1.3680.89
17_T29_D1.3630.89
3_A7_L1.3040.86
14_S20_Y1.2950.85
68_C71_C1.2830.85
48_H54_E1.2700.84
11_E78_D1.2680.84
7_L11_E1.2400.82
90_D94_P1.2340.81
71_C74_H1.2300.81
34_I55_G1.2240.81
29_D70_H1.2200.80
64_I67_C1.2200.80
29_D73_R1.2040.79
32_S36_A1.1960.79
53_L76_Q1.1890.78
65_P69_P1.1870.78
67_C81_H1.1840.78
38_N59_E1.1770.77
54_E81_H1.1630.76
70_H73_R1.1620.76
12_T56_T1.1530.75
62_Q72_P1.1480.74
50_H53_L1.1480.74
60_L68_C1.1470.74
9_L92_Q1.1420.74
45_R52_R1.1110.71
34_I37_R1.0810.68
16_D56_T1.0810.68
47_N88_V1.0750.67
41_E65_P1.0740.67
78_D84_E1.0730.67
55_G88_V1.0720.67
32_S88_V1.0620.66
58_S87_D1.0600.66
12_T16_D1.0530.65
4_V82_V1.0450.64
68_C74_H1.0260.62
82_V94_P1.0140.61
85_A93_K1.0060.60
56_T59_E1.0050.60
3_A11_E1.0000.59
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  
4wwsA50.73415.90.943Contact Map
2wnfA10.319113.90.945Contact Map
1t0tV50.73413.40.945Contact Map
1vdhA50.702111.40.947Contact Map
3nsjA10.96819.50.949Contact Map
4esjA20.48948.30.95Contact Map
2xocA20.15967.80.951Contact Map
3axsA10.94685.80.953Contact Map
3l0aA10.77665.70.953Contact Map
3buaE40.12775.20.954Contact 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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