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2K2U

ID: 1515673806 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 115 (101)
Sequences: 206 (137)
Seq/Len: 2.040
Nf(neff/√len): 13.6

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: 2.040).

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
101_K105_Q2.0030.99
27_L62_L1.9610.99
58_M104_L1.7820.97
59_M63_I1.7050.96
30_R37_V1.5980.94
18_I27_L1.5230.92
18_I109_S1.5000.91
52_P57_K1.4930.91
97_M101_K1.4890.91
39_T108_I1.4880.91
53_A90_S1.4480.89
9_F108_I1.4430.89
19_N62_L1.4300.89
18_I100_I1.3730.86
48_L51_T1.3530.85
7_A16_I1.3140.82
4_S98_D1.3110.82
49_Q52_P1.2970.81
60_L91_F1.2180.75
45_I52_P1.2170.75
40_V48_L1.2160.75
54_S62_L1.2090.74
94_R98_D1.2040.74
10_E104_L1.2030.74
103_T114_A1.1980.73
81_V114_A1.1820.72
33_D36_K1.1790.71
15_I67_D1.1690.71
30_R34_G1.1650.70
27_L54_S1.1620.70
83_K94_R1.1580.70
55_S88_M1.1470.68
9_F67_D1.1240.66
27_L61_R1.1220.66
88_M92_N1.1200.66
7_A29_W1.1160.65
22_V54_S1.1150.65
9_F12_V1.1140.65
103_T109_S1.1120.65
68_E80_V1.1100.65
83_K90_S1.1080.65
47_K63_I1.1000.64
45_I57_K1.0900.63
56_E112_K1.0830.62
103_T108_I1.0590.59
17_A61_R1.0570.59
2_S17_A1.0520.59
51_T54_S1.0490.58
51_T97_M1.0470.58
69_S80_V1.0420.58
58_M97_M1.0280.56
10_E52_P1.0090.54
54_S100_I1.0090.54
29_W57_K1.0060.54
26_E112_K1.0050.53
28_T100_I1.0040.53
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  
1y5oA111000.112Contact Map
1pfjA10.817499.90.272Contact Map
2cayA20.817489.40.847Contact Map
3fssA10.721779.60.866Contact Map
4ifsA10.773978.30.867Contact Map
2hthB10.895778.10.868Contact Map
4khbD40.791377.80.868Contact Map
4pq0A10.739175.80.87Contact Map
4tyzA20.756563.90.881Contact Map
2yf0A10.773959.40.884Contact 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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