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chey_edited

ID: 1504721551 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 112 (108)
Sequences: 206863 (142446)
Seq/Len: 1915.398
Nf(neff/√len): 13706.9

Jackhmmer Results: (2016_04)
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: 1915.398).

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
10_R27_E3.0651.00
14_R27_E2.7671.00
10_R29_E2.7161.00
3_V34_A2.4031.00
26_E43_Y2.3161.00
32_V54_N2.1161.00
35_L63_T2.0691.00
68_G71_S2.0621.00
51_N81_E2.0221.00
31_G55_M2.0151.00
39_Q67_D1.9661.00
55_M63_T1.9381.00
28_A37_K1.9151.00
26_E37_K1.9011.00
48_S60_L1.8761.00
26_E41_G1.8091.00
77_M95_A1.7891.00
16_L105_A1.7721.00
30_D54_N1.7631.00
61_L75_V1.7411.00
29_E33_D1.6891.00
65_R96_S1.5241.00
62_K93_A1.4881.00
14_R18_K1.4481.00
50_W58_L1.4471.00
63_T67_D1.4361.00
37_K41_G1.4081.00
30_D33_D1.3440.99
31_G60_L1.3170.99
81_E86_N1.3150.99
55_M59_E1.3150.99
38_L64_I1.3150.99
37_K40_A1.3030.99
32_V55_M1.2730.99
84_K88_I1.2530.99
56_D59_E1.2520.99
37_K43_Y1.2450.98
46_V73_L1.1960.98
63_T66_A1.1880.98
35_L60_L1.1750.98
58_L90_A1.1750.98
88_I92_Q1.1710.98
5_D49_D1.1180.96
7_S29_E1.1150.96
89_A93_A1.1090.96
61_L77_M1.0970.96
78_V103_F1.0590.95
83_K86_N1.0500.94
58_L89_A1.0490.94
77_M90_A1.0410.94
28_A34_A1.0190.93
34_A60_L1.0050.93
2_V13_V1.0020.92
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  
4g97A10.946499.90.077Contact Map
1w25A20.991199.80.079Contact Map
3n0rA10.946499.80.084Contact Map
3breA20.991199.80.088Contact Map
3dzdA20.973299.80.106Contact Map
3eq2A20.973299.80.114Contact Map
4l4uA10.973299.80.123Contact Map
3lufA20.991199.80.128Contact Map
2ayxA10.973299.80.129Contact Map
3rqiA10.964399.80.136Contact 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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