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103

ID: 1500058622 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 90 (90)
Sequences: 364 (229.1)
Seq/Len: 4.044
Nf(neff/√len): 24.1

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: 4.044).

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
27_N30_I1.8551.00
40_A44_L1.8121.00
46_S49_L1.7200.99
87_E90_D1.7080.99
39_S44_L1.6570.99
45_V49_L1.6020.99
24_F27_N1.5680.98
62_P65_A1.5450.98
61_S67_G1.5280.98
66_R70_V1.4790.97
28_I39_S1.4740.97
48_K52_Y1.4660.97
2_V5_L1.4390.97
24_F29_I1.4370.97
80_D83_A1.4270.97
53_Q56_R1.3580.95
50_A54_A1.3320.94
3_T6_L1.3050.93
38_F44_L1.2950.93
59_S62_P1.2610.92
71_C74_S1.2420.91
81_L85_A1.2240.90
61_S64_P1.2170.90
2_V7_G1.1770.88
77_Y89_I1.1620.87
67_G70_V1.1480.86
67_G71_C1.1450.86
59_S63_N1.1410.86
13_Q17_C1.1370.85
43_K49_L1.1290.85
83_A86_S1.1230.84
8_G22_E1.1190.84
54_A57_K1.1110.83
65_A71_C1.0960.82
5_L19_P1.0950.82
8_G48_K1.0930.82
67_G72_S1.0920.82
10_M22_E1.0790.81
43_K46_S1.0490.78
51_S54_A1.0160.75
49_L52_Y1.0110.75
3_T8_G1.0080.74
2_V9_D1.0030.74
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  
2xl1A10.16672.10.937Contact Map
4xk8F201.60.942Contact Map
2ly1A10.83331.40.943Contact Map
3r4dB20.11111.30.944Contact Map
4h14A10.45561.30.945Contact Map
2wscF10.52221.20.946Contact Map
3tcqA10.17781.20.946Contact Map
1jb0F10.61.10.948Contact Map
4kt0F10.610.948Contact Map
4l6vF30.610.949Contact 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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