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3oss

ID: 1500381927 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 65 (65)
Sequences: 220 (144.7)
Seq/Len: 3.385
Nf(neff/√len): 17.9

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: 3.385).

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
43_I46_I4.1061.00
21_I51_V2.0101.00
27_Q64_L1.8600.99
2_T62_L1.8070.99
2_T53_L1.7860.99
21_I62_L1.6510.98
50_H61_R1.6010.98
53_L62_L1.3820.94
8_L11_I1.3470.93
61_R65_A1.3420.93
2_T8_L1.3410.93
18_G29_V1.3070.91
9_R12_A1.2730.90
42_V54_R1.2520.89
2_T51_V1.2500.89
39_H63_S1.2430.88
41_A55_Y1.2350.88
41_A64_L1.2340.88
29_V39_H1.2110.86
11_I26_K1.1940.85
52_M61_R1.1750.84
18_G34_E1.1660.83
13_F21_I1.1360.81
8_L21_I1.1200.80
43_I51_V1.1110.79
14_G34_E1.1040.79
21_I60_E1.1020.78
7_V31_L1.0920.78
14_G50_H1.0910.77
28_Q37_D1.0700.76
1_E42_V1.0650.75
22_E42_V1.0450.73
42_V45_E1.0360.72
3_R45_E1.0350.72
50_H63_S1.0240.71
42_V53_L1.0060.69
48_R58_K1.0030.69
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  
3ossC1199.70.185Contact Map
2lnvA1199.70.204Contact Map
4av2M12179.20.796Contact Map
2ivwA11490.834Contact Map
2lc4A11480.835Contact Map
2y4xA20.9846380.845Contact Map
2f5tX10.846214.20.874Contact Map
3qphA10.830811.40.879Contact Map
2fauA10.81546.90.89Contact Map
4toiA10.55385.80.894Contact 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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