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T0829

ID: 1505448606 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 67 (67)
Sequences: 654 (493)
Seq/Len: 9.761
Nf(neff/√len): 60.2

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: 9.761).

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
2_R23_E2.9791.00
23_E33_Q2.7311.00
44_N54_F2.3041.00
39_E43_Q2.1361.00
41_A54_F2.0611.00
55_F60_K1.7331.00
2_R12_S1.6751.00
5_V13_I1.6741.00
42_H46_M1.5881.00
7_S52_G1.5671.00
22_L59_I1.4961.00
52_G60_K1.4411.00
35_L64_L1.4090.99
45_F54_F1.3910.99
38_P63_F1.3900.99
17_P39_E1.3810.99
25_Q31_T1.3580.99
2_R25_Q1.3390.99
21_M33_Q1.3170.99
10_I55_F1.2970.99
46_M51_K1.2790.99
36_G64_L1.2650.99
35_L66_R1.2190.98
15_Y20_R1.2040.98
13_I24_I1.1890.98
56_D60_K1.1240.96
52_G56_D1.1100.96
41_A63_F1.0760.95
53_R56_D1.0750.95
38_P41_A1.0560.94
7_S50_S1.0480.94
9_R55_F1.0300.93
39_E42_H1.0220.93
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  
4rgiA1199.90.035Contact Map
3fssA10.776129.20.853Contact Map
3f5rA10.970127.90.855Contact Map
4khbD40.955224.20.859Contact Map
4c5wA10.895521.80.862Contact Map
3k8rA20.8657170.868Contact Map
2x8nA10.940314.90.872Contact Map
4hs5A20.970190.884Contact Map
2xppB10.35828.30.886Contact Map
2qmeI10.34337.50.888Contact 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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