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1G2E_A

ID: 1515161491 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 83 (81)
Sequences: 32930 (19099.3)
Seq/Len: 406.543
Nf(neff/√len): 2122.1

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: 406.543).

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
53_D56_D2.2741.00
28_E52_I2.2671.00
18_E70_Q2.2241.00
30_E52_I2.2161.00
15_T18_E2.2131.00
26_I63_T2.1641.00
4_N50_N1.7911.00
59_K63_T1.7241.00
58_E78_Y1.6901.00
54_P78_Y1.6891.00
54_P58_E1.6311.00
8_N75_K1.6211.00
35_V46_Y1.6151.00
68_R73_T1.5571.00
22_L67_L1.5561.00
37_D40_T1.5161.00
28_E56_D1.5151.00
12_Q72_K1.5091.00
26_I64_L1.5001.00
16_Q20_R1.4881.00
20_R24_G1.3700.99
3_T57_A1.3640.99
69_L74_I1.3230.99
66_G73_T1.3220.99
12_Q42_Q1.2960.99
11_P14_M1.2880.99
30_E50_N1.2810.99
31_S50_N1.2630.99
57_A78_Y1.2360.98
52_I56_D1.2360.98
64_L67_L1.2310.98
5_L61_I1.2310.98
5_L57_A1.2010.98
21_S24_G1.1880.98
13_N70_Q1.1830.98
34_L43_S1.1610.97
7_V23_F1.1360.97
22_L64_L1.1180.96
8_N77_S1.1180.96
51_Y60_A1.1150.96
58_E62_N1.1050.96
35_V48_F1.1050.96
23_F49_V1.1040.96
34_L47_G1.1000.96
61_I78_Y1.0930.96
4_N31_S1.0530.95
68_R71_T1.0480.94
55_K59_K1.0460.94
12_Q45_G1.0270.94
3_T30_E1.0240.93
22_L69_L1.0190.93
17_E21_S1.0150.93
59_K62_N1.0030.93
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  
3pgwS2199.1-0.193Contact Map
3q2sC20.975999-0.158Contact Map
3n9uC20.975999-0.154Contact Map
1rk8A10.98899-0.146Contact Map
1u6fA1199-0.134Contact Map
2jrsA1199-0.131Contact Map
4wikA20.975999-0.13Contact Map
2kxnB1198.9-0.125Contact Map
2mtgA1198.9-0.123Contact Map
1oo0B1198.9-0.122Contact 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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