GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
4F25 cut to pdb length

ID: 1377323210 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 0% gaps before running GREMLIN.
Length: 81 (81)
Sequences: 13235 (8140.5)
Seq/Len: 163.395
Nf(neff/√len): 904.5

HHblits Results: (2013_03)
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: 163.395).

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 > 0% 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
50_T53_A2.6471.00
17_A67_N2.5721.00
27_N49_E2.5671.00
14_D17_A2.3531.00
11_K69_R2.2331.00
25_F60_K2.0221.00
56_R60_K2.0191.00
55_E75_R1.9391.00
29_L49_E1.8261.00
7_K72_F1.7111.00
4_I58_I1.6491.00
19_Y23_S1.6431.00
27_N53_A1.6031.00
51_Q55_E1.5561.00
25_F61_M1.5561.00
66_L71_V1.5041.00
21_T64_M1.4891.00
65_L68_D1.4891.00
34_V43_Y1.4801.00
20_D23_S1.4661.00
3_N47_H1.4461.00
10_D13_I1.3670.99
55_E59_E1.3620.99
18_L44_G1.3550.99
33_V40_S1.3490.99
51_Q75_R1.3320.99
65_L70_K1.3230.99
12_S67_N1.3170.99
63_G70_K1.3130.99
15_N19_Y1.2710.99
49_E53_A1.2610.99
4_I54_A1.2530.99
29_L47_H1.2260.98
22_F46_V1.2190.98
54_A75_R1.2050.98
56_R59_E1.1330.97
21_T61_M1.1260.97
30_S47_H1.1250.97
13_I67_N1.1220.97
52_E56_R1.1210.97
6_I22_F1.0900.96
21_T66_L1.0550.95
48_F57_A1.0070.93
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: (08Feb14)
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  
3pgwS20.987799.60.058Contact Map
2errA1199.50.075Contact Map
4f02A2199.50.078Contact Map
2l9wA10.950699.50.084Contact Map
3q2sC20.987799.50.084Contact Map
1rk8A10.987799.50.084Contact Map
2cq3A1199.50.086Contact Map
2i2yA10.96399.50.09Contact Map
2cqiA1199.50.094Contact Map
2fy1A1199.50.094Contact 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.

Page generated in 0.0601 seconds.