GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
4cu5

ID: 1501760598 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 85 (80)
Sequences: 594 (592)
Seq/Len: 7.425
Nf(neff/√len): 66.2

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: 7.425).

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 > 50% 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
78_K81_D2.8641.00
16_S76_L2.7231.00
76_L80_L2.5971.00
47_V54_E2.5761.00
65_I82_F2.4991.00
17_A48_V2.4561.00
71_D74_D2.4051.00
74_D78_K1.9111.00
5_T42_T1.8121.00
3_K43_Q1.8121.00
4_H46_Y1.7701.00
44_N65_I1.7691.00
45_L64_F1.6001.00
72_R75_T1.5851.00
50_G68_K1.4250.99
9_D53_C1.4080.99
32_C54_E1.3840.99
10_G31_I1.3400.98
17_A26_D1.2690.98
32_C38_V1.2640.97
48_V79_A1.2580.97
20_V26_D1.2360.97
42_T62_E1.2280.97
10_G14_K1.2210.97
12_V72_R1.1930.96
18_T22_W1.1880.96
13_D72_R1.1450.95
45_L62_E1.1310.94
13_D50_G1.1310.94
54_E66_M1.1270.94
4_H24_Y1.1130.94
20_V79_A1.1120.94
49_G66_M1.0940.93
6_I21_G1.0700.92
77_Y80_L1.0650.92
6_I46_Y1.0540.91
16_S46_Y1.0520.91
20_V83_I1.0430.90
27_G30_L1.0180.89
70_N74_D1.0000.88
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  
4cu2A10.917699.70.052Contact Map
4cu5A6199.20.285Contact Map
1kl7A20.870612.60.854Contact Map
2eguA10.89418.50.864Contact Map
1o58A40.95297.70.867Contact Map
2xveA30.97657.40.868Contact Map
4rg3A10.97657.10.869Contact Map
4r2vA20.95296.70.871Contact Map
4ql4A10.95296.60.871Contact Map
4usrA10.98826.10.873Contact 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 0.0242 seconds.