OPENSEQ.org
cdomain 1-82 -force run

ID: 1516681069 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 82 (82)
Sequences: 51 (31.5)
Seq/Len: 0.622
Nf(neff/√len): 3.5

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: 0.622).

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
22_Y30_Y2.0110.90
12_Y34_S1.7840.81
12_Y25_S1.7040.77
25_S34_S1.6730.75
10_E71_I1.6280.72
70_N76_P1.4990.63
57_L61_E1.3580.52
67_L78_A1.3390.50
5_H20_L1.3320.49
23_D36_N1.3290.49
15_M18_K1.3120.48
24_W74_V1.2500.43
46_F53_S1.2460.43
17_Q20_L1.2420.42
3_I9_K1.2330.41
6_S10_E1.2020.39
17_Q44_D1.1960.39
63_I81_L1.1910.38
20_L30_Y1.1730.37
23_D81_L1.1650.36
41_E63_I1.1240.33
60_N72_F1.1220.33
70_N73_Q1.1150.33
23_D45_E1.1070.32
15_M75_S1.1020.32
36_N45_E1.0990.31
75_S78_A1.0920.31
48_N52_Q1.0810.30
43_Q62_S1.0780.30
14_S31_F1.0750.30
7_T12_Y1.0680.29
18_K82_L1.0670.29
43_Q82_L1.0610.29
1_D55_P1.0610.29
22_Y31_F1.0560.28
24_W40_P1.0480.28
5_H30_Y1.0410.27
8_S81_L1.0340.27
16_I36_N1.0290.27
16_I23_D1.0290.27
40_P74_V1.0280.27
5_H22_Y1.0240.26
26_T49_P1.0240.26
54_S60_N1.0160.26
14_S73_Q1.0150.26
7_T24_W1.0130.26
3_I6_S1.0120.26
7_T74_V1.0050.25
72_F75_S1.0040.25
70_N80_M1.0030.25
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  
4i9oA10.256144.40.912Contact Map
2gutA10.402429.50.92Contact Map
2k0nA10.43923.90.923Contact Map
2oniA10.96349.20.936Contact Map
3olmA10.96346.70.94Contact Map
1nd7A10.96345.90.942Contact Map
1zvdA10.96345.80.942Contact Map
1sumB10.41464.10.946Contact Map
2g40A10.3784.10.946Contact Map
4dr0A20.682940.946Contact 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 0.0271 seconds.