OPENSEQ.org
2_1divpdb

ID: 1516869526 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 149 (147)
Sequences: 3540 (2187.8)
Seq/Len: 24.082
Nf(neff/√len): 180.4

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: 24.082).

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_K20_N3.2311.00
62_L66_K2.8651.00
103_Q109_K2.6871.00
128_N140_T2.6151.00
7_K35_L2.5801.00
128_N142_K2.4471.00
126_Y144_H2.4001.00
59_A63_A2.2711.00
80_P146_T2.1361.00
78_T146_T2.0581.00
123_A127_T2.0251.00
5_F19_K1.9751.00
78_T144_H1.9211.00
48_E51_K1.8911.00
101_S104_A1.8781.00
55_Q59_A1.8111.00
5_F13_G1.7751.00
67_K71_Q1.7481.00
26_A31_F1.7231.00
134_H137_V1.6921.00
67_K70_E1.6801.00
63_A66_K1.6531.00
9_V35_L1.6351.00
130_P138_T1.6291.00
45_K48_E1.6021.00
102_L110_L1.5921.00
30_L36_A1.5781.00
70_E73_E1.5691.00
53_K57_Q1.5661.00
65_A134_H1.5641.00
46_A50_Q1.5501.00
41_P45_K1.5251.00
56_R60_E1.5241.00
64_N67_K1.4841.00
66_K70_E1.4811.00
77_V102_L1.4701.00
63_A67_K1.4631.00
99_A115_I1.4581.00
69_K73_E1.4201.00
52_Q55_Q1.3940.99
77_V101_S1.3820.99
2_K44_L1.3580.99
129_V143_V1.3510.99
81_A93_I1.3500.99
1_M26_A1.3480.99
18_I44_L1.3400.99
79_I101_S1.3360.99
66_K69_K1.3240.99
5_F12_K1.3070.99
45_K49_A1.3030.99
60_E64_N1.2990.99
81_A89_L1.2750.99
130_P140_T1.2720.99
4_I43_N1.2710.99
8_D14_K1.2700.99
3_V26_A1.2660.99
54_E58_A1.2590.99
121_I145_V1.2470.99
121_I143_V1.2370.98
42_A46_A1.2360.98
37_I43_N1.2090.98
69_K139_A1.2040.98
75_L106_H1.1960.98
51_K55_Q1.1960.98
6_L37_I1.1920.98
49_A52_Q1.1670.97
2_K18_I1.1620.97
39_A44_L1.1620.97
43_N46_A1.1590.97
124_L147_E1.1540.97
101_S105_Q1.1500.97
51_K54_E1.1460.97
76_T144_H1.1430.97
100_E104_A1.1390.97
53_K56_R1.1320.97
132_K138_T1.1250.97
58_A61_E1.1180.96
115_I131_V1.0880.96
31_F34_G1.0870.96
44_L48_E1.0770.95
126_Y142_K1.0700.95
57_Q61_E1.0680.95
12_K25_Y1.0660.95
102_L106_H1.0660.95
92_S122_R1.0370.94
49_A53_K1.0340.94
58_A62_L1.0170.93
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  
1divA11100-0.038Contact Map
3bboJ10.9866100-0.018Contact Map
4rb6I10.9799100-0.015Contact Map
4tp9H10.9866100-0.014Contact Map
1nkwF10.3491000.003Contact Map
3j7yH10.36241000.08Contact Map
2hbaA20.34999.80.493Contact Map
1vw4G10.30299.80.517Contact Map
4qjty10.859199.70.561Contact Map
3pxgA60.657726.20.919Contact 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 0.0357 seconds.