OPENSEQ.org
9_1tenpdb

ID: 1516869706 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 89 (89)
Sequences: 1275 (921.7)
Seq/Len: 14.326
Nf(neff/√len): 97.7

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: 14.326).

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
17_A87_F3.0381.00
33_L71_L2.4351.00
9_V85_E2.3871.00
13_T16_T2.2881.00
33_L56_Y2.2101.00
35_Y58_I2.0321.00
12_V87_F1.9341.00
6_Q22_F1.8951.00
73_S80_S1.8741.00
61_L67_Y1.8681.00
12_V17_A1.7311.00
58_I69_V1.7051.00
11_D18_L1.4070.99
17_A69_V1.3960.99
2_D26_A1.3840.99
14_D64_D1.3780.99
4_P73_S1.3730.99
28_I73_S1.3540.99
7_I19_I1.3210.99
32_E79_S1.2860.99
34_T58_I1.2820.99
75_R78_M1.2810.99
31_I73_S1.2720.99
72_I82_P1.2430.98
30_G74_R1.2090.98
47_I50_T1.2090.98
29_D78_M1.2040.98
19_I69_V1.1960.98
2_D80_S1.1790.98
37_I65_T1.1730.98
8_E62_K1.1670.97
7_I71_L1.1610.97
9_V87_F1.1600.97
4_P80_S1.0870.96
9_V19_I1.0770.95
38_K86_T1.0740.95
8_E20_T1.0590.95
18_L55_Q1.0450.94
66_E86_T1.0340.94
68_E84_K1.0240.93
10_K20_T1.0240.93
29_D75_R1.0110.93
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  
3csgA1199.30.055Contact Map
3qwqB10.988899.20.088Contact Map
2rb8A1199.20.091Contact Map
4lpvA2199.20.102Contact Map
3teuA1199.20.103Contact Map
2h41A1199.20.109Contact Map
3b83A8199.20.112Contact Map
1j8kA1199.10.115Contact Map
2ha1A1199.10.117Contact Map
1qr4A20.988899.10.119Contact 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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