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1ayaA

ID: 1507296321 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 101 (96)
Sequences: 4610 (2615)
Seq/Len: 48.021
Nf(neff/√len): 266.9

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: 48.021).

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
42_S51_H2.9281.00
18_L42_S2.5301.00
71_T74_E2.4521.00
60_Y70_A2.3241.00
5_F31_P2.2551.00
4_W29_A2.0461.00
90_N93_V2.0431.00
7_P31_P2.0391.00
13_E16_N1.9271.00
10_T13_E1.9061.00
43_V52_I1.8791.00
69_F78_Y1.8751.00
70_A74_E1.8411.00
24_D45_R1.8291.00
24_D46_N1.7801.00
32_S40_T1.7221.00
69_F79_Y1.6561.00
40_T53_K1.6281.00
60_Y68_K1.6241.00
11_G30_R1.5961.00
2_R73_A1.5451.00
8_N31_P1.5131.00
11_G51_H1.5121.00
57_T60_Y1.4721.00
31_P37_G1.4060.99
27_F80_M1.3960.99
77_Q80_M1.3540.99
22_G26_S1.3520.99
29_A76_V1.3300.99
30_R42_S1.3250.99
88_E91_G1.2840.99
6_H9_I1.2670.99
80_M84_G1.2060.98
6_H17_L1.1960.98
12_V15_E1.1830.98
41_L54_I1.1710.98
54_I61_Y1.1630.97
92_D95_E1.1490.97
14_A18_L1.1440.97
40_T51_H1.1110.96
35_N38_D1.1080.96
15_E51_H1.0890.96
26_S44_R1.0810.95
6_H28_L1.0640.95
19_L49_V1.0600.95
29_A54_I1.0570.95
38_D53_K1.0500.94
90_N96_L1.0260.94
73_A77_Q1.0160.93
23_V26_S1.0030.93
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  
3ps5A1199.90.101Contact Map
2b3oA10.990199.90.105Contact Map
4fl3A1199.90.112Contact Map
2ozoA1199.90.127Contact Map
2shpA2199.90.134Contact Map
3eazA10.950599.90.138Contact Map
2oq1A1199.90.14Contact Map
2ysxA1199.90.14Contact Map
3us4A10.940699.90.141Contact Map
1rjaA10.970399.90.143Contact 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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