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yym

ID: 1491895460 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 116 (116)
Sequences: 682 (426.4)
Seq/Len: 5.879
Nf(neff/√len): 39.6

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: 5.879).

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
45_H77_T4.3871.00
62_C69_C2.5171.00
68_N104_A2.1941.00
6_F10_H2.1871.00
5_R9_Q2.0081.00
26_M30_R1.7711.00
27_M32_M1.7591.00
5_R8_R1.7531.00
10_H23_C1.6731.00
54_I101_V1.6401.00
41_N114_H1.6271.00
23_C55_C1.5790.99
37_C90_C1.5490.99
11_V51_I1.5140.99
9_Q38_K1.5080.99
12_H22_Y1.4250.98
46_E50_N1.4100.98
30_R33_T1.3840.98
79_C105_C1.3710.98
3_Y7_L1.3520.98
38_K43_F1.3120.97
38_K114_H1.3100.97
44_I115_F1.2960.97
54_I67_M1.2630.96
22_Y32_M1.2610.96
22_Y77_T1.2330.95
9_Q104_A1.2280.95
26_M45_H1.2270.95
92_Y105_C1.2160.95
27_M45_H1.2140.95
46_E80_R1.1850.94
76_V99_R1.1750.93
36_H97_S1.1410.92
24_N77_T1.1220.91
69_C104_A1.1110.90
51_I103_I1.1090.90
30_R44_I1.1040.90
12_H45_H1.0980.90
56_S100_R1.0860.89
44_I101_V1.0800.89
2_M5_R1.0770.89
58_T70_H1.0650.88
62_C70_H1.0560.87
49_W52_R1.0450.86
25_M29_R1.0390.86
26_M100_R1.0390.86
84_S88_P1.0330.86
2_M67_M1.0290.85
80_R95_M1.0290.85
9_Q114_H1.0220.85
8_R30_R1.0220.85
22_Y26_M1.0210.85
10_H38_K1.0150.84
54_I66_K1.0110.84
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  
1rnfA211000.038Contact Map
3mwqA111000.047Contact Map
2e0jA211000.057Contact Map
1dy5A20.99141000.059Contact Map
1rraA111000.061Contact Map
1agiA10.97411000.067Contact Map
2apqA10.97411000.067Contact Map
2j4tA20.96551000.088Contact Map
4aohA10.95691000.099Contact Map
3zbvA10.96551000.103Contact 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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