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KaiB

ID: 1476808649 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 102 (92)
Sequences: 344 (250)
Seq/Len: 3.739
Nf(neff/√len): 26.1

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: 3.739).

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
31_L35_F2.0081.00
28_K32_E1.9471.00
28_K41_L1.6140.98
66_K69_P1.5490.98
46_V61_T1.5220.97
53_A73_R1.4650.97
20_S81_D1.4130.96
6_T40_A1.4100.96
65_A79_L1.4010.95
68_L90_D1.3950.95
64_L75_I1.3730.95
9_L86_L1.3490.94
9_L88_G1.3470.94
79_L89_L1.3300.93
12_Y56_D1.2690.91
10_K42_K1.2680.91
65_A74_R1.2680.91
26_T80_S1.2620.91
23_A37_G1.2570.91
70_L90_D1.2390.90
66_K90_D1.2370.90
16_N46_V1.2310.89
13_V30_I1.2050.88
24_L41_L1.2050.88
14_A47_L1.1950.87
55_E92_L1.1900.87
56_D65_A1.1860.87
34_E61_T1.1580.85
56_D67_V1.1570.85
68_L87_I1.1510.85
32_E39_Y1.1450.84
30_I85_V1.1400.84
35_F45_D1.1280.83
49_N52_L1.1280.83
5_K67_V1.1070.81
25_K93_Y1.0970.80
78_D89_L1.0960.80
31_L42_K1.0820.79
27_L79_L1.0730.78
5_K33_V1.0630.78
12_Y91_L1.0510.76
68_L72_V1.0500.76
42_K84_K1.0470.76
43_V54_E1.0460.76
31_L38_V1.0450.76
72_V90_D1.0290.74
85_V89_L1.0290.74
43_V68_L1.0260.74
16_N85_V1.0200.73
12_Y87_I1.0150.73
51_Q55_E1.0080.72
32_E41_L1.0050.72
12_Y52_L1.0050.72
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  
1t4yA10.960899.90.346Contact Map
4kunA20.882499.80.458Contact Map
1wwjA40.960899.80.484Contact Map
1fo5A10.8333950.837Contact Map
1qgvA10.970694.60.84Contact Map
4cdoA20.990294.10.844Contact Map
2av4A10.990293.70.847Contact Map
1iloA10.754993.60.847Contact Map
3d22A10.951930.85Contact Map
3cxgA20.8824930.851Contact 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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