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OPENSEQ.org

SasA

ID: 1493410027 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 105 (97)
Sequences: 116 (82.9)
Seq/Len: 1.196
Nf(neff/√len): 8.4

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: 1.196).

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
52_V59_V2.7291.00
93_Q96_Q2.0290.97
51_N59_V1.7790.93
52_V57_Q1.6090.87
60_E72_K1.5520.84
25_S84_I1.5300.83
69_A82_S1.4680.79
28_I52_V1.4550.78
23_P62_Y1.4230.76
65_V82_S1.3600.72
45_I94_L1.3390.70
43_V80_V1.3250.69
31_R71_V1.3100.67
59_V71_V1.3050.67
46_S55_Q1.2970.66
45_I100_Q1.2930.66
18_F62_Y1.2680.64
81_L86_L1.2630.63
33_K52_V1.2610.63
28_I59_V1.2490.62
24_L62_Y1.2350.61
64_L95_P1.2300.60
44_P86_L1.2150.59
30_Q51_N1.2020.58
16_Q82_S1.1950.57
21_T35_I1.1790.55
55_Q90_L1.1620.54
79_Q93_Q1.1590.53
24_L86_L1.1580.53
92_N99_V1.1570.53
35_I91_A1.1540.53
43_V69_A1.1520.53
79_Q87_T1.1470.52
33_K59_V1.1380.51
51_N85_D1.1360.51
12_P37_A1.1220.50
22_R67_T1.1160.49
6_P34_N1.1110.49
25_S33_K1.1080.48
32_V65_V1.0900.47
26_Q36_L1.0720.45
51_N93_Q1.0650.44
34_N71_V1.0500.43
5_S9_L1.0320.41
40_E87_T1.0260.41
67_T86_L1.0200.40
46_S53_A1.0090.39
29_V87_T1.0040.39
13_L45_I1.0030.38
29_V72_K1.0010.38
48_Q90_L1.0000.38
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  
1t4yA111000.215Contact Map
4kunA20.838199.20.719Contact Map
1wwjA40.923898.60.771Contact Map
1iloA10.723858.40.916Contact Map
2fgxA10.790550.90.92Contact Map
1nhoA10.850.40.92Contact Map
1wjkA10.885749.40.92Contact Map
3cxgA20.904849.10.92Contact Map
4wxtA10.923848.70.921Contact Map
2vm1A40.942945.40.922Contact 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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