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sub_b

ID: 1502119673 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 105 (105)
Sequences: 4252 (3024.5)
Seq/Len: 40.495
Nf(neff/√len): 295.2

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: 40.495).

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
7_D11_N2.4281.00
17_L21_R2.1951.00
25_E29_K2.1231.00
10_D14_Q2.0961.00
24_E28_G2.0281.00
50_Q54_N2.0141.00
18_N22_N1.9811.00
65_N69_S1.8781.00
14_Q18_N1.8631.00
89_Q93_I1.7291.00
32_E36_K1.7281.00
70_T74_L1.7101.00
13_K17_L1.6291.00
62_E65_N1.6271.00
21_R25_E1.5811.00
34_L38_R1.5581.00
53_V57_S1.5561.00
86_Q90_Q1.5311.00
60_E64_M1.5131.00
64_M68_N1.5001.00
43_K47_D1.4951.00
11_N15_R1.4701.00
75_E79_N1.4491.00
57_S61_R1.4481.00
39_A43_K1.4401.00
78_E82_N1.4241.00
74_L77_F1.4111.00
69_S73_T1.3820.99
36_K40_R1.3780.99
79_N83_E1.3670.99
28_G32_E1.3580.99
35_E39_A1.3560.99
76_Q80_Y1.3230.99
10_D13_K1.3200.99
68_N71_Y1.3190.99
53_V56_Y1.2930.99
72_K76_Q1.2890.99
15_R19_T1.2790.99
43_K46_M1.2440.98
71_Y75_E1.2430.98
49_D53_V1.2330.98
88_E91_K1.2240.98
72_K75_E1.2210.98
35_E38_R1.2100.98
47_D50_Q1.2050.98
60_E63_K1.1790.98
63_K66_L1.1610.97
31_I35_E1.1610.97
27_R31_I1.1560.97
95_Q99_R1.1500.97
22_N26_L1.1450.97
80_Y83_E1.1360.97
4_V7_D1.1220.97
68_N72_K1.1020.96
28_G31_I1.0950.96
11_N14_Q1.0860.96
90_Q94_N1.0780.95
62_E66_L1.0680.95
44_V48_A1.0570.95
63_K67_I1.0540.95
87_F91_K1.0450.94
29_K32_E1.0380.94
40_R43_K1.0380.94
37_A40_R1.0270.94
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  
2khkA10.504896.80.511Contact Map
1l2pA10.58194.70.585Contact Map
2dm9A20.066789.50.647Contact Map
3v6iA20.790576.50.699Contact Map
4efaG10.8476410.76Contact Map
2clyA20.952428.20.78Contact Map
4cfgA20.923824.40.787Contact Map
4efaE10.838123.50.789Contact Map
4aurA1120.50.794Contact Map
3v6iB20.876219.20.797Contact 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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