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2H24

ID: 1515673251 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 139 (136)
Sequences: 230 (126.8)
Seq/Len: 1.691
Nf(neff/√len): 10.9

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: 1.691).

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
118_K122_E2.1560.99
13_F17_K2.0270.99
57_M129_Y1.6930.95
31_S104_V1.6200.93
50_Q54_E1.5620.91
111_L118_K1.5570.91
119_A122_E1.4590.86
118_K126_F1.4450.86
16_V94_C1.4230.85
25_N64_D1.4170.84
64_D104_V1.4140.84
119_A124_D1.4120.84
21_D28_L1.4010.83
123_F127_I1.4000.83
129_Y133_Y1.3980.83
6_L14_S1.3920.83
122_E126_F1.3810.82
57_M78_L1.3770.82
52_Y94_C1.3200.78
24_D71_V1.3080.77
121_S127_I1.3050.77
10_R16_V1.3020.77
75_G78_L1.2970.76
118_K121_S1.2880.76
115_G127_I1.2510.72
45_L80_T1.2380.71
51_F78_L1.2280.70
118_K123_F1.2050.68
22_Q84_R1.2020.68
72_N136_M1.1900.67
78_L123_F1.1780.66
48_M57_M1.1770.66
10_R94_C1.1750.66
48_M126_F1.1740.65
43_Q92_L1.1690.65
119_A129_Y1.1660.65
2_L136_M1.1610.64
27_L51_F1.1480.63
25_N72_N1.1480.63
23_L36_F1.1450.63
111_L121_S1.1370.62
130_I133_Y1.1290.61
62_N90_R1.0910.57
77_N104_V1.0860.57
57_M75_G1.0780.56
5_M10_R1.0770.56
56_V119_A1.0760.55
115_G122_E1.0750.55
5_M16_V1.0750.55
15_R109_N1.0720.55
42_C88_C1.0670.55
74_L108_F1.0590.54
73_S114_K1.0580.54
26_L85_L1.0580.54
55_E78_L1.0480.53
27_L58_P1.0450.52
37_K59_Q1.0380.51
116_I119_A1.0340.51
36_F100_A1.0240.50
9_L16_V1.0240.50
12_A62_N1.0230.50
115_G118_K1.0210.50
88_C94_C1.0190.49
83_L112_Q1.0160.49
120_M126_F1.0080.48
12_A78_L1.0060.48
130_I136_M1.0050.48
17_K66_D1.0020.48
4_N124_D1.0010.48
95_E105_K1.0010.48
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  
2ilkA111000.089Contact Map
1lqsL20.94241000.163Contact Map
4dohA20.9641000.17Contact Map
1n1fA10.97841000.172Contact Map
3dlqI10.87771000.238Contact Map
4o6kA40.87771000.246Contact Map
1fyhA20.884936.20.923Contact Map
2rigA10.805819.50.932Contact Map
1wb9A20.935317.30.934Contact Map
1d9cA20.820116.40.935Contact 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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