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OPENSEQ.org

1oee

ID: 1492603460 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 193 (191)
Sequences: 306 (201.7)
Seq/Len: 1.602
Nf(neff/√len): 14.6

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: 1.602).

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
27_V112_I3.4611.00
50_K183_S2.8601.00
29_N107_Y2.7741.00
90_G104_K2.2680.99
16_K19_N2.1860.99
92_V139_I2.1850.99
177_Y189_E2.1740.99
145_I149_R2.0180.98
139_I156_I2.0040.98
106_D129_K1.9500.98
38_V84_M1.7980.96
86_G95_H1.6670.93
45_L183_S1.6190.92
103_C128_C1.6160.92
57_K60_D1.6010.91
10_L14_E1.5760.91
36_D88_E1.5290.89
23_D26_N1.5220.88
83_E97_N1.5200.88
135_A160_N1.4890.87
103_C135_A1.4780.86
165_S168_N1.4730.86
35_W157_F1.4030.82
182_S185_E1.3940.82
108_D127_E1.3920.82
128_C135_A1.3860.81
166_L170_M1.3770.81
157_F166_L1.3650.80
17_A26_N1.3570.79
181_L189_E1.3400.78
21_V117_S1.3330.78
125_L170_M1.3280.77
25_A31_T1.2890.74
71_K75_H1.2860.74
55_F71_K1.2830.74
128_C131_P1.2820.74
18_A76_K1.2720.73
52_D71_K1.2650.72
68_A184_E1.2570.71
111_K157_F1.2520.71
124_Y168_N1.2430.70
84_M95_H1.2400.70
92_V156_I1.2390.70
127_E163_Q1.2330.69
57_K184_E1.2130.68
84_M179_Y1.2120.67
8_K11_T1.1840.65
38_V95_H1.1760.64
153_H174_P1.1750.64
155_H174_P1.1750.64
55_F67_F1.1690.63
177_Y190_M1.1560.62
21_V24_D1.1530.62
17_A21_V1.1500.61
66_T181_L1.1500.61
23_D129_K1.1470.61
48_S183_S1.1450.61
16_K187_V1.1370.60
115_Y142_S1.1250.59
116_K185_E1.1170.58
89_D156_I1.1150.58
103_C133_S1.1140.58
75_H79_A1.1130.58
110_Y191_M1.1080.57
95_H179_Y1.1060.57
45_L64_T1.0950.56
80_T176_Y1.0930.56
60_D187_V1.0860.55
15_Q110_Y1.0850.55
18_A63_K1.0850.55
66_T108_D1.0820.54
64_T70_I1.0800.54
70_I73_Y1.0790.54
7_G10_L1.0770.54
14_E18_A1.0770.54
45_L48_S1.0740.54
56_Q60_D1.0700.53
103_C160_N1.0570.52
72_D75_H1.0510.51
18_A157_F1.0480.51
32_L94_F1.0420.50
117_S120_K1.0410.50
25_A104_K1.0370.50
8_K13_V1.0290.49
41_S44_P1.0280.49
21_V119_K1.0270.49
48_S98_N1.0220.48
36_D130_D1.0190.48
157_F170_M1.0180.48
28_Q147_A1.0160.48
16_K23_D1.0110.47
23_D99_E1.0080.47
15_Q71_K1.0060.47
5_S10_L1.0030.46
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  
1txlA10.97411000.004Contact Map
2lwxA10.367926.50.958Contact Map
4a60A10.637319.70.96Contact Map
3q6lA10.585515.80.962Contact Map
2dgaA10.554413.70.963Contact Map
3ptmA20.497413.10.963Contact Map
4aznA20.61148.70.966Contact Map
3oiqB10.15548.70.966Contact Map
3wbgA40.59078.20.966Contact Map
4hudA60.12447.40.967Contact 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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