OPENSEQ.org
Apobec

ID: 1517592878 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 166 (157)
Sequences: 526 (285)
Seq/Len: 3.350
Nf(neff/√len): 22.7

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: 3.350).

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
73_C87_C2.4071.00
12_P15_K2.0851.00
69_T95_K1.9521.00
19_S158_E1.9401.00
20_C158_E1.8420.99
43_E87_C1.8350.99
40_K48_M1.6670.98
135_M147_E1.6400.98
158_E162_Q1.6190.98
122_V125_L1.6020.98
9_F12_P1.5990.98
12_P20_C1.5880.98
19_S38_S1.5720.98
15_K20_C1.5690.98
43_E73_C1.5370.97
39_K67_Y1.4930.96
11_H158_E1.4750.96
63_Q104_V1.4650.96
9_F13_R1.3940.94
101_V108_T1.3750.94
144_A148_E1.3700.93
9_F16_S1.3420.92
10_Y13_R1.3250.92
4_E9_F1.3110.91
133_E153_T1.3050.91
13_R20_C1.3010.91
70_M111_C1.2990.91
144_A147_E1.2910.90
122_V135_M1.2840.90
9_F14_S1.2560.89
67_Y71_Q1.2540.89
6_C132_L1.2500.88
20_C28_D1.2430.88
4_E12_P1.2380.88
160_H164_L1.2310.87
89_E141_K1.2250.87
12_P35_Y1.1690.83
10_Y15_K1.1680.83
4_E152_D1.1630.83
12_P16_S1.1510.82
16_S19_S1.1430.82
42_A65_T1.1270.80
161_N164_L1.1220.80
8_A14_S1.1190.80
109_H122_V1.1180.80
56_H94_A1.1160.79
12_P158_E1.1140.79
12_P38_S1.1140.79
96_E104_V1.1110.79
31_L38_S1.1060.79
26_G124_K1.1020.78
13_R16_S1.0990.78
4_E10_Y1.0990.78
4_E13_R1.0970.78
122_V147_E1.0960.78
96_E128_T1.0840.77
35_Y165_E1.0700.75
48_M96_E1.0700.75
143_Y147_E1.0670.75
123_R134_C1.0660.75
108_T140_W1.0610.74
3_K10_Y1.0590.74
90_V132_L1.0550.74
4_E15_K1.0490.73
135_M144_A1.0420.72
66_M69_T1.0420.72
76_T86_S1.0350.72
158_E165_E1.0300.71
94_A105_I1.0260.71
46_F70_M1.0260.71
102_E133_E1.0250.71
66_M71_Q1.0200.70
135_M148_E1.0200.70
89_E120_K1.0160.70
20_C67_Y1.0160.70
100_N107_P1.0130.69
56_H154_S1.0130.69
64_I88_C1.0080.69
12_P152_D1.0020.68
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  
4j4jA20.92771000.179Contact Map
3v4kA20.92171000.185Contact Map
4xxoA201000.19Contact Map
2mzzA101000.191Contact Map
3vowA20.92771000.192Contact Map
2nytA40.921799.80.578Contact Map
1zy7A20.915799.20.73Contact Map
4p9cA120.632596.80.856Contact Map
2hvwA30.692893.40.884Contact Map
3g8qA40.74191.90.89Contact 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.

Page generated in 0.0218 seconds.