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RatApobecStart

ID: 1517593014 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 165 (149)
Sequences: 267 (150.1)
Seq/Len: 1.792
Nf(neff/√len): 12.3

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: 1.792).

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
3_F7_F2.6181.00
3_F9_P2.3831.00
144_E147_W2.3171.00
90_V97_A1.8530.97
69_S84_L1.7940.97
3_F37_N1.7310.96
66_W69_S1.5340.91
97_A129_S1.5310.91
19_L22_I1.4630.88
83_F132_C1.4430.87
7_F37_N1.4310.86
47_I69_S1.3820.83
64_I77_S1.3740.83
145_A148_P1.3630.82
47_I67_F1.3310.80
47_I119_V1.3290.80
40_K48_E1.3240.80
73_C98_R1.3090.79
19_L144_E1.3010.78
66_W92_L1.2980.78
73_C76_C1.2930.77
17_C93_F1.2730.76
3_F6_F1.2730.76
16_T20_Y1.2560.75
5_V12_L1.2390.73
111_L124_M1.2320.72
131_Y135_N1.2290.72
144_E149_R1.2290.72
111_L114_L1.2260.72
13_R98_R1.2250.72
21_E128_E1.2210.72
70_W100_Y1.2170.71
143_N148_P1.2170.71
6_F12_L1.2150.71
89_H96_I1.2150.71
131_Y141_P1.2040.70
87_Y125_T1.2010.70
143_N146_H1.2010.70
73_C114_L1.1980.69
46_F99_L1.1970.69
63_S93_F1.1950.69
33_H62_C1.1740.67
114_L124_M1.1650.66
85_S93_F1.1600.66
142_S145_A1.1490.65
144_E148_P1.1230.62
38_T66_W1.1220.62
78_R130_G1.1170.62
63_S121_I1.1110.61
107_N138_N1.1090.61
144_E150_Y1.1080.61
22_I84_L1.1060.60
129_S146_H1.1010.60
47_I65_T1.1010.60
18_L137_V1.1000.60
73_C124_M1.0980.60
18_L22_I1.0970.59
68_L96_I1.0930.59
5_V8_D1.0890.59
20_Y57_C1.0890.59
19_L35_S1.0810.58
94_I132_C1.0800.58
46_F133_W1.0780.57
41_H76_C1.0740.57
22_I64_I1.0730.57
16_T91_T1.0720.57
33_H126_E1.0690.57
4_E8_D1.0660.56
55_Y97_A1.0650.56
17_C51_T1.0580.55
66_W94_I1.0510.55
48_E66_W1.0450.54
16_T19_L1.0430.54
142_S146_H1.0400.53
142_S148_P1.0340.53
52_T68_L1.0330.53
64_I71_S1.0330.53
66_W80_I1.0320.53
23_N88_P1.0250.52
70_W83_F1.0210.51
66_W105_P1.0200.51
12_L15_E1.0170.51
80_I97_A1.0050.50
23_N28_H1.0020.49
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  
4j4jA20.98791000.157Contact Map
3v4kA20.98181000.163Contact Map
3vowA20.98791000.174Contact Map
4xxoA201000.18Contact Map
2mzzA101000.186Contact Map
2nytA40.98181000.572Contact Map
4p9cA120.624297.90.874Contact Map
2hvwA30.703970.893Contact Map
1vq2A10.763696.50.899Contact Map
3g8qA40.763695.20.909Contact 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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