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VV TRAP COMPLEX

Genes: A B A+B
Length: 429 172 569
Sequences: 6035 5605 4512
Seq/Len: 14.07 32.59 7.93
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 7.42
2 0.01 0.00 7.50
5 0.03 0.02 7.51
10 0.05 0.04 7.52
20 0.08 0.06 7.51
100 0.15 0.12 7.54
0.22 0.20 7.57
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!

GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution.
Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
246_L 30_T 4.31 1.00 1.00
25_I 100_S 3.62 1.00 1.00
234_K 37_W 2.08 1.00 0.99
52_D 51_R 2.05 1.00 0.99
273_N 68_R 1.96 1.00 0.99
268_L 23_A 1.93 1.00 0.99
26_F 96_A 1.62 1.00 0.96
243_V 33_I 1.52 1.00 0.94
245_S 26_L 1.51 0.99 0.94
18_M 93_L 1.43 0.99 0.91
271_T 22_M 1.43 0.99 0.91
268_L 19_V 1.40 0.99 0.90
273_N 70_T 1.35 0.99 0.88
276_A 61_G 1.34 0.99 0.88
280_L 62_C 1.33 0.98 0.87
272_V 61_G 1.25 0.98 0.83
277_V 65_A 1.23 0.97 0.82
272_V 18_T 1.21 0.97 0.80
17_G 73_N 1.19 0.96 0.79
48_L 52_V 1.15 0.95 0.76
269_R 15_E 1.13 0.95 0.74
57_L 50_A 1.11 0.94 0.72
52_D 55_M 1.10 0.94 0.72
239_E 36_R 1.10 0.94 0.71
54_F 29_L 1.08 0.93 0.69
26_F 100_S 1.07 0.93 0.69
276_A 65_A 1.07 0.93 0.68
269_R 19_V 1.07 0.93 0.68
242_V 30_T 1.03 0.91 0.64
51_I 55_M 1.03 0.90 0.64
265_V 19_V 1.02 0.90 0.63
275_T 58_S 1.02 0.90 0.62
47_M 59_L 1.01 0.90 0.62
47_M 104_I 1.01 0.89 0.61
51_I 59_L 0.98 0.88 0.59
22_F 97_V 0.96 0.86 0.55
246_L 26_L 0.95 0.85 0.55
279_A 54_F 0.95 0.85 0.54
15_F 77_F 0.94 0.85 0.54
16_A 92_S 0.91 0.82 0.50
246_L 34_A 0.88 0.79 0.46
272_V 22_M 0.86 0.77 0.44
16_A 81_L 0.86 0.77 0.43
57_L 25_L 0.84 0.73 0.40
17_G 78_S 0.84 0.73 0.40
273_N 65_A 0.81 0.70 0.37
281_M 72_V 0.80 0.69 0.36
264_F 23_A 0.80 0.68 0.35
242_V 29_L 0.79 0.67 0.34
249_L 27_V 0.78 0.66 0.33
382_S 72_V 0.76 0.62 0.30
64_L 26_L 0.75 0.62 0.29
51_I 58_S 0.73 0.59 0.27
279_A 58_S 0.73 0.58 0.27
390_H 75_T 0.70 0.54 0.24
48_L 130_M 0.70 0.54 0.24
243_V 30_T 0.70 0.54 0.24
52_D 52_V 0.69 0.52 0.23
22_F 101_I 0.68 0.51 0.22
277_V 72_V 0.68 0.51 0.22
16_A 89_L 0.67 0.49 0.21
234_K 39_L 0.67 0.49 0.21
64_L 23_A 0.67 0.49 0.21
14_L 74_I 0.66 0.48 0.20
265_V 23_A 0.66 0.47 0.20
277_V 71_H 0.66 0.47 0.20
29_L 103_A 0.65 0.46 0.19
283_M 59_L 0.63 0.42 0.17
18_M 96_A 0.62 0.41 0.16
26_F 99_V 0.62 0.41 0.16
21_G 62_C 0.62 0.41 0.16
61_F 26_L 0.61 0.40 0.15
20_V 72_V 0.59 0.36 0.14
57_L 29_L 0.59 0.36 0.14
18_M 97_V 0.59 0.36 0.14
280_L 137_G 0.59 0.36 0.14
22_F 141_M 0.58 0.35 0.13
44_A 107_L 0.57 0.34 0.13
61_F 25_L 0.57 0.34 0.13
331_E 128_K 0.57 0.33 0.12
149_L 76_F 0.57 0.33 0.12
269_R 64_I 0.56 0.33 0.12
18_M 92_S 0.56 0.32 0.12
74_I 115_T 0.56 0.32 0.12
367_I 122_T 0.55 0.30 0.11
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)

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