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OPENSEQ.org
T142_COMPLEX
Genes: A B A+B
Length: 72 89 143
Sequences: 223 4148 84
Seq/Len: 3.1 46.61 0.59
MirrorTree (Pazo et al. 2001) 0.71
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 0.04 0.02 0.47
2 0.04 0.03 0.48
5 0.04 0.04 0.49
10 0.05 0.05 0.50
20 0.05 0.06 0.52
100 0.06 0.09 0.55
∞ 0.08 0.16 0.78
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
55_L 65_L 1.54 0.64 0.00
8_L 8_R 1.42 0.55 0.00
26_M 66_G 1.37 0.51 0.00
43_W 23_I 1.36 0.50 0.00
43_W 10_K 1.33 0.48 0.00
39_D 13_M 1.31 0.46 0.00
24_I 10_K 1.30 0.46 0.00
8_L 72_L 1.28 0.44 0.00
50_K 40_K 1.19 0.37 0.00
22_F 76_D 1.15 0.34 0.00
50_K 21_V 1.11 0.31 0.00
18_T 46_Y 1.10 0.30 0.00
26_M 16_R 1.08 0.29 0.00
39_D 58_I 1.08 0.29 0.00
4_D 76_D 1.07 0.28 0.00
18_T 5_T 1.06 0.28 0.00
25_A 23_I 1.06 0.28 0.00
38_N 56_N 1.06 0.28 0.00
32_T 42_T 1.05 0.27 0.00
8_L 74_G 1.05 0.27 0.00
55_L 74_G 1.05 0.27 0.00
62_I 56_N 1.05 0.27 0.00
56_E 17_N 1.04 0.26 0.00
36_K 61_L 1.01 0.24 0.00
65_Y 71_W 0.99 0.24 0.00
28_L 23_I 0.99 0.24 0.00
43_W 43_L 0.98 0.23 0.00
52_V 17_N 0.98 0.23 0.00
18_T 64_T 0.97 0.23 0.00
56_E 48_N 0.95 0.21 0.00
39_D 23_I 0.95 0.21 0.00
51_A 43_L 0.95 0.21 0.00
68_N 27_S 0.94 0.21 0.00
37_L 44_S 0.94 0.21 0.00
58_N 4_D 0.94 0.20 0.00
34_S 12_I 0.92 0.20 0.00
18_T 15_E 0.92 0.20 0.00
48_I 55_Q 0.91 0.19 0.00
57_L 75_F 0.90 0.19 0.00
7_S 26_L 0.89 0.18 0.00
1_M 22_D 0.89 0.18 0.00
72_H 45_Q 0.89 0.18 0.00
4_D 46_Y 0.88 0.18 0.00
13_T 63_K 0.88 0.18 0.00
48_I 76_D 0.88 0.18 0.00
36_K 18_L 0.88 0.18 0.00
39_D 9_L 0.88 0.17 0.00
16_C 17_N 0.87 0.17 0.00
47_E 62_A 0.87 0.17 0.00
64_K 25_N 0.86 0.17 0.00
8_L 77_V 0.86 0.17 0.00
66_F 69_E 0.86 0.17 0.00
68_N 68_S 0.86 0.17 0.00
66_F 37_K 0.85 0.17 0.00
51_A 47_V 0.85 0.17 0.00
57_L 8_R 0.85 0.17 0.00
18_T 8_R 0.85 0.16 0.00
8_L 71_W 0.85 0.16 0.00
3_Y 57_R 0.85 0.16 0.00
71_V 56_N 0.85 0.16 0.00
64_K 2_Q 0.84 0.16 0.00
21_N 77_V 0.84 0.16 0.00
26_M 78_P 0.84 0.16 0.00
1_M 19_K 0.84 0.16 0.00
16_C 68_S 0.83 0.15 0.00
7_S 67_V 0.83 0.15 0.00
12_I 67_V 0.82 0.15 0.00
43_W 47_V 0.82 0.15 0.00
27_G 14_A 0.82 0.15 0.00
26_M 39_S 0.81 0.15 0.00
34_S 24_L 0.81 0.15 0.00
69_A 62_A 0.81 0.15 0.00
67_F 8_R 0.81 0.14 0.00
11_K 50_V 0.81 0.14 0.00
51_A 13_M 0.81 0.14 0.00
32_T 46_Y 0.80 0.14 0.00
39_D 56_N 0.80 0.14 0.00
65_Y 67_V 0.79 0.14 0.00
38_N 16_R 0.79 0.14 0.00
67_F 61_L 0.79 0.14 0.00
60_Q 70_A 0.78 0.14 0.00
66_F 65_L 0.78 0.14 0.00
34_S 54_D 0.78 0.13 0.00
45_D 58_I 0.78 0.13 0.00
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)
ID Seq/Len Name Options I_Prob Status
8908 0.14 H0974 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
8905 0.59 T142_COMPLEX Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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