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OPENSEQ.org
Ig2ACTA
Genes: A B A+B
Length: 96 377 469
Sequences: 23371 13012 231
Seq/Len: 243.45 34.51 0.49
MirrorTree (Pazo et al. 2001) 0.05
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.20 0.04 0.05
2 0.22 0.04 0.08
5 0.23 0.05 0.15
10 0.25 0.06 0.29
20 0.25 0.06 0.49
100 0.27 0.12 1.00
∞ 0.28 0.17 1.29
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
90_L 10_L 1.23 0.35 0.00
93_T 100_P 1.20 0.34 0.00
15_G 155_L 1.12 0.28 0.00
17_S 155_L 1.10 0.27 0.00
77_A 14_N 1.10 0.27 0.00
67_K 33_F 1.08 0.26 0.00
12_V 136_V 1.08 0.26 0.00
77_A 87_I 1.00 0.21 0.00
90_L 191_L 0.98 0.20 0.00
73_Y 344_G 0.97 0.20 0.00
20_L 361_K 0.97 0.20 0.00
20_L 347_I 0.95 0.19 0.00
41_V 293_K 0.95 0.19 0.00
34_W 158_G 0.95 0.19 0.00
38_N 195_L 0.95 0.19 0.00
20_L 208_R 0.94 0.18 0.00
18_V 137_A 0.93 0.18 0.00
62_I 322_L 0.93 0.18 0.00
10_K 313_D 0.93 0.18 0.00
41_V 127_E 0.92 0.17 0.00
20_L 251_T 0.92 0.17 0.00
24_I 291_I 0.91 0.17 0.00
7_P 91_T 0.91 0.17 0.00
68_K 108_T 0.90 0.17 0.00
28_P 167_I 0.87 0.15 0.00
82_G 15_G 0.87 0.15 0.00
38_N 211_V 0.86 0.15 0.00
92_V 191_L 0.86 0.15 0.00
6_K 195_L 0.86 0.15 0.00
10_K 82_D 0.85 0.15 0.00
77_A 141_V 0.85 0.15 0.00
43_F 301_M 0.85 0.15 0.00
89_R 134_M 0.85 0.15 0.00
19_K 56_V 0.85 0.14 0.00
22_C 303_G 0.84 0.14 0.00
68_K 195_L 0.84 0.14 0.00
58_V 284_I 0.83 0.14 0.00
47_R 33_F 0.83 0.14 0.00
58_V 73_I 0.83 0.14 0.00
79_N 291_I 0.83 0.14 0.00
3_F 42_H 0.82 0.14 0.00
34_W 344_G 0.82 0.14 0.00
18_V 59_E 0.82 0.13 0.00
82_G 285_M 0.82 0.13 0.00
88_T 296_Y 0.82 0.13 0.00
36_R 261_E 0.81 0.13 0.00
22_C 319_I 0.81 0.13 0.00
71_G 158_G 0.81 0.13 0.00
96_P 211_V 0.81 0.13 0.00
34_W 303_G 0.80 0.13 0.00
85_T 280_T 0.80 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
2040 0.54 Ig2ACTA Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.00 Done
2039 0.13 Ig2ACTA Δgene:(1, 20) A:(1E-60, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) Killed - Shared
2035 0.37 Ig2ACTA Δgene:(1, 100) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.00 Done - Shared
2031 0.08 Ig2ACTA Δgene:(1, 20) A:(1E-80, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) Killed - Shared
2030 1.3 Ig2ACTA Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2028 1.01 Ig2ACTA Δgene:(1, 100) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.01 Done - Shared
2020 0.43 Ig2ACTA Δgene:(1, 20) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2019 0.49 Ig2ACTA Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
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