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OPENSEQ.org
Ig2ACTA
Genes: A B A+B
Length: 96 377 469
Sequences: 21457 13012 204
Seq/Len: 223.51 34.51 0.43
MirrorTree (Pazo et al. 2001) 0.07
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 0.19 0.04 0.04
2 0.21 0.04 0.07
5 0.23 0.05 0.14
10 0.24 0.06 0.26
20 0.25 0.06 0.43
100 0.27 0.12 0.87
∞ 0.28 0.17 1.10
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
92_V 37_V 1.15 0.28 0.00
73_Y 344_G 1.15 0.28 0.00
90_L 311_I 1.13 0.26 0.00
92_V 92_F 1.12 0.26 0.00
32_L 102_E 1.05 0.22 0.00
73_Y 155_L 1.00 0.19 0.00
68_K 164_N 0.99 0.19 0.00
18_V 284_I 0.99 0.19 0.00
90_L 191_L 0.99 0.19 0.00
15_G 96_L 0.98 0.19 0.00
7_P 91_T 0.98 0.19 0.00
34_W 158_G 0.98 0.18 0.00
18_V 137_A 0.97 0.18 0.00
77_A 14_N 0.96 0.18 0.00
77_A 156_D 0.96 0.18 0.00
50_L 207_E 0.96 0.18 0.00
38_N 76_G 0.95 0.18 0.00
24_I 291_I 0.95 0.17 0.00
20_L 251_T 0.94 0.17 0.00
18_V 129_F 0.94 0.17 0.00
92_V 250_I 0.94 0.17 0.00
1_P 274_A 0.93 0.17 0.00
65_V 183_A 0.93 0.17 0.00
37_N 194_I 0.93 0.16 0.00
67_K 33_F 0.91 0.16 0.00
77_A 204_T 0.91 0.16 0.00
8_Q 195_L 0.90 0.15 0.00
17_S 155_L 0.90 0.15 0.00
35_K 87_I 0.90 0.15 0.00
18_V 283_S 0.88 0.15 0.00
7_P 107_L 0.88 0.14 0.00
67_K 195_L 0.88 0.14 0.00
60_L 303_G 0.87 0.14 0.00
91_D 108_T 0.87 0.14 0.00
30_P 274_A 0.87 0.14 0.00
88_T 296_Y 0.87 0.14 0.00
20_L 347_I 0.87 0.14 0.00
18_V 59_E 0.87 0.14 0.00
22_C 303_G 0.86 0.14 0.00
66_N 10_L 0.86 0.14 0.00
60_L 158_G 0.86 0.14 0.00
72_W 288_D 0.86 0.14 0.00
34_W 344_G 0.85 0.14 0.00
65_V 129_F 0.84 0.13 0.00
3_F 42_H 0.84 0.13 0.00
41_V 116_A 0.84 0.13 0.00
62_I 299_N 0.84 0.13 0.00
44_N 107_L 0.84 0.13 0.00
60_L 56_V 0.83 0.13 0.00
60_L 153_I 0.83 0.13 0.00
41_V 127_E 0.83 0.13 0.00
15_G 13_D 0.82 0.13 0.00
82_G 230_A 0.82 0.13 0.00
92_V 57_G 0.81 0.12 0.00
62_I 322_L 0.81 0.12 0.00
34_W 15_G 0.81 0.12 0.00
34_W 303_G 0.81 0.12 0.00
12_V 9_A 0.81 0.12 0.00
1_P 300_V 0.81 0.12 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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