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OPENSEQ.org
Ig2ACTA
Genes: A B A+B
Length: 96 377 470
Sequences: 23371 13012 474
Seq/Len: 243.45 34.51 1.01
MirrorTree (Pazo et al. 2001) 0.02
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
20_L 317_K 1.41 0.70 0.01
90_L 331_I 1.25 0.57 0.00
60_L 361_K 1.13 0.45 0.00
34_W 158_G 1.09 0.42 0.00
90_L 58_D 1.04 0.38 0.00
20_L 313_D 1.04 0.38 0.00
28_P 169_E 0.98 0.33 0.00
30_P 280_T 0.96 0.31 0.00
90_L 317_K 0.95 0.30 0.00
16_D 108_T 0.94 0.29 0.00
32_L 254_N 0.92 0.28 0.00
69_D 169_E 0.91 0.27 0.00
77_A 82_D 0.89 0.26 0.00
21_E 56_V 0.89 0.25 0.00
35_K 87_I 0.87 0.24 0.00
20_L 251_T 0.86 0.23 0.00
69_D 252_I 0.85 0.23 0.00
3_F 72_P 0.85 0.23 0.00
18_V 220_Y 0.84 0.23 0.00
65_V 66_I 0.84 0.23 0.00
24_I 317_K 0.84 0.22 0.00
15_G 56_V 0.84 0.22 0.00
32_L 185_R 0.82 0.21 0.00
90_L 311_I 0.82 0.21 0.00
3_F 216_E 0.82 0.21 0.00
96_P 329_I 0.81 0.20 0.00
34_W 303_G 0.81 0.20 0.00
33_F 299_N 0.80 0.20 0.00
22_C 185_R 0.78 0.19 0.00
74_T 299_N 0.78 0.19 0.00
91_D 205_T 0.78 0.19 0.00
71_G 252_I 0.78 0.18 0.00
78_V 121_M 0.77 0.18 0.00
43_F 301_M 0.77 0.18 0.00
47_R 257_F 0.77 0.18 0.00
30_P 137_A 0.77 0.18 0.00
22_C 319_I 0.76 0.18 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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