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OPENSEQ.org
Ig2ACTA
Genes: A B A+B
Length: 96 377 469
Sequences: 14203 4910 172
Seq/Len: 147.95 13.02 0.37
MirrorTree (Pazo et al. 2001) 0.07
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 0.17 0.01 0.01
2 0.20 0.01 0.02
5 0.24 0.01 0.04
10 0.26 0.01 0.08
20 0.27 0.02 0.16
100 0.31 0.05 0.36
∞ 0.32 0.18 0.54
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
77_A 82_D 1.66 0.58 0.00
90_L 69_L 1.44 0.43 0.00
90_L 295_L 1.28 0.33 0.00
62_I 299_N 1.12 0.24 0.00
90_L 349_A 1.10 0.22 0.00
50_L 296_Y 1.09 0.22 0.00
20_L 136_V 1.09 0.22 0.00
96_P 250_I 1.02 0.19 0.00
68_K 296_Y 1.00 0.18 0.00
18_V 162_T 1.00 0.18 0.00
92_V 184_G 1.00 0.18 0.00
62_I 300_V 0.98 0.17 0.00
16_D 99_A 0.97 0.17 0.00
23_Q 284_I 0.96 0.16 0.00
15_G 344_G 0.95 0.16 0.00
75_V 342_W 0.94 0.15 0.00
75_V 260_P 0.93 0.15 0.00
52_Q 73_I 0.92 0.15 0.00
3_F 102_E 0.91 0.14 0.00
75_V 264_F 0.91 0.14 0.00
82_G 72_P 0.90 0.14 0.00
22_C 22_G 0.90 0.14 0.00
26_A 184_G 0.90 0.14 0.00
15_G 303_G 0.89 0.14 0.00
34_W 158_G 0.89 0.14 0.00
72_W 82_D 0.89 0.14 0.00
71_G 299_N 0.89 0.14 0.00
22_C 166_P 0.89 0.14 0.00
75_V 166_P 0.88 0.13 0.00
75_V 22_G 0.88 0.13 0.00
1_P 169_E 0.88 0.13 0.00
38_N 25_G 0.88 0.13 0.00
71_G 12_C 0.88 0.13 0.00
46_D 236_S 0.87 0.13 0.00
60_L 314_R 0.87 0.13 0.00
24_I 234_S 0.87 0.13 0.00
10_K 37_V 0.84 0.12 0.00
30_P 164_N 0.84 0.12 0.00
30_P 173_L 0.83 0.12 0.00
34_W 315_M 0.83 0.12 0.00
22_C 314_R 0.82 0.12 0.00
76_S 105_T 0.82 0.11 0.00
75_V 314_R 0.82 0.11 0.00
26_A 154_V 0.81 0.11 0.00
73_Y 158_G 0.81 0.11 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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