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OPENSEQ.org
IscSfdx
Genes: A B A+B
Length: 404 111 511
Sequences: 31466 1721 349
Seq/Len: 77.89 15.5 0.68
MirrorTree (Pazo et al. 2001) 0.72
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 0.07 0.00 0.15
2 0.09 0.01 0.16
5 0.11 0.01 0.68
10 0.12 0.01 0.77
20 0.15 0.01 0.88
100 0.25 0.01 1.45
∞ 0.29 0.03 2.23
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
71_F 28_L 1.80 0.84 0.09
366_I 97_V 1.44 0.61 0.04
27_M 86_S 1.39 0.57 0.03
274_R 97_V 1.27 0.47 0.02
204_G 70_D 1.21 0.42 0.02
230_M 55_V 1.17 0.39 0.01
356_S 44_K 1.17 0.39 0.01
21_E 60_D 1.16 0.38 0.01
383_L 86_S 1.13 0.35 0.01
204_G 25_E 1.12 0.35 0.01
357_L 107_H 1.09 0.33 0.01
217_Y 59_F 1.07 0.31 0.01
52_D 28_L 1.04 0.29 0.01
98_I 60_D 1.00 0.26 0.01
332_S 65_S 0.99 0.26 0.01
377_I 30_A 0.99 0.26 0.01
391_K 100_I 0.98 0.25 0.01
370_I 26_T 0.98 0.25 0.01
362_T 15_D 0.96 0.24 0.01
135_K 55_V 0.96 0.24 0.01
141_M 55_V 0.96 0.24 0.01
377_I 5_V 0.93 0.22 0.01
224_V 30_A 0.92 0.21 0.01
176_I 38_I 0.92 0.21 0.01
79_D 100_I 0.91 0.21 0.01
399_I 54_I 0.91 0.21 0.01
317_L 65_S 0.91 0.21 0.01
184_S 31_A 0.91 0.21 0.01
71_F 19_L 0.90 0.20 0.01
97_I 64_E 0.90 0.20 0.01
299_N 109_R 0.90 0.20 0.01
180_D 73_L 0.90 0.20 0.01
206_K 73_L 0.90 0.20 0.01
69_I 62_L 0.89 0.20 0.01
145_T 79_L 0.89 0.20 0.01
383_L 28_L 0.89 0.20 0.01
97_I 105_I 0.89 0.20 0.01
100_S 22_N 0.89 0.20 0.01
113_Q 31_A 0.88 0.19 0.01
71_F 105_I 0.88 0.19 0.01
166_I 49_T 0.87 0.19 0.01
376_S 82_E 0.87 0.19 0.01
150_I 31_A 0.87 0.19 0.01
173_R 11_D 0.87 0.19 0.01
299_N 107_H 0.87 0.19 0.01
342_L 46_C 0.86 0.18 0.01
218_V 94_E 0.86 0.18 0.01
259_A 21_A 0.86 0.18 0.01
152_H 31_A 0.85 0.18 0.01
79_D 86_S 0.85 0.18 0.01
193_S 44_K 0.85 0.18 0.01
184_S 6_I 0.85 0.18 0.01
197_V 57_E 0.85 0.18 0.01
279_N 89_A 0.85 0.18 0.01
402_A 107_H 0.85 0.18 0.01
69_I 58_G 0.85 0.18 0.01
226_I 21_A 0.85 0.18 0.01
135_K 93_D 0.85 0.18 0.01
125_A 26_T 0.84 0.18 0.01
57_Q 55_V 0.84 0.18 0.01
58_I 28_L 0.84 0.17 0.01
297_A 27_I 0.84 0.17 0.01
124_L 26_T 0.84 0.17 0.01
391_K 29_D 0.84 0.17 0.01
53_I 28_L 0.84 0.17 0.01
79_D 37_E 0.84 0.17 0.01
66_P 38_I 0.84 0.17 0.01
314_I 60_D 0.83 0.17 0.01
182_T 96_L 0.83 0.17 0.01
26_F 26_T 0.83 0.17 0.01
400_E 82_E 0.83 0.17 0.00
133_D 109_R 0.83 0.17 0.00
43_F 31_A 0.83 0.17 0.00
397_N 44_K 0.83 0.17 0.00
299_N 108_A 0.83 0.17 0.00
83_I 55_V 0.82 0.17 0.00
216_L 43_E 0.82 0.16 0.00
70_V 43_E 0.82 0.16 0.00
52_D 53_C 0.82 0.16 0.00
399_I 35_G 0.82 0.16 0.00
126_P 109_R 0.81 0.16 0.00
204_G 45_S 0.81 0.16 0.00
116_R 97_V 0.81 0.16 0.00
283_D 92_T 0.81 0.16 0.00
346_D 110_E 0.81 0.16 0.00
92_K 43_E 0.81 0.16 0.00
235_H 40_H 0.80 0.16 0.00
28_T 107_H 0.80 0.16 0.00
112_R 78_G 0.80 0.15 0.00
360_F 35_G 0.80 0.15 0.00
136_E 55_V 0.80 0.15 0.00
382_D 63_P 0.79 0.15 0.00
392_Q 105_I 0.79 0.15 0.00
368_Y 89_A 0.79 0.15 0.00
162_D 102_R 0.79 0.15 0.00
233_G 71_D 0.79 0.15 0.00
7_L 109_R 0.79 0.15 0.00
365_E 91_V 0.79 0.15 0.00
202_F 60_D 0.79 0.15 0.00
58_I 78_G 0.78 0.15 0.00
235_H 9_H 0.78 0.15 0.00
150_I 109_R 0.78 0.15 0.00
83_I 95_D 0.78 0.14 0.00
356_S 36_I 0.77 0.14 0.00
364_E 98_V 0.77 0.14 0.00
383_L 22_N 0.77 0.14 0.00
7_L 26_T 0.77 0.14 0.00
42_R 28_L 0.77 0.14 0.00
314_I 105_I 0.77 0.14 0.00
322_V 41_A 0.77 0.14 0.00
319_D 90_R 0.77 0.14 0.00
308_V 104_T 0.77 0.14 0.00
365_E 37_E 0.77 0.14 0.00
366_I 64_E 0.77 0.14 0.00
226_I 108_A 0.77 0.14 0.00
165_A 94_E 0.77 0.14 0.00
230_M 29_D 0.77 0.14 0.00
317_L 31_A 0.77 0.14 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)
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