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OPENSEQ.org
Anc-I 435 Trial
Genes: A B A+B
Length: 480 104 574
Sequences: 652 450 152
Seq/Len: 1.36 4.33 0.26
MirrorTree (Pazo et al. 2001) 0.83
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 0.09 0.10 0.23
2 0.09 0.10 0.26
5 0.10 0.11 0.26
10 0.10 0.11 0.26
20 0.10 0.11 0.26
100 0.10 0.11 0.26
∞ 0.12 0.14 0.26
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
427_Q 18_Q 1.76 0.55 0.00
151_H 10_Y 1.70 0.50 0.00
128_L 64_V 1.62 0.46 0.00
318_L 81_R 1.53 0.40 0.00
143_V 81_R 1.49 0.38 0.00
318_L 85_Y 1.44 0.35 0.00
459_T 85_Y 1.37 0.30 0.00
180_A 10_Y 1.30 0.27 0.00
181_K 55_L 1.26 0.25 0.00
286_G 85_Y 1.20 0.22 0.00
127_A 61_P 1.17 0.20 0.00
127_A 63_E 1.16 0.20 0.00
180_A 85_Y 1.15 0.20 0.00
348_R 81_R 1.14 0.20 0.00
286_G 10_Y 1.14 0.19 0.00
227_E 74_A 1.12 0.19 0.00
98_Y 27_L 1.12 0.19 0.00
211_R 87_N 1.12 0.19 0.00
211_R 55_L 1.11 0.18 0.00
71_L 87_N 1.11 0.18 0.00
82_C 64_V 1.10 0.18 0.00
324_L 97_V 1.10 0.18 0.00
116_S 10_Y 1.08 0.17 0.00
180_A 32_V 1.08 0.17 0.00
282_C 26_I 1.08 0.17 0.00
23_Y 55_L 1.06 0.16 0.00
392_F 24_Q 1.06 0.16 0.00
62_G 6_E 1.06 0.16 0.00
222_A 99_H 1.06 0.16 0.00
458_E 10_Y 1.05 0.16 0.00
361_Y 10_Y 1.03 0.15 0.00
288_L 85_Y 1.03 0.15 0.00
198_T 53_L 1.03 0.15 0.00
155_V 91_C 1.02 0.15 0.00
475_V 18_Q 1.02 0.15 0.00
370_P 85_Y 1.01 0.15 0.00
172_I 53_L 1.01 0.15 0.00
140_V 82_I 1.01 0.15 0.00
198_T 81_R 1.01 0.15 0.00
144_K 96_F 1.01 0.15 0.00
222_A 55_L 1.00 0.14 0.00
163_Y 18_Q 1.00 0.14 0.00
172_I 51_W 0.99 0.14 0.00
268_L 85_Y 0.98 0.14 0.00
424_A 86_D 0.98 0.14 0.00
204_I 43_P 0.97 0.14 0.00
221_E 51_W 0.97 0.14 0.00
436_V 18_Q 0.97 0.13 0.00
158_D 90_Q 0.97 0.13 0.00
367_A 24_Q 0.96 0.13 0.00
463_I 73_K 0.96 0.13 0.00
243_P 69_E 0.96 0.13 0.00
286_G 7_T 0.96 0.13 0.00
71_L 55_L 0.96 0.13 0.00
223_V 61_P 0.95 0.13 0.00
86_E 26_I 0.95 0.13 0.00
181_K 51_W 0.95 0.13 0.00
370_P 7_T 0.95 0.13 0.00
371_A 32_V 0.95 0.13 0.00
211_R 46_H 0.94 0.13 0.00
463_I 33_P 0.94 0.13 0.00
218_F 32_V 0.94 0.12 0.00
243_P 49_T 0.93 0.12 0.00
303_K 79_Y 0.93 0.12 0.00
218_F 7_T 0.92 0.12 0.00
355_D 74_A 0.92 0.12 0.00
146_F 79_Y 0.92 0.12 0.00
243_P 55_L 0.92 0.12 0.00
155_V 92_Q 0.91 0.12 0.00
97_A 18_Q 0.91 0.12 0.00
394_D 75_H 0.91 0.12 0.00
95_Y 93_V 0.91 0.12 0.00
276_T 6_E 0.91 0.12 0.00
340_T 3_M 0.91 0.12 0.00
385_M 53_L 0.90 0.12 0.00
221_E 77_D 0.90 0.12 0.00
392_F 70_A 0.90 0.12 0.00
98_Y 93_V 0.90 0.11 0.00
448_R 18_Q 0.90 0.11 0.00
409_W 55_L 0.90 0.11 0.00
284_K 35_I 0.90 0.11 0.00
412_A 10_Y 0.89 0.11 0.00
128_L 61_P 0.89 0.11 0.00
128_L 68_I 0.89 0.11 0.00
218_F 18_Q 0.88 0.11 0.00
62_G 42_D 0.88 0.11 0.00
65_T 9_S 0.88 0.11 0.00
70_D 9_S 0.88 0.11 0.00
211_R 10_Y 0.88 0.11 0.00
302_Q 79_Y 0.88 0.11 0.00
295_M 90_Q 0.87 0.11 0.00
356_P 85_Y 0.87 0.11 0.00
71_L 93_V 0.87 0.11 0.00
198_T 51_W 0.87 0.11 0.00
211_R 53_L 0.86 0.10 0.00
368_S 24_Q 0.86 0.10 0.00
84_R 61_P 0.85 0.10 0.00
151_H 92_Q 0.85 0.10 0.00
221_E 95_S 0.85 0.10 0.00
39_R 79_Y 0.85 0.10 0.00
163_Y 7_T 0.85 0.10 0.00
124_G 53_L 0.84 0.10 0.00
163_Y 85_Y 0.84 0.10 0.00
450_S 84_G 0.84 0.10 0.00
263_I 61_P 0.83 0.10 0.00
116_S 85_Y 0.83 0.10 0.00
49_E 13_P 0.83 0.10 0.00
372_V 7_T 0.83 0.10 0.00
48_P 79_Y 0.83 0.10 0.00
308_S 27_L 0.83 0.10 0.00
427_Q 78_C 0.82 0.10 0.00
287_M 10_Y 0.82 0.10 0.00
146_F 37_Y 0.82 0.10 0.00
131_L 53_L 0.82 0.10 0.00
382_V 87_N 0.82 0.10 0.00
76_E 83_T 0.82 0.10 0.00
459_T 55_L 0.82 0.09 0.00
158_D 92_Q 0.82 0.09 0.00
39_R 80_I 0.82 0.09 0.00
426_V 37_Y 0.81 0.09 0.00
247_E 3_M 0.81 0.09 0.00
41_T 27_L 0.81 0.09 0.00
150_P 63_E 0.81 0.09 0.00
367_A 55_L 0.81 0.09 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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