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OPENSEQ.org
Mikhail
Genes: A B A+B
Length: 452 191 597
Sequences: 6410 4749 264
Seq/Len: 14.18 24.86 0.44
MirrorTree (Pazo et al. 2001) 0.40
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 0.06 0.04 0.11
2 0.06 0.04 0.20
5 0.06 0.05 0.30
10 0.06 0.05 0.33
20 0.06 0.05 0.41
100 0.10 0.08 0.74
∞ 0.22 0.15 2.56
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
431_T 94_I 2.33 0.93 0.73
80_V 125_H 1.41 0.46 0.12
133_P 28_G 1.37 0.43 0.10
338_L 32_S 1.37 0.43 0.10
431_T 129_D 1.36 0.42 0.10
272_C 63_E 1.31 0.39 0.08
159_V 121_V 1.25 0.35 0.07
416_S 138_D 1.21 0.31 0.06
214_M 122_L 1.19 0.30 0.05
326_E 32_S 1.17 0.29 0.05
78_L 36_R 1.15 0.28 0.05
70_S 32_S 1.13 0.27 0.04
264_V 48_D 1.13 0.27 0.04
411_S 105_E 1.12 0.26 0.04
263_A 143_A 1.10 0.25 0.04
264_V 143_A 1.10 0.25 0.04
52_D 103_E 1.09 0.24 0.04
40_E 80_E 1.08 0.24 0.04
250_V 32_S 1.08 0.24 0.03
212_I 125_H 1.07 0.23 0.03
364_A 49_L 1.04 0.22 0.03
143_A 76_Q 1.04 0.22 0.03
45_I 69_R 1.04 0.22 0.03
41_G 23_I 1.03 0.21 0.03
265_A 107_A 1.02 0.21 0.03
330_D 30_G 1.02 0.21 0.03
251_V 106_A 1.00 0.20 0.03
207_I 29_A 1.00 0.20 0.02
37_A 43_K 0.99 0.19 0.02
348_I 148_I 0.99 0.19 0.02
201_L 77_A 0.98 0.19 0.02
32_A 29_A 0.98 0.19 0.02
348_I 61_I 0.98 0.19 0.02
374_V 166_Q 0.97 0.19 0.02
216_I 124_V 0.97 0.18 0.02
274_I 96_S 0.96 0.18 0.02
201_L 52_E 0.96 0.18 0.02
21_T 94_I 0.96 0.18 0.02
78_L 129_D 0.94 0.17 0.02
69_F 110_L 0.94 0.17 0.02
38_L 103_E 0.93 0.17 0.02
299_A 63_E 0.93 0.17 0.02
347_Q 166_Q 0.93 0.17 0.02
388_K 166_Q 0.93 0.17 0.02
337_V 102_V 0.92 0.17 0.02
281_S 100_G 0.92 0.16 0.02
47_G 35_G 0.91 0.16 0.02
250_V 62_P 0.91 0.16 0.02
411_S 162_C 0.91 0.16 0.02
385_V 34_A 0.91 0.16 0.02
188_M 62_P 0.91 0.16 0.02
272_C 168_H 0.90 0.16 0.02
238_I 127_D 0.90 0.16 0.02
212_I 29_A 0.90 0.15 0.02
199_L 129_D 0.90 0.15 0.02
368_Q 21_I 0.89 0.15 0.01
261_P 112_I 0.89 0.15 0.01
20_V 32_S 0.89 0.15 0.01
375_Q 66_R 0.89 0.15 0.01
320_I 95_F 0.89 0.15 0.01
127_A 58_G 0.88 0.15 0.01
218_M 59_M 0.87 0.15 0.01
415_L 18_D 0.87 0.14 0.01
350_G 167_Y 0.86 0.14 0.01
294_R 32_S 0.86 0.14 0.01
338_L 77_A 0.85 0.14 0.01
286_A 148_I 0.85 0.14 0.01
398_E 96_S 0.85 0.14 0.01
37_A 104_T 0.85 0.14 0.01
364_A 35_G 0.84 0.14 0.01
351_I 18_D 0.84 0.14 0.01
431_T 39_S 0.84 0.13 0.01
375_Q 34_A 0.84 0.13 0.01
20_V 22_F 0.84 0.13 0.01
88_Q 167_Y 0.84 0.13 0.01
409_A 97_C 0.84 0.13 0.01
348_I 62_P 0.83 0.13 0.01
294_R 106_A 0.83 0.13 0.01
200_R 64_I 0.83 0.13 0.01
173_E 32_S 0.83 0.13 0.01
274_I 63_E 0.83 0.13 0.01
143_A 32_S 0.83 0.13 0.01
255_A 131_V 0.83 0.13 0.01
16_L 47_V 0.83 0.13 0.01
44_R 21_I 0.83 0.13 0.01
425_I 97_C 0.83 0.13 0.01
93_P 87_K 0.83 0.13 0.01
272_C 103_E 0.82 0.13 0.01
25_S 142_P 0.82 0.13 0.01
442_L 19_R 0.82 0.13 0.01
159_V 29_A 0.82 0.13 0.01
170_G 137_R 0.81 0.12 0.01
286_A 169_S 0.81 0.12 0.01
414_V 171_H 0.81 0.12 0.01
237_L 34_A 0.81 0.12 0.01
369_L 39_S 0.81 0.12 0.01
294_R 52_E 0.81 0.12 0.01
371_K 54_E 0.81 0.12 0.01
334_T 83_Q 0.80 0.12 0.01
39_G 102_V 0.80 0.12 0.01
372_F 156_K 0.80 0.12 0.01
168_A 112_I 0.80 0.12 0.01
374_V 39_S 0.80 0.12 0.01
174_L 32_S 0.80 0.12 0.01
336_A 96_S 0.79 0.12 0.01
450_L 129_D 0.79 0.12 0.01
286_A 163_S 0.79 0.12 0.01
78_L 170_P 0.79 0.12 0.01
20_V 52_E 0.79 0.12 0.01
302_Q 96_S 0.79 0.12 0.01
102_A 148_I 0.79 0.12 0.01
265_A 151_V 0.79 0.12 0.01
427_E 101_I 0.78 0.12 0.01
97_G 48_D 0.78 0.12 0.01
400_I 150_E 0.78 0.11 0.01
93_P 29_A 0.78 0.11 0.01
362_I 82_L 0.78 0.11 0.01
162_D 29_A 0.78 0.11 0.01
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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