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OPENSEQ.org
hass
Genes: A B A+B
Length: 317 112 414
Sequences: 5021 932 810
Seq/Len: 15.84 8.32 1.96
MirrorTree (Pazo et al. 2001) 0.62
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 0.06 0.04 1.66
2 0.06 0.05 1.77
5 0.09 0.06 1.81
10 0.12 0.08 1.86
20 0.14 0.09 1.89
100 0.20 0.14 1.94
∞ 0.23 0.18 2.04
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
284_S 40_F 3.09 1.00 1.00
246_R 32_E 2.56 1.00 0.99
253_R 46_D 1.64 0.95 0.90
288_A 37_Q 1.55 0.93 0.86
183_A 21_Q 1.44 0.88 0.80
251_I 39_F 1.33 0.82 0.71
248_W 32_E 1.28 0.79 0.67
252_D 24_Q 1.22 0.74 0.60
287_F 39_F 1.20 0.72 0.58
248_W 35_G 1.17 0.69 0.55
137_S 8_A 1.10 0.62 0.47
285_G 39_F 1.07 0.60 0.44
137_S 59_V 1.06 0.59 0.43
250_V 32_E 1.05 0.57 0.41
248_W 31_A 1.03 0.55 0.39
249_L 70_N 1.00 0.52 0.36
286_V 31_A 1.00 0.52 0.36
36_L 75_R 0.98 0.50 0.34
252_D 25_S 0.98 0.50 0.34
260_L 11_A 0.97 0.49 0.33
267_R 84_L 0.97 0.48 0.33
221_Q 27_M 0.97 0.48 0.32
285_G 34_A 0.96 0.48 0.32
179_G 83_V 0.95 0.47 0.31
264_N 39_F 0.95 0.46 0.30
302_E 39_F 0.90 0.40 0.25
150_V 14_K 0.89 0.40 0.24
86_A 38_V 0.89 0.39 0.24
243_A 41_D 0.88 0.39 0.24
52_L 64_R 0.88 0.39 0.24
247_G 40_F 0.87 0.37 0.22
90_A 11_A 0.87 0.37 0.22
200_S 70_N 0.86 0.37 0.22
286_V 28_L 0.85 0.35 0.20
141_L 50_A 0.84 0.34 0.19
22_G 104_V 0.83 0.34 0.19
48_Q 21_Q 0.83 0.34 0.19
159_F 37_Q 0.82 0.32 0.18
116_V 19_A 0.82 0.32 0.18
13_A 24_Q 0.81 0.31 0.17
273_A 38_V 0.81 0.31 0.17
91_V 46_D 0.80 0.31 0.17
73_A 19_A 0.79 0.29 0.15
195_Q 44_K 0.79 0.29 0.15
260_L 19_A 0.78 0.29 0.15
46_L 31_A 0.78 0.29 0.15
305_A 39_F 0.78 0.28 0.15
281_R 41_D 0.77 0.28 0.15
231_Q 49_Q 0.77 0.28 0.14
289_L 30_F 0.77 0.28 0.14
267_R 72_V 0.77 0.27 0.14
53_W 21_Q 0.76 0.27 0.14
300_R 39_F 0.76 0.27 0.14
13_A 31_A 0.76 0.27 0.14
269_T 30_F 0.76 0.27 0.13
20_A 31_A 0.75 0.26 0.13
89_A 30_F 0.75 0.26 0.13
136_G 45_L 0.75 0.26 0.13
46_L 39_F 0.75 0.26 0.13
167_A 106_G 0.75 0.26 0.13
69_P 91_N 0.74 0.26 0.13
252_D 28_L 0.74 0.25 0.12
123_V 26_A 0.74 0.25 0.12
160_I 48_M 0.74 0.25 0.12
57_G 24_Q 0.74 0.25 0.12
252_D 106_G 0.74 0.25 0.12
201_V 83_V 0.73 0.25 0.12
247_G 84_L 0.73 0.24 0.12
302_E 62_G 0.73 0.24 0.12
292_L 38_V 0.73 0.24 0.12
137_S 9_Q 0.73 0.24 0.12
236_R 96_A 0.73 0.24 0.12
299_I 70_N 0.72 0.24 0.11
141_L 70_N 0.72 0.23 0.11
281_R 42_E 0.72 0.23 0.11
284_S 24_Q 0.71 0.23 0.11
93_L 90_A 0.71 0.23 0.11
215_R 53_L 0.71 0.23 0.11
281_R 38_V 0.71 0.23 0.10
217_L 70_N 0.70 0.22 0.10
280_T 62_G 0.70 0.22 0.10
30_R 98_A 0.70 0.22 0.10
90_A 87_L 0.70 0.22 0.10
115_T 11_A 0.70 0.22 0.10
243_A 45_L 0.70 0.22 0.10
201_V 34_A 0.70 0.22 0.10
251_I 14_K 0.70 0.22 0.10
229_N 6_S 0.69 0.22 0.10
242_D 86_R 0.69 0.21 0.10
150_V 72_V 0.69 0.21 0.10
204_H 27_M 0.69 0.21 0.10
298_A 37_Q 0.69 0.21 0.10
9_R 39_F 0.69 0.21 0.10
79_R 49_Q 0.69 0.21 0.09
293_D 44_K 0.69 0.21 0.09
260_L 28_L 0.68 0.21 0.09
299_I 39_F 0.68 0.21 0.09
309_N 83_V 0.68 0.20 0.09
91_V 68_G 0.68 0.20 0.09
249_L 32_E 0.68 0.20 0.09
287_F 50_A 0.68 0.20 0.09
223_Q 8_A 0.68 0.20 0.09
306_R 105_L 0.67 0.20 0.09
191_A 22_P 0.67 0.20 0.09
237_Q 34_A 0.67 0.20 0.09
202_H 57_M 0.67 0.20 0.08
38_A 68_G 0.66 0.19 0.08
224_A 74_F 0.66 0.19 0.08
228_R 60_E 0.66 0.19 0.08
46_L 59_V 0.66 0.19 0.08
221_Q 99_L 0.66 0.19 0.08
51_L 86_R 0.66 0.19 0.08
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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