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OPENSEQ.org
2801
Genes: A B A+B
Length: 113 100 195
Sequences: 11125 1973 198
Seq/Len: 98.45 19.73 1.02
MirrorTree (Pazo et al. 2001) 0.77
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 0.04 0.01 0.93
2 0.05 0.01 0.94
5 0.07 0.02 1.00
10 0.08 0.02 1.09
20 0.09 0.03 1.18
100 0.14 0.04 1.73
∞ 0.18 0.09 3.27
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
9_T 41_D 2.20 0.98 0.92
66_T 51_D 1.85 0.93 0.78
72_N 45_A 1.66 0.86 0.64
76_A 45_A 1.61 0.84 0.61
18_E 39_K 1.48 0.76 0.48
69_F 39_K 1.44 0.73 0.44
69_F 55_P 1.27 0.59 0.29
74_Q 75_V 1.23 0.55 0.25
21_E 26_R 1.20 0.52 0.23
62_V 15_L 1.19 0.51 0.22
9_T 37_S 1.14 0.47 0.19
18_E 42_I 1.12 0.45 0.17
19_Y 58_N 1.09 0.42 0.16
20_L 81_L 1.09 0.42 0.16
42_S 36_L 1.05 0.39 0.14
61_K 79_Y 1.04 0.38 0.13
9_T 20_V 1.03 0.37 0.13
14_I 10_F 1.03 0.37 0.12
31_A 63_L 1.02 0.37 0.12
36_V 19_F 1.02 0.36 0.12
56_A 23_T 1.02 0.36 0.12
59_L 46_A 1.01 0.35 0.11
49_R 10_F 1.00 0.35 0.11
76_A 41_D 1.00 0.34 0.11
67_V 43_I 1.00 0.34 0.11
77_V 28_I 0.99 0.33 0.10
80_W 10_F 0.97 0.32 0.10
52_T 46_A 0.97 0.32 0.10
59_L 68_Q 0.97 0.32 0.10
71_L 31_E 0.97 0.32 0.10
51_L 34_T 0.96 0.31 0.09
45_I 19_F 0.96 0.31 0.09
44_L 81_L 0.94 0.30 0.09
73_L 19_F 0.94 0.30 0.09
38_R 75_V 0.93 0.29 0.08
71_L 39_K 0.93 0.29 0.08
52_T 20_V 0.93 0.29 0.08
20_L 88_G 0.93 0.29 0.08
73_L 42_I 0.93 0.29 0.08
65_T 11_R 0.92 0.28 0.08
29_E 81_L 0.91 0.28 0.08
41_V 58_N 0.90 0.27 0.07
19_Y 39_K 0.90 0.27 0.07
85_N 20_V 0.89 0.26 0.07
93_G 44_N 0.89 0.26 0.07
20_L 40_L 0.89 0.26 0.07
70_W 46_A 0.88 0.25 0.07
21_E 79_Y 0.88 0.25 0.07
25_L 77_K 0.88 0.25 0.07
83_E 17_D 0.88 0.25 0.07
35_H 35_T 0.88 0.25 0.06
82_V 64_S 0.87 0.25 0.06
19_Y 54_S 0.87 0.24 0.06
93_G 64_S 0.87 0.24 0.06
72_N 46_A 0.87 0.24 0.06
80_W 41_D 0.86 0.24 0.06
48_N 6_N 0.86 0.24 0.06
32_E 62_E 0.86 0.24 0.06
48_N 17_D 0.86 0.24 0.06
9_T 17_D 0.85 0.23 0.06
18_E 54_S 0.85 0.23 0.06
26_K 93_L 0.85 0.23 0.06
18_E 38_R 0.85 0.23 0.06
54_E 51_D 0.84 0.23 0.06
78_D 45_A 0.84 0.22 0.05
85_N 18_F 0.84 0.22 0.05
55_M 61_E 0.84 0.22 0.05
49_R 83_F 0.84 0.22 0.05
14_I 42_I 0.84 0.22 0.05
90_E 16_A 0.84 0.22 0.05
25_L 61_E 0.84 0.22 0.05
85_N 93_L 0.83 0.22 0.05
14_I 39_K 0.83 0.21 0.05
83_E 9_S 0.83 0.21 0.05
73_L 35_T 0.82 0.21 0.05
33_L 81_L 0.82 0.21 0.05
45_I 11_R 0.82 0.21 0.05
13_D 38_R 0.82 0.21 0.05
25_L 45_A 0.82 0.21 0.05
72_N 19_F 0.82 0.21 0.05
39_N 36_L 0.82 0.21 0.05
52_T 34_T 0.81 0.21 0.05
6_R 41_D 0.81 0.21 0.05
65_T 27_K 0.81 0.20 0.05
73_L 41_D 0.81 0.20 0.05
39_N 61_E 0.81 0.20 0.04
63_F 71_S 0.80 0.20 0.04
53_T 14_W 0.80 0.20 0.04
36_V 57_G 0.80 0.20 0.04
91_E 13_A 0.80 0.20 0.04
81_E 39_K 0.80 0.20 0.04
93_G 89_K 0.80 0.20 0.04
84_N 73_I 0.80 0.20 0.04
44_L 72_S 0.79 0.20 0.04
69_F 82_I 0.79 0.20 0.04
25_L 91_E 0.79 0.19 0.04
92_L 78_Q 0.79 0.19 0.04
63_F 83_F 0.79 0.19 0.04
20_L 75_V 0.79 0.19 0.04
19_Y 36_L 0.79 0.19 0.04
77_V 92_E 0.79 0.19 0.04
55_M 56_P 0.79 0.19 0.04
51_L 46_A 0.78 0.19 0.04
49_R 57_G 0.78 0.19 0.04
64_D 92_E 0.78 0.19 0.04
49_R 52_L 0.78 0.19 0.04
39_N 74_R 0.78 0.19 0.04
52_T 9_S 0.78 0.19 0.04
58_R 98_H 0.77 0.18 0.04
9_T 95_L 0.77 0.18 0.04
24_D 92_E 0.77 0.18 0.04
77_V 17_D 0.77 0.18 0.04
8_P 41_D 0.77 0.18 0.04
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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