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OPENSEQ.org
4ME7
Genes: A B A+B
Length: 116 93 206
Sequences: 3031 842 155
Seq/Len: 26.13 9.05 0.75
MirrorTree (Pazo et al. 2001) 0.70
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 0.01 0.01 0.74
2 0.01 0.01 0.75
5 0.01 0.01 0.75
10 0.02 0.01 0.77
20 0.03 0.02 0.79
100 0.06 0.02 0.88
∞ 0.10 0.05 1.46
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
44_V 70_N 2.11 0.95 0.74
83_I 10_M 1.53 0.70 0.29
82_T 61_Y 1.37 0.59 0.19
10_F 86_V 1.37 0.58 0.18
95_L 82_A 1.36 0.57 0.18
63_D 45_V 1.32 0.54 0.16
109_I 49_T 1.28 0.51 0.14
67_Y 87_E 1.26 0.49 0.13
69_F 9_E 1.24 0.47 0.12
93_T 82_A 1.23 0.46 0.12
10_F 89_L 1.21 0.45 0.11
86_Q 86_V 1.17 0.41 0.09
90_D 82_A 1.16 0.40 0.09
66_R 81_E 1.15 0.39 0.09
90_D 89_L 1.14 0.38 0.08
30_I 17_N 1.13 0.38 0.08
29_V 6_A 1.13 0.38 0.08
2_I 92_G 1.13 0.38 0.08
29_V 50_T 1.12 0.37 0.08
80_I 45_V 1.10 0.36 0.07
30_I 20_A 1.09 0.35 0.07
111_L 9_E 1.08 0.34 0.07
52_Q 90_V 1.08 0.34 0.07
29_V 16_E 1.07 0.33 0.06
86_Q 82_A 1.06 0.33 0.06
29_V 48_R 1.05 0.32 0.06
62_I 57_M 1.05 0.32 0.06
42_A 71_I 1.05 0.32 0.06
66_R 82_A 1.05 0.32 0.06
104_D 6_A 1.05 0.32 0.06
65_K 88_R 1.03 0.31 0.06
101_D 36_L 1.02 0.29 0.05
38_F 71_I 1.02 0.29 0.05
95_L 89_L 1.01 0.29 0.05
75_I 55_D 1.01 0.29 0.05
75_I 80_C 1.01 0.28 0.05
86_Q 62_M 1.00 0.28 0.05
44_V 26_A 0.99 0.28 0.05
59_H 64_M 0.99 0.27 0.04
110_S 64_M 0.99 0.27 0.04
72_D 32_S 0.99 0.27 0.04
86_Q 73_S 0.98 0.27 0.04
97_D 12_I 0.98 0.27 0.04
51_I 64_M 0.97 0.26 0.04
66_R 87_E 0.97 0.26 0.04
76_L 64_M 0.96 0.26 0.04
44_V 66_K 0.96 0.25 0.04
52_Q 74_E 0.96 0.25 0.04
93_T 74_E 0.96 0.25 0.04
71_R 79_E 0.96 0.25 0.04
2_I 88_R 0.95 0.25 0.04
55_K 64_M 0.95 0.25 0.04
78_E 64_M 0.95 0.25 0.04
32_N 61_Y 0.94 0.24 0.04
51_I 60_G 0.94 0.24 0.04
30_I 16_E 0.94 0.24 0.04
108_Q 6_A 0.94 0.24 0.04
93_T 83_E 0.93 0.24 0.04
49_A 85_T 0.92 0.23 0.03
93_T 86_V 0.92 0.23 0.03
74_V 64_M 0.92 0.23 0.03
86_Q 81_E 0.92 0.23 0.03
34_I 39_Q 0.92 0.23 0.03
29_V 7_R 0.91 0.23 0.03
83_I 29_E 0.91 0.22 0.03
86_Q 75_A 0.91 0.22 0.03
71_R 83_E 0.90 0.22 0.03
69_F 83_E 0.90 0.22 0.03
93_T 90_V 0.90 0.22 0.03
10_F 90_V 0.90 0.22 0.03
114_I 33_R 0.90 0.22 0.03
14_S 59_R 0.90 0.22 0.03
90_D 81_E 0.90 0.21 0.03
59_H 60_G 0.89 0.21 0.03
108_Q 85_T 0.89 0.21 0.03
92_I 22_L 0.89 0.21 0.03
62_I 49_T 0.88 0.21 0.03
1_M 37_I 0.88 0.21 0.03
23_G 64_M 0.88 0.20 0.03
66_R 89_L 0.88 0.20 0.03
96_D 53_N 0.87 0.20 0.03
59_H 67_I 0.87 0.20 0.03
58_T 64_M 0.87 0.20 0.03
8_V 83_E 0.87 0.20 0.03
90_D 86_V 0.87 0.20 0.03
86_Q 79_E 0.87 0.20 0.03
40_P 68_N 0.87 0.20 0.03
35_G 68_N 0.86 0.20 0.03
30_I 6_A 0.86 0.19 0.03
8_V 34_N 0.85 0.19 0.03
103_V 25_V 0.85 0.19 0.03
114_I 14_L 0.85 0.19 0.03
50_Q 55_D 0.85 0.19 0.03
46_A 64_M 0.85 0.19 0.02
76_L 60_G 0.85 0.19 0.02
10_F 88_R 0.85 0.19 0.02
89_T 86_V 0.85 0.19 0.02
4_K 7_R 0.84 0.19 0.02
40_P 65_A 0.84 0.19 0.02
49_A 88_R 0.84 0.19 0.02
4_K 52_H 0.84 0.18 0.02
100_M 59_R 0.83 0.18 0.02
28_L 68_N 0.83 0.18 0.02
47_I 44_Y 0.83 0.18 0.02
9_Y 10_M 0.83 0.18 0.02
69_F 86_V 0.83 0.18 0.02
19_S 10_M 0.82 0.18 0.02
3_V 90_V 0.82 0.17 0.02
95_L 74_E 0.82 0.17 0.02
32_N 64_M 0.82 0.17 0.02
68_G 51_R 0.81 0.17 0.02
80_I 34_N 0.81 0.17 0.02
51_I 67_I 0.81 0.17 0.02
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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