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OPENSEQ.org
e6-e7
Genes: A B A+B
Length: 158 105 249
Sequences: 273 79 79
Seq/Len: 1.73 0.75 0.32
MirrorTree (Pazo et al. 2001) 0.79
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 0.00 0.00 0.30
2 0.00 0.00 0.30
5 0.00 0.00 0.30
10 0.00 0.00 0.30
20 0.00 0.00 0.30
100 0.00 0.00 0.30
∞ 0.00 0.00 0.30
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
63_A 100_W 1.66 0.54 0.00
9_R 91_L 1.65 0.54 0.00
76_R 11_I 1.41 0.38 0.00
54_V 81_D 1.37 0.35 0.00
49_F 2_H 1.34 0.33 0.00
51_D 56_P 1.33 0.33 0.00
137_Q 79_S 1.33 0.33 0.00
45_F 61_M 1.32 0.32 0.00
126_R 92_N 1.30 0.31 0.00
81_Y 61_M 1.30 0.30 0.00
56_Y 61_M 1.29 0.30 0.00
125_R 63_C 1.27 0.29 0.00
84_S 60_T 1.26 0.28 0.00
78_L 87_Q 1.25 0.28 0.00
98_L 83_L 1.25 0.28 0.00
50_K 87_Q 1.24 0.27 0.00
64_A 38_N 1.24 0.27 0.00
82_S 10_D 1.23 0.27 0.00
43_E 7_T 1.23 0.27 0.00
37_T 23_V 1.19 0.24 0.00
131_A 60_T 1.19 0.24 0.00
57_R 31_L 1.19 0.24 0.00
14_L 78_S 1.17 0.24 0.00
76_R 56_P 1.17 0.23 0.00
135_R 91_L 1.17 0.23 0.00
75_I 40_E 1.15 0.23 0.00
62_H 72_I 1.14 0.22 0.00
94_T 75_V 1.13 0.22 0.00
71_F 66_C 1.12 0.21 0.00
22_N 38_N 1.12 0.21 0.00
53_F 90_F 1.11 0.21 0.00
63_A 35_E 1.11 0.21 0.00
63_A 63_C 1.11 0.21 0.00
115_A 12_V 1.10 0.20 0.00
100_N 77_E 1.10 0.20 0.00
90_L 61_M 1.10 0.20 0.00
146_R 2_H 1.10 0.20 0.00
17_L 17_P 1.10 0.20 0.00
139_H 87_Q 1.08 0.20 0.00
81_Y 58_R 1.08 0.19 0.00
34_Y 10_D 1.07 0.19 0.00
55_V 31_L 1.07 0.19 0.00
120_H 93_T 1.07 0.19 0.00
62_H 95_S 1.06 0.19 0.00
137_Q 96_F 1.06 0.19 0.00
58_D 87_Q 1.05 0.18 0.00
107_R 18_Q 1.05 0.18 0.00
106_L 75_V 1.04 0.18 0.00
121_L 100_W 1.04 0.18 0.00
77_E 33_D 1.04 0.18 0.00
134_Y 90_F 1.04 0.18 0.00
29_E 53_R 1.03 0.18 0.00
82_S 47_Q 1.03 0.18 0.00
56_Y 51_A 1.03 0.18 0.00
83_D 73_K 1.03 0.17 0.00
146_R 63_C 1.03 0.17 0.00
103_I 31_L 1.02 0.17 0.00
50_K 36_E 1.02 0.17 0.00
120_H 79_S 1.02 0.17 0.00
14_L 28_H 1.02 0.17 0.00
115_A 96_F 1.01 0.17 0.00
33_V 15_L 1.01 0.17 0.00
101_L 14_H 1.01 0.17 0.00
86_Y 2_H 1.01 0.17 0.00
131_A 11_I 1.00 0.16 0.00
133_H 85_A 1.00 0.16 0.00
137_Q 90_F 1.00 0.16 0.00
27_D 89_L 0.99 0.16 0.00
74_R 62_L 0.98 0.16 0.00
75_I 32_S 0.98 0.16 0.00
23_T 10_D 0.97 0.15 0.00
110_K 75_V 0.97 0.15 0.00
131_A 12_V 0.97 0.15 0.00
25_L 88_Q 0.97 0.15 0.00
76_R 75_V 0.97 0.15 0.00
126_R 15_L 0.96 0.15 0.00
48_A 89_L 0.95 0.14 0.00
30_I 57_Q 0.94 0.14 0.00
80_H 91_L 0.94 0.14 0.00
43_E 34_S 0.94 0.14 0.00
69_I 63_C 0.94 0.14 0.00
69_I 34_S 0.94 0.14 0.00
37_T 50_P 0.94 0.14 0.00
34_Y 9_Q 0.94 0.14 0.00
78_L 57_Q 0.94 0.14 0.00
87_G 35_E 0.94 0.14 0.00
79_R 24_D 0.93 0.14 0.00
54_V 47_Q 0.93 0.14 0.00
125_R 26_L 0.93 0.14 0.00
124_K 39_D 0.93 0.14 0.00
50_K 63_C 0.93 0.14 0.00
113_N 71_R 0.93 0.14 0.00
85_V 52_R 0.92 0.13 0.00
60_I 32_S 0.92 0.13 0.00
51_D 71_R 0.92 0.13 0.00
116_E 34_S 0.91 0.13 0.00
127_F 29_E 0.91 0.13 0.00
46_E 96_F 0.91 0.13 0.00
101_L 66_C 0.90 0.13 0.00
75_I 87_Q 0.90 0.13 0.00
5_E 70_A 0.89 0.13 0.00
94_T 83_L 0.89 0.13 0.00
61_P 56_P 0.89 0.13 0.00
101_L 103_S 0.89 0.12 0.00
134_Y 96_F 0.89 0.12 0.00
77_E 95_S 0.89 0.12 0.00
95_N 39_D 0.89 0.12 0.00
116_E 31_L 0.88 0.12 0.00
106_L 56_P 0.88 0.12 0.00
118_L 91_L 0.88 0.12 0.00
51_D 28_H 0.88 0.12 0.00
44_V 14_H 0.88 0.12 0.00
127_F 25_L 0.88 0.12 0.00
130_I 24_D 0.87 0.12 0.00
38_V 102_A 0.87 0.12 0.00
63_A 53_R 0.87 0.12 0.00
107_R 22_P 0.87 0.12 0.00
62_H 89_L 0.87 0.12 0.00
62_H 64_M 0.87 0.12 0.00
73_S 15_L 0.86 0.12 0.00
14_L 71_R 0.86 0.12 0.00
22_N 35_E 0.86 0.12 0.00
30_I 19_N 0.86 0.12 0.00
96_T 48_H 0.86 0.12 0.00
74_R 82_D 0.86 0.12 0.00
21_L 37_E 0.86 0.12 0.00
12_Y 33_D 0.86 0.12 0.00
119_R 80_A 0.86 0.12 0.00
11_P 84_R 0.86 0.12 0.00
71_F 79_S 0.86 0.12 0.00
33_V 14_H 0.85 0.12 0.00
34_Y 89_L 0.85 0.12 0.00
79_R 29_E 0.85 0.12 0.00
59_S 72_I 0.85 0.12 0.00
69_I 96_F 0.85 0.11 0.00
25_L 57_Q 0.85 0.11 0.00
129_N 56_P 0.84 0.11 0.00
76_R 83_L 0.84 0.11 0.00
59_S 4_P 0.84 0.11 0.00
54_V 96_F 0.84 0.11 0.00
63_A 10_D 0.84 0.11 0.00
145_A 78_S 0.84 0.11 0.00
11_P 103_S 0.84 0.11 0.00
38_V 35_E 0.84 0.11 0.00
38_V 36_E 0.84 0.11 0.00
89_T 12_V 0.83 0.11 0.00
78_L 71_R 0.83 0.11 0.00
97_G 32_S 0.83 0.11 0.00
109_Q 15_L 0.83 0.11 0.00
119_R 87_Q 0.83 0.11 0.00
113_N 26_L 0.83 0.11 0.00
139_H 33_D 0.82 0.11 0.00
116_E 38_N 0.82 0.11 0.00
129_N 37_E 0.82 0.11 0.00
66_H 80_A 0.82 0.11 0.00
134_Y 59_H 0.82 0.11 0.00
20_E 2_H 0.82 0.11 0.00
79_R 25_L 0.82 0.11 0.00
103_I 92_N 0.81 0.10 0.00
99_Y 100_W 0.81 0.10 0.00
121_L 72_I 0.81 0.10 0.00
76_R 23_V 0.81 0.10 0.00
90_L 91_L 0.81 0.10 0.00
97_G 9_Q 0.81 0.10 0.00
59_S 54_A 0.81 0.10 0.00
133_H 23_V 0.80 0.10 0.00
81_Y 55_E 0.80 0.10 0.00
132_G 33_D 0.80 0.10 0.00
50_K 62_L 0.80 0.10 0.00
59_S 6_A 0.80 0.10 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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