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OPENSEQ.org
mlad_mlab
Genes: A B A+B
Length: 183 97 273
Sequences: 2454 119 101
Seq/Len: 13.41 1.23 0.37
MirrorTree (Pazo et al. 2001) 0.69
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 0.00 0.01
2 0.01 0.00 0.36
5 0.02 0.00 0.36
10 0.03 0.00 0.36
20 0.04 0.00 0.36
100 0.06 0.00 0.36
∞ 0.16 0.00 0.36
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
16_A 80_K 1.66 0.58 0.00
153_G 81_V 1.58 0.53 0.00
139_S 60_H 1.51 0.48 0.00
24_V 85_A 1.49 0.47 0.00
30_N 59_L 1.46 0.45 0.00
37_E 53_G 1.46 0.44 0.00
40_Y 83_T 1.45 0.44 0.00
28_A 24_V 1.40 0.40 0.00
28_A 81_V 1.34 0.36 0.00
27_K 95_L 1.33 0.36 0.00
112_L 60_H 1.33 0.35 0.00
41_T 83_T 1.30 0.34 0.00
155_K 55_L 1.30 0.34 0.00
153_G 26_L 1.29 0.33 0.00
35_R 52_T 1.26 0.31 0.00
22_L 39_I 1.25 0.31 0.00
155_K 35_A 1.23 0.29 0.00
139_S 90_L 1.22 0.28 0.00
104_S 83_T 1.18 0.27 0.00
100_S 89_N 1.18 0.27 0.00
84_L 11_G 1.17 0.26 0.00
27_K 83_T 1.17 0.26 0.00
41_T 95_L 1.15 0.25 0.00
111_Y 66_K 1.15 0.25 0.00
121_P 69_G 1.15 0.25 0.00
83_T 19_E 1.14 0.24 0.00
40_Y 74_L 1.14 0.24 0.00
133_T 89_N 1.12 0.24 0.00
78_Y 83_T 1.10 0.22 0.00
40_Y 95_L 1.10 0.22 0.00
37_E 36_V 1.09 0.22 0.00
59_S 52_T 1.08 0.21 0.00
159_N 44_L 1.08 0.21 0.00
91_N 17_S 1.08 0.21 0.00
96_T 69_G 1.07 0.21 0.00
133_T 60_H 1.06 0.21 0.00
35_R 85_A 1.06 0.21 0.00
30_N 22_Q 1.06 0.20 0.00
116_V 79_D 1.05 0.20 0.00
116_V 39_I 1.05 0.20 0.00
100_S 60_H 1.05 0.20 0.00
18_L 86_K 1.05 0.20 0.00
95_D 5_L 1.04 0.20 0.00
133_T 49_R 1.04 0.19 0.00
81_R 32_R 1.02 0.19 0.00
141_M 4_S 1.01 0.18 0.00
132_D 32_R 1.01 0.18 0.00
70_D 41_C 1.01 0.18 0.00
111_Y 92_A 1.01 0.18 0.00
122_E 12_D 1.00 0.18 0.00
55_R 65_A 1.00 0.18 0.00
153_G 24_V 0.99 0.18 0.00
3_T 60_H 0.99 0.18 0.00
100_S 49_R 0.99 0.18 0.00
34_I 77_V 0.99 0.17 0.00
126_A 2_S 0.99 0.17 0.00
163_G 26_L 0.98 0.17 0.00
92_H 62_I 0.98 0.17 0.00
59_S 62_I 0.98 0.17 0.00
104_S 95_L 0.98 0.17 0.00
32_T 52_T 0.98 0.17 0.00
12_I 78_N 0.97 0.17 0.00
155_K 94_V 0.97 0.17 0.00
89_R 78_N 0.97 0.17 0.00
38_P 63_D 0.97 0.16 0.00
112_L 24_V 0.96 0.16 0.00
134_I 43_D 0.94 0.15 0.00
20_A 60_H 0.94 0.15 0.00
35_R 22_Q 0.94 0.15 0.00
100_S 53_G 0.93 0.15 0.00
139_S 89_N 0.93 0.15 0.00
40_Y 64_L 0.93 0.15 0.00
157_D 73_T 0.93 0.15 0.00
55_R 61_L 0.93 0.15 0.00
55_R 79_D 0.92 0.15 0.00
35_R 93_D 0.92 0.15 0.00
16_A 42_I 0.92 0.15 0.00
59_S 59_L 0.92 0.15 0.00
141_M 17_S 0.92 0.14 0.00
28_A 47_V 0.91 0.14 0.00
78_Y 95_L 0.91 0.14 0.00
3_T 49_R 0.91 0.14 0.00
86_I 93_D 0.91 0.14 0.00
81_R 89_N 0.91 0.14 0.00
2_Q 7_W 0.91 0.14 0.00
133_T 62_I 0.90 0.14 0.00
158_D 31_M 0.90 0.14 0.00
42_L 31_M 0.90 0.14 0.00
155_K 42_I 0.90 0.14 0.00
139_S 28_L 0.89 0.14 0.00
54_A 10_T 0.89 0.14 0.00
35_R 44_L 0.89 0.14 0.00
21_A 13_T 0.89 0.14 0.00
79_L 44_L 0.89 0.14 0.00
45_T 41_C 0.88 0.13 0.00
79_L 91_P 0.88 0.13 0.00
75_P 46_R 0.88 0.13 0.00
47_D 90_L 0.88 0.13 0.00
126_A 28_L 0.87 0.13 0.00
101_I 23_D 0.87 0.13 0.00
163_G 27_P 0.87 0.13 0.00
30_N 66_K 0.87 0.13 0.00
155_K 22_Q 0.86 0.13 0.00
59_S 22_Q 0.86 0.13 0.00
28_A 22_Q 0.86 0.13 0.00
24_V 52_T 0.86 0.13 0.00
156_G 55_L 0.86 0.13 0.00
114_L 93_D 0.86 0.13 0.00
40_Y 80_K 0.85 0.12 0.00
123_L 35_A 0.85 0.12 0.00
123_L 42_I 0.85 0.12 0.00
123_L 82_Y 0.85 0.12 0.00
127_I 23_D 0.85 0.12 0.00
40_Y 96_P 0.85 0.12 0.00
169_A 47_V 0.84 0.12 0.00
25_C 69_G 0.84 0.12 0.00
127_I 46_R 0.84 0.12 0.00
79_L 65_A 0.84 0.12 0.00
81_R 60_H 0.84 0.12 0.00
19_L 35_A 0.84 0.12 0.00
33_S 50_V 0.84 0.12 0.00
84_L 75_Q 0.84 0.12 0.00
14_L 58_L 0.83 0.12 0.00
139_S 27_P 0.83 0.12 0.00
166_P 61_L 0.83 0.12 0.00
31_V 44_L 0.82 0.12 0.00
92_H 43_D 0.82 0.11 0.00
139_S 57_L 0.82 0.11 0.00
16_A 36_V 0.82 0.11 0.00
83_T 70_N 0.81 0.11 0.00
130_D 94_V 0.81 0.11 0.00
156_G 64_L 0.81 0.11 0.00
6_N 15_A 0.81 0.11 0.00
36_T 47_V 0.81 0.11 0.00
8_I 68_Q 0.80 0.11 0.00
19_L 9_Q 0.80 0.11 0.00
91_N 19_E 0.80 0.11 0.00
58_V 28_L 0.80 0.11 0.00
45_T 58_L 0.80 0.11 0.00
153_G 22_Q 0.80 0.11 0.00
42_L 48_S 0.79 0.11 0.00
6_N 35_A 0.79 0.11 0.00
155_K 24_V 0.79 0.11 0.00
161_N 17_S 0.79 0.11 0.00
21_A 9_Q 0.78 0.10 0.00
22_L 80_K 0.78 0.10 0.00
122_E 95_L 0.78 0.10 0.00
173_N 86_K 0.78 0.10 0.00
42_L 78_N 0.78 0.10 0.00
158_D 71_N 0.78 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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