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OPENSEQ.org
5198
Genes: A B A+B
Length: 146 93 235
Sequences: 71 3969 55
Seq/Len: 0.49 42.68 0.23
MirrorTree (Pazo et al. 2001) 0.64
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 0.02 0.23
2 0.00 0.03 0.24
5 0.00 0.04 0.24
10 0.00 0.05 0.24
20 0.00 0.06 0.24
100 0.00 0.08 0.24
∞ 0.00 0.14 0.26
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
118_A 82_V 1.82 0.54 0.00
119_I 80_L 1.57 0.39 0.00
112_R 53_R 1.54 0.37 0.00
131_A 79_V 1.53 0.37 0.00
137_A 16_I 1.52 0.36 0.00
124_P 12_D 1.51 0.36 0.00
131_A 10_L 1.44 0.32 0.00
53_I 50_R 1.40 0.30 0.00
124_P 6_K 1.33 0.26 0.00
106_A 65_H 1.28 0.24 0.00
99_K 49_Y 1.27 0.23 0.00
118_A 80_L 1.21 0.21 0.00
106_A 38_I 1.20 0.20 0.00
34_L 77_L 1.18 0.20 0.00
120_D 14_E 1.18 0.19 0.00
30_G 46_P 1.17 0.19 0.00
3_P 50_R 1.16 0.19 0.00
111_F 83_L 1.16 0.18 0.00
69_V 69_I 1.15 0.18 0.00
38_Y 87_L 1.15 0.18 0.00
108_D 57_T 1.12 0.17 0.00
127_S 10_L 1.11 0.17 0.00
46_A 90_P 1.10 0.17 0.00
111_F 57_T 1.08 0.16 0.00
77_D 81_R 1.08 0.16 0.00
57_K 29_I 1.07 0.16 0.00
4_E 13_R 1.06 0.15 0.00
29_Q 7_P 1.05 0.15 0.00
137_A 37_A 1.05 0.15 0.00
117_A 77_L 1.02 0.14 0.00
116_Q 40_E 1.02 0.14 0.00
25_V 60_A 1.02 0.14 0.00
53_I 58_H 1.01 0.14 0.00
126_L 77_L 1.00 0.14 0.00
108_D 53_R 1.00 0.14 0.00
20_V 54_V 0.99 0.13 0.00
130_E 39_A 0.99 0.13 0.00
115_V 57_T 0.98 0.13 0.00
124_P 16_I 0.98 0.13 0.00
27_G 43_C 0.98 0.13 0.00
20_V 23_D 0.97 0.13 0.00
42_E 53_R 0.97 0.13 0.00
17_S 58_H 0.97 0.13 0.00
98_L 48_M 0.97 0.12 0.00
128_H 51_A 0.96 0.12 0.00
114_Q 18_E 0.96 0.12 0.00
123_R 66_Y 0.96 0.12 0.00
131_A 39_A 0.96 0.12 0.00
50_S 86_A 0.96 0.12 0.00
120_D 10_L 0.95 0.12 0.00
25_V 42_A 0.95 0.12 0.00
111_F 69_I 0.95 0.12 0.00
58_R 50_R 0.94 0.12 0.00
112_R 57_T 0.94 0.12 0.00
50_S 43_C 0.94 0.12 0.00
68_D 14_E 0.94 0.12 0.00
110_W 81_R 0.93 0.12 0.00
136_A 36_E 0.93 0.12 0.00
119_I 71_Q 0.93 0.12 0.00
143_L 85_T 0.93 0.11 0.00
127_S 30_A 0.93 0.11 0.00
125_A 79_V 0.92 0.11 0.00
127_S 79_V 0.92 0.11 0.00
139_K 77_L 0.92 0.11 0.00
34_L 43_C 0.92 0.11 0.00
111_F 53_R 0.91 0.11 0.00
92_P 56_G 0.91 0.11 0.00
116_Q 62_V 0.90 0.11 0.00
133_S 43_C 0.90 0.11 0.00
72_A 26_L 0.90 0.11 0.00
131_A 9_S 0.90 0.11 0.00
26_I 67_V 0.90 0.11 0.00
27_G 88_Q 0.90 0.11 0.00
139_K 13_R 0.90 0.11 0.00
134_L 10_L 0.89 0.11 0.00
68_D 69_I 0.89 0.10 0.00
114_Q 13_R 0.89 0.10 0.00
128_H 71_Q 0.89 0.10 0.00
106_A 66_Y 0.89 0.10 0.00
117_A 54_V 0.88 0.10 0.00
121_D 23_D 0.88 0.10 0.00
107_Y 65_H 0.88 0.10 0.00
59_L 72_V 0.88 0.10 0.00
29_Q 42_A 0.87 0.10 0.00
135_F 33_N 0.87 0.10 0.00
19_V 53_R 0.87 0.10 0.00
132_K 62_V 0.87 0.10 0.00
110_W 52_G 0.86 0.10 0.00
106_A 86_A 0.86 0.10 0.00
7_D 27_A 0.86 0.10 0.00
132_K 3_L 0.86 0.10 0.00
112_R 90_P 0.86 0.10 0.00
83_P 18_E 0.85 0.10 0.00
45_L 28_A 0.85 0.10 0.00
82_D 86_A 0.84 0.10 0.00
106_A 16_I 0.84 0.10 0.00
133_S 19_Y 0.84 0.09 0.00
130_E 73_E 0.84 0.09 0.00
42_E 88_Q 0.83 0.09 0.00
99_K 42_A 0.83 0.09 0.00
81_Y 90_P 0.82 0.09 0.00
17_S 11_S 0.82 0.09 0.00
76_V 1_M 0.82 0.09 0.00
89_T 15_Q 0.82 0.09 0.00
17_S 21_S 0.82 0.09 0.00
115_V 27_A 0.81 0.09 0.00
118_A 64_P 0.81 0.09 0.00
2_A 11_S 0.81 0.09 0.00
111_F 52_G 0.81 0.09 0.00
138_R 3_L 0.81 0.09 0.00
68_D 4_E 0.81 0.09 0.00
121_D 79_V 0.81 0.09 0.00
67_K 63_R 0.81 0.09 0.00
3_P 17_M 0.81 0.09 0.00
132_K 6_K 0.80 0.09 0.00
67_K 86_A 0.80 0.09 0.00
124_P 66_Y 0.80 0.09 0.00
5_T 27_A 0.80 0.09 0.00
109_A 67_V 0.80 0.09 0.00
36_V 79_V 0.80 0.09 0.00
100_R 86_A 0.80 0.09 0.00
93_D 56_G 0.80 0.09 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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