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OPENSEQ.org
PE20_PPE31
Genes: A B A+B
Length: 99 399 485
Sequences: 474 381 147
Seq/Len: 4.79 0.95 0.3
MirrorTree (Pazo et al. 2001) 0.30
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.09 0.33 0.20
2 0.11 0.38 0.21
5 0.19 0.41 0.24
10 0.24 0.43 0.26
20 0.28 0.44 0.30
100 0.36 0.49 0.38
∞ 0.40 0.54 0.39
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
42_A 158_S 1.98 0.72 0.03
74_E 326_V 1.56 0.45 0.01
25_I 21_S 1.45 0.38 0.01
3_F 185_A 1.38 0.34 0.01
22_G 72_Y 1.36 0.33 0.01
38_E 110_I 1.34 0.32 0.01
12_A 22_A 1.30 0.29 0.01
46_E 14_R 1.29 0.29 0.01
95_I 288_D 1.29 0.29 0.01
59_A 37_E 1.27 0.28 0.01
84_A 29_S 1.26 0.28 0.01
74_E 61_A 1.22 0.25 0.00
74_E 179_L 1.20 0.24 0.00
6_V 47_S 1.20 0.24 0.00
75_A 86_A 1.20 0.24 0.00
40_A 47_S 1.20 0.24 0.00
19_R 24_M 1.20 0.24 0.00
62_Y 34_L 1.17 0.23 0.00
76_F 56_E 1.17 0.23 0.00
84_A 67_A 1.17 0.22 0.00
67_A 110_I 1.17 0.22 0.00
38_E 21_S 1.16 0.22 0.00
15_A 15_M 1.15 0.22 0.00
13_I 63_A 1.13 0.21 0.00
75_A 170_P 1.13 0.21 0.00
97_A 61_A 1.12 0.21 0.00
21_V 303_V 1.11 0.20 0.00
4_V 24_M 1.10 0.20 0.00
66_G 121_I 1.10 0.20 0.00
72_M 171_V 1.10 0.19 0.00
74_E 131_P 1.09 0.19 0.00
85_D 186_I 1.08 0.18 0.00
67_A 132_A 1.07 0.18 0.00
23_S 325_T 1.07 0.18 0.00
62_Y 156_G 1.06 0.18 0.00
89_A 183_S 1.05 0.17 0.00
51_T 93_A 1.04 0.17 0.00
32_A 66_T 1.04 0.17 0.00
90_T 13_A 1.03 0.17 0.00
13_I 64_S 1.02 0.17 0.00
9_D 174_T 1.02 0.16 0.00
65_V 141_A 1.02 0.16 0.00
58_H 93_A 1.02 0.16 0.00
40_A 3_F 1.01 0.16 0.00
23_S 215_L 1.01 0.16 0.00
49_A 369_P 1.00 0.16 0.00
11_L 347_S 1.00 0.16 0.00
58_H 167_F 1.00 0.15 0.00
20_H 178_G 1.00 0.15 0.00
86_S 28_A 0.99 0.15 0.00
53_T 74_A 0.98 0.15 0.00
95_I 21_S 0.97 0.15 0.00
10_A 72_Y 0.97 0.14 0.00
60_A 326_V 0.97 0.14 0.00
29_N 310_G 0.97 0.14 0.00
84_A 153_G 0.97 0.14 0.00
90_T 389_P 0.96 0.14 0.00
74_E 73_V 0.96 0.14 0.00
55_F 30_A 0.96 0.14 0.00
85_D 182_Q 0.96 0.14 0.00
93_A 82_R 0.96 0.14 0.00
81_G 169_E 0.95 0.14 0.00
68_Q 17_S 0.95 0.14 0.00
59_A 285_A 0.95 0.14 0.00
2_A 156_G 0.95 0.14 0.00
88_A 41_S 0.94 0.14 0.00
20_H 62_S 0.94 0.14 0.00
24_V 149_M 0.94 0.14 0.00
59_A 190_T 0.94 0.14 0.00
39_L 4_A 0.93 0.13 0.00
99_S 61_A 0.93 0.13 0.00
59_A 315_T 0.92 0.13 0.00
17_Q 3_F 0.92 0.13 0.00
64_A 19_A 0.92 0.13 0.00
72_M 374_G 0.91 0.13 0.00
31_V 206_A 0.91 0.13 0.00
78_A 76_M 0.91 0.13 0.00
23_S 343_S 0.91 0.13 0.00
56_N 97_Y 0.91 0.13 0.00
72_M 366_P 0.91 0.13 0.00
79_M 162_T 0.91 0.13 0.00
22_G 135_A 0.90 0.12 0.00
60_A 108_P 0.90 0.12 0.00
46_E 209_P 0.90 0.12 0.00
73_N 72_Y 0.90 0.12 0.00
62_Y 4_A 0.90 0.12 0.00
29_N 50_S 0.90 0.12 0.00
57_F 192_A 0.90 0.12 0.00
76_F 72_Y 0.89 0.12 0.00
12_A 184_A 0.89 0.12 0.00
76_F 174_T 0.89 0.12 0.00
62_Y 66_T 0.89 0.12 0.00
99_S 115_A 0.89 0.12 0.00
67_A 22_A 0.89 0.12 0.00
2_A 185_A 0.88 0.12 0.00
59_A 213_Q 0.88 0.12 0.00
3_F 5_T 0.88 0.12 0.00
14_A 174_T 0.88 0.12 0.00
15_A 64_S 0.88 0.12 0.00
90_T 109_V 0.88 0.12 0.00
13_I 119_A 0.88 0.12 0.00
40_A 23_P 0.88 0.12 0.00
46_E 1_L 0.87 0.12 0.00
61_M 126_L 0.87 0.12 0.00
35_A 145_S 0.87 0.12 0.00
82_A 116_Q 0.87 0.12 0.00
67_A 155_A 0.87 0.12 0.00
76_F 158_S 0.87 0.12 0.00
53_T 336_T 0.87 0.12 0.00
59_A 2_D 0.86 0.11 0.00
13_I 176_A 0.86 0.11 0.00
66_G 65_M 0.86 0.11 0.00
65_V 194_A 0.86 0.11 0.00
35_A 35_S 0.86 0.11 0.00
70_I 47_S 0.86 0.11 0.00
58_H 3_F 0.86 0.11 0.00
54_Q 24_M 0.85 0.11 0.00
15_A 182_Q 0.85 0.11 0.00
9_D 169_E 0.85 0.11 0.00
93_A 134_A 0.85 0.11 0.00
77_V 375_G 0.85 0.11 0.00
45_D 154_Y 0.85 0.11 0.00
73_N 234_V 0.84 0.11 0.00
92_A 304_A 0.84 0.11 0.00
2_A 1_L 0.84 0.11 0.00
20_H 338_A 0.84 0.11 0.00
60_A 24_M 0.84 0.11 0.00
29_N 166_P 0.84 0.11 0.00
4_V 327_G 0.84 0.11 0.00
27_A 316_V 0.83 0.10 0.00
74_E 221_A 0.83 0.10 0.00
10_A 199_T 0.83 0.10 0.00
51_T 24_M 0.82 0.10 0.00
21_V 116_Q 0.82 0.10 0.00
96_I 43_L 0.82 0.10 0.00
8_P 327_G 0.82 0.10 0.00
43_A 329_L 0.82 0.10 0.00
44_A 85_Q 0.82 0.10 0.00
7_C 61_A 0.82 0.10 0.00
67_A 163_Q 0.82 0.10 0.00
51_T 126_L 0.82 0.10 0.00
6_V 336_T 0.81 0.10 0.00
72_M 388_R 0.81 0.10 0.00
59_A 371_G 0.81 0.10 0.00
6_V 364_G 0.81 0.10 0.00
65_V 338_A 0.81 0.10 0.00
77_V 187_A 0.81 0.10 0.00
83_S 116_Q 0.81 0.10 0.00
13_I 319_G 0.81 0.10 0.00
64_A 23_P 0.81 0.10 0.00
65_V 158_S 0.81 0.10 0.00
85_D 86_A 0.81 0.10 0.00
77_V 394_R 0.81 0.10 0.00
33_A 110_I 0.81 0.10 0.00
71_A 189_A 0.81 0.10 0.00
42_A 23_P 0.81 0.10 0.00
70_I 244_L 0.80 0.10 0.00
86_S 24_M 0.80 0.10 0.00
47_V 154_Y 0.80 0.10 0.00
96_I 126_L 0.80 0.10 0.00
52_A 128_Q 0.80 0.10 0.00
41_P 24_M 0.80 0.10 0.00
50_L 24_M 0.80 0.10 0.00
51_T 167_F 0.80 0.10 0.00
22_G 388_R 0.80 0.10 0.00
16_G 175_N 0.80 0.10 0.00
15_A 31_W 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.44 > 0.4) of paralogs.
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