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OPENSEQ.org
PE20-PPE31
Genes: A B A+B
Length: 399 99 485
Sequences: 381 474 147
Seq/Len: 0.95 4.79 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 0.33 0.09 0.21
2 0.38 0.11 0.21
5 0.41 0.19 0.24
10 0.43 0.24 0.26
20 0.44 0.28 0.30
100 0.49 0.36 0.38
∞ 0.54 0.40 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
158_S 42_A 1.98 0.72 0.03
326_V 74_E 1.56 0.45 0.01
21_S 25_I 1.44 0.38 0.01
185_A 3_F 1.38 0.34 0.01
110_I 38_E 1.35 0.32 0.01
72_Y 22_G 1.35 0.32 0.01
22_A 12_A 1.30 0.29 0.01
288_D 95_I 1.29 0.29 0.01
14_R 46_E 1.28 0.28 0.01
37_E 59_A 1.26 0.28 0.01
29_S 84_A 1.26 0.27 0.01
47_S 40_A 1.25 0.27 0.00
61_A 74_E 1.22 0.25 0.00
47_S 6_V 1.21 0.24 0.00
179_L 74_E 1.20 0.24 0.00
24_M 19_R 1.19 0.24 0.00
121_I 66_G 1.18 0.23 0.00
34_L 62_Y 1.17 0.23 0.00
110_I 67_A 1.16 0.22 0.00
67_A 84_A 1.16 0.22 0.00
56_E 76_F 1.16 0.22 0.00
21_S 38_E 1.15 0.22 0.00
15_M 15_A 1.15 0.21 0.00
63_A 13_I 1.13 0.21 0.00
61_A 97_A 1.12 0.21 0.00
86_A 75_A 1.11 0.20 0.00
303_V 21_V 1.11 0.20 0.00
24_M 4_V 1.10 0.20 0.00
66_T 32_A 1.10 0.20 0.00
131_P 74_E 1.10 0.20 0.00
171_V 72_M 1.09 0.19 0.00
186_I 85_D 1.07 0.18 0.00
132_A 67_A 1.07 0.18 0.00
156_G 62_Y 1.05 0.18 0.00
13_A 90_T 1.04 0.17 0.00
93_A 51_T 1.03 0.17 0.00
174_T 9_D 1.03 0.17 0.00
64_S 13_I 1.02 0.16 0.00
93_A 58_H 1.01 0.16 0.00
215_L 23_S 1.01 0.16 0.00
369_P 49_A 1.00 0.16 0.00
115_A 99_S 0.99 0.15 0.00
178_G 20_H 0.99 0.15 0.00
167_F 58_H 0.99 0.15 0.00
347_S 11_L 0.99 0.15 0.00
28_A 86_S 0.99 0.15 0.00
183_S 89_A 0.98 0.15 0.00
74_A 53_T 0.97 0.15 0.00
325_T 23_S 0.97 0.15 0.00
72_Y 10_A 0.97 0.15 0.00
21_S 95_I 0.97 0.15 0.00
73_V 74_E 0.97 0.14 0.00
153_G 84_A 0.97 0.14 0.00
310_G 29_N 0.97 0.14 0.00
326_V 60_A 0.96 0.14 0.00
389_P 90_T 0.96 0.14 0.00
170_P 75_A 0.96 0.14 0.00
182_Q 85_D 0.96 0.14 0.00
30_A 55_F 0.95 0.14 0.00
3_F 40_A 0.95 0.14 0.00
23_P 40_A 0.95 0.14 0.00
285_A 59_A 0.95 0.14 0.00
169_E 81_G 0.94 0.14 0.00
156_G 2_A 0.94 0.14 0.00
41_S 88_A 0.94 0.14 0.00
149_M 24_V 0.94 0.14 0.00
19_A 64_A 0.94 0.14 0.00
61_A 99_S 0.93 0.13 0.00
62_S 20_H 0.93 0.13 0.00
190_T 59_A 0.93 0.13 0.00
315_T 59_A 0.93 0.13 0.00
126_L 61_M 0.93 0.13 0.00
17_S 30_A 0.92 0.13 0.00
4_A 39_L 0.92 0.13 0.00
3_F 17_Q 0.92 0.13 0.00
66_T 62_Y 0.92 0.13 0.00
108_P 60_A 0.91 0.13 0.00
76_M 78_A 0.91 0.13 0.00
206_A 31_V 0.91 0.13 0.00
135_A 22_G 0.91 0.13 0.00
374_G 72_M 0.91 0.13 0.00
65_M 66_G 0.91 0.13 0.00
110_I 33_A 0.91 0.13 0.00
162_T 79_M 0.90 0.12 0.00
366_P 72_M 0.90 0.12 0.00
97_Y 56_N 0.90 0.12 0.00
343_S 23_S 0.90 0.12 0.00
72_Y 73_N 0.90 0.12 0.00
174_T 76_F 0.90 0.12 0.00
209_P 46_E 0.89 0.12 0.00
4_A 62_Y 0.89 0.12 0.00
192_A 57_F 0.89 0.12 0.00
22_A 67_A 0.89 0.12 0.00
50_S 29_N 0.89 0.12 0.00
72_Y 76_F 0.88 0.12 0.00
174_T 14_A 0.88 0.12 0.00
185_A 2_A 0.88 0.12 0.00
141_A 65_V 0.88 0.12 0.00
184_A 12_A 0.88 0.12 0.00
5_T 3_F 0.88 0.12 0.00
119_A 13_I 0.88 0.12 0.00
64_S 15_A 0.88 0.12 0.00
213_Q 59_A 0.88 0.12 0.00
109_V 90_T 0.87 0.12 0.00
1_L 46_E 0.87 0.12 0.00
145_S 35_A 0.87 0.12 0.00
155_A 67_A 0.87 0.12 0.00
158_S 76_F 0.87 0.12 0.00
176_A 13_I 0.86 0.11 0.00
336_T 53_T 0.86 0.11 0.00
2_D 59_A 0.86 0.11 0.00
47_S 70_I 0.86 0.11 0.00
116_Q 82_A 0.86 0.11 0.00
187_A 77_V 0.86 0.11 0.00
194_A 65_V 0.86 0.11 0.00
35_S 35_A 0.86 0.11 0.00
159_A 33_A 0.85 0.11 0.00
24_M 54_Q 0.85 0.11 0.00
182_Q 15_A 0.85 0.11 0.00
3_F 58_H 0.85 0.11 0.00
169_E 9_D 0.85 0.11 0.00
338_A 20_H 0.85 0.11 0.00
134_A 93_A 0.85 0.11 0.00
154_Y 45_D 0.84 0.11 0.00
304_A 92_A 0.84 0.11 0.00
166_P 29_N 0.84 0.11 0.00
207_A 40_A 0.84 0.11 0.00
23_P 64_A 0.84 0.11 0.00
234_V 73_N 0.84 0.11 0.00
327_G 4_V 0.84 0.11 0.00
375_G 77_V 0.84 0.11 0.00
1_L 2_A 0.84 0.11 0.00
316_V 27_A 0.83 0.11 0.00
244_L 70_I 0.83 0.11 0.00
24_M 60_A 0.83 0.10 0.00
221_A 74_E 0.82 0.10 0.00
199_T 10_A 0.82 0.10 0.00
17_S 68_Q 0.82 0.10 0.00
327_G 8_P 0.82 0.10 0.00
329_L 43_A 0.82 0.10 0.00
163_Q 67_A 0.81 0.10 0.00
24_M 51_T 0.81 0.10 0.00
61_A 7_C 0.81 0.10 0.00
175_N 61_M 0.81 0.10 0.00
85_Q 44_A 0.81 0.10 0.00
116_Q 21_V 0.81 0.10 0.00
126_L 51_T 0.81 0.10 0.00
371_G 59_A 0.81 0.10 0.00
336_T 6_V 0.81 0.10 0.00
364_G 6_V 0.81 0.10 0.00
319_G 13_I 0.81 0.10 0.00
338_A 65_V 0.81 0.10 0.00
86_A 85_D 0.81 0.10 0.00
189_A 71_A 0.81 0.10 0.00
158_S 65_V 0.81 0.10 0.00
394_R 77_V 0.80 0.10 0.00
388_R 72_M 0.80 0.10 0.00
116_Q 83_S 0.80 0.10 0.00
23_P 42_A 0.80 0.10 0.00
43_L 96_I 0.80 0.10 0.00
167_F 51_T 0.80 0.10 0.00
82_R 93_A 0.80 0.10 0.00
86_A 61_M 0.80 0.10 0.00
128_Q 52_A 0.80 0.10 0.00
24_M 86_S 0.80 0.10 0.00
154_Y 47_V 0.80 0.10 0.00
126_L 96_I 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 A, there is a high ratio (0.44 > 0.4) of paralogs.
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