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OPENSEQ.org
myco5
Genes: A B A+B
Length: 187 624 795
Sequences: 1458 1769 868
Seq/Len: 7.8 2.83 1.09
MirrorTree (Pazo et al. 2001) 0.33
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.02
100 0.00 0.00 0.11
∞ 0.06 0.03 1.07
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
154_L 332_L 1.09 0.44 0.00
17_G 330_T 1.06 0.41 0.00
63_A 514_L 0.99 0.35 0.00
64_T 315_A 0.99 0.35 0.00
89_E 101_V 0.98 0.34 0.00
22_I 156_V 0.97 0.33 0.00
160_I 291_L 0.96 0.33 0.00
113_V 459_V 0.93 0.30 0.00
46_S 604_A 0.93 0.30 0.00
8_K 329_W 0.92 0.29 0.00
15_I 456_V 0.92 0.29 0.00
19_L 418_A 0.91 0.29 0.00
145_S 529_I 0.91 0.28 0.00
46_S 198_G 0.90 0.28 0.00
69_D 261_Y 0.90 0.28 0.00
12_V 557_A 0.89 0.27 0.00
133_V 219_A 0.89 0.27 0.00
55_N 85_D 0.89 0.27 0.00
117_N 276_V 0.88 0.27 0.00
21_T 514_L 0.88 0.26 0.00
55_N 211_A 0.87 0.25 0.00
94_P 129_T 0.86 0.24 0.00
172_L 271_E 0.86 0.24 0.00
98_V 305_D 0.85 0.24 0.00
170_D 478_T 0.85 0.24 0.00
123_I 430_L 0.84 0.24 0.00
19_L 315_A 0.84 0.24 0.00
44_V 244_F 0.84 0.23 0.00
13_L 246_P 0.83 0.23 0.00
94_P 431_A 0.83 0.23 0.00
121_L 134_H 0.83 0.23 0.00
86_Q 322_A 0.82 0.22 0.00
56_A 409_G 0.81 0.22 0.00
12_V 416_F 0.81 0.21 0.00
170_D 550_R 0.81 0.21 0.00
2_A 337_E 0.80 0.21 0.00
133_V 531_V 0.80 0.21 0.00
173_K 332_L 0.80 0.21 0.00
12_V 315_A 0.80 0.21 0.00
112_Q 580_I 0.80 0.21 0.00
44_V 320_L 0.80 0.20 0.00
1_M 315_A 0.79 0.20 0.00
141_Q 485_H 0.79 0.20 0.00
185_V 545_L 0.79 0.20 0.00
166_I 140_Y 0.78 0.20 0.00
105_L 188_L 0.78 0.20 0.00
85_S 8_V 0.77 0.19 0.00
100_D 466_V 0.77 0.19 0.00
133_V 51_L 0.77 0.19 0.00
65_V 180_A 0.77 0.19 0.00
5_A 397_D 0.76 0.18 0.00
174_V 441_E 0.76 0.18 0.00
87_D 177_L 0.76 0.18 0.00
44_V 129_T 0.76 0.18 0.00
180_S 578_I 0.76 0.18 0.00
141_Q 387_T 0.76 0.18 0.00
113_V 336_V 0.76 0.18 0.00
125_L 197_V 0.75 0.18 0.00
32_K 419_Q 0.75 0.18 0.00
118_G 585_T 0.75 0.18 0.00
30_P 419_Q 0.75 0.18 0.00
19_L 385_C 0.75 0.18 0.00
104_F 350_D 0.75 0.18 0.00
133_V 93_D 0.74 0.18 0.00
99_G 600_A 0.74 0.17 0.00
154_L 316_Y 0.74 0.17 0.00
131_L 319_G 0.74 0.17 0.00
158_A 126_D 0.74 0.17 0.00
180_S 284_F 0.74 0.17 0.00
55_N 129_T 0.74 0.17 0.00
78_S 34_I 0.74 0.17 0.00
124_E 255_A 0.73 0.17 0.00
174_V 532_M 0.73 0.17 0.00
5_A 519_I 0.73 0.17 0.00
166_I 392_I 0.73 0.17 0.00
12_V 518_P 0.73 0.17 0.00
115_F 562_I 0.73 0.17 0.00
96_A 440_D 0.73 0.17 0.00
39_T 218_Q 0.73 0.17 0.00
9_N 481_F 0.72 0.17 0.00
23_T 180_A 0.72 0.16 0.00
141_Q 600_A 0.72 0.16 0.00
46_S 178_V 0.72 0.16 0.00
26_Q 482_L 0.72 0.16 0.00
116_H 180_A 0.72 0.16 0.00
73_L 562_I 0.72 0.16 0.00
91_H 510_A 0.71 0.16 0.00
94_P 432_Q 0.71 0.16 0.00
7_F 365_A 0.71 0.16 0.00
69_D 221_V 0.71 0.16 0.00
35_A 580_I 0.71 0.16 0.00
113_V 50_R 0.71 0.16 0.00
56_A 607_R 0.71 0.16 0.00
68_R 294_Q 0.71 0.16 0.00
19_L 557_A 0.70 0.15 0.00
170_D 355_V 0.70 0.15 0.00
7_F 533_P 0.70 0.15 0.00
21_T 315_A 0.70 0.15 0.00
14_V 533_P 0.70 0.15 0.00
146_S 383_A 0.70 0.15 0.00
88_Y 587_L 0.70 0.15 0.00
7_F 393_P 0.69 0.15 0.00
99_G 203_A 0.69 0.15 0.00
51_D 546_L 0.69 0.15 0.00
46_S 22_R 0.69 0.15 0.00
61_D 533_P 0.69 0.15 0.00
72_Y 275_A 0.69 0.15 0.00
55_N 46_R 0.69 0.15 0.00
96_A 420_I 0.69 0.15 0.00
136_T 553_Q 0.69 0.15 0.00
123_I 100_V 0.69 0.15 0.00
185_V 456_V 0.69 0.15 0.00
183_G 422_A 0.69 0.15 0.00
46_S 246_P 0.69 0.15 0.00
172_L 82_R 0.69 0.15 0.00
87_D 311_A 0.69 0.14 0.00
122_Y 332_L 0.68 0.14 0.00
182_L 71_G 0.68 0.14 0.00
36_F 481_F 0.68 0.14 0.00
73_L 264_F 0.68 0.14 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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