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OPENSEQ.org
cI_G_cIII_cytb
Genes: A B A+B
Length: 100 440 519
Sequences: 1241 3168 517
Seq/Len: 12.41 7.2 1
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.02
2 0.00 0.00 0.03
5 0.00 0.00 0.13
10 0.00 0.00 0.17
20 0.00 0.00 0.23
100 0.01 0.00 0.30
∞ 0.02 0.01 0.96
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
60_V 205_I 1.76 0.90 0.31
60_V 113_F 1.47 0.74 0.15
38_M 134_L 1.34 0.65 0.10
65_A 134_L 1.27 0.58 0.08
46_F 369_L 1.24 0.56 0.07
37_I 180_L 1.18 0.50 0.06
98_M 174_E 1.18 0.50 0.06
4_L 375_V 1.16 0.48 0.06
38_M 26_V 1.16 0.48 0.06
16_V 342_V 1.15 0.47 0.05
84_H 284_N 1.13 0.45 0.05
41_A 354_V 1.12 0.44 0.05
38_M 406_I 1.10 0.43 0.05
34_G 57_L 1.09 0.42 0.04
90_L 404_F 1.07 0.40 0.04
65_A 366_W 1.07 0.40 0.04
63_I 34_M 1.04 0.38 0.04
47_V 328_A 1.04 0.37 0.04
35_L 61_T 1.03 0.36 0.04
62_Y 410_L 1.02 0.35 0.03
52_Y 396_G 1.01 0.35 0.03
41_A 71_P 1.00 0.34 0.03
89_N 64_V 1.00 0.34 0.03
11_A 277_P 1.00 0.34 0.03
10_L 344_A 1.00 0.34 0.03
99_R 367_F 1.00 0.34 0.03
87_R 131_V 0.99 0.33 0.03
41_A 411_L 0.98 0.33 0.03
75_I 211_V 0.98 0.32 0.03
52_Y 376_V 0.97 0.32 0.03
99_R 262_V 0.97 0.32 0.03
79_L 42_N 0.97 0.32 0.03
76_G 143_A 0.96 0.31 0.03
89_N 341_L 0.96 0.31 0.03
78_A 269_F 0.95 0.30 0.03
93_D 20_H 0.95 0.30 0.03
46_F 298_F 0.95 0.30 0.03
89_N 93_L 0.94 0.29 0.03
34_G 385_A 0.93 0.28 0.02
19_L 355_R 0.93 0.28 0.02
17_L 44_W 0.92 0.27 0.02
99_R 214_W 0.91 0.27 0.02
80_L 168_A 0.90 0.27 0.02
10_L 244_F 0.90 0.26 0.02
26_R 61_T 0.90 0.26 0.02
73_A 196_S 0.89 0.26 0.02
11_A 414_I 0.89 0.25 0.02
28_L 339_A 0.89 0.25 0.02
27_N 260_L 0.89 0.25 0.02
23_V 258_V 0.89 0.25 0.02
55_Q 93_L 0.88 0.25 0.02
49_A 180_L 0.88 0.25 0.02
33_I 56_V 0.88 0.25 0.02
42_S 260_L 0.88 0.24 0.02
22_L 143_A 0.87 0.24 0.02
86_R 23_L 0.87 0.24 0.02
66_I 356_S 0.87 0.24 0.02
73_A 15_F 0.86 0.24 0.02
96_S 17_R 0.86 0.23 0.02
24_I 105_F 0.85 0.23 0.02
56_T 116_L 0.85 0.23 0.02
41_A 136_Y 0.85 0.23 0.02
19_L 61_T 0.85 0.23 0.02
65_A 83_I 0.84 0.22 0.02
29_L 254_F 0.84 0.22 0.02
32_L 220_G 0.84 0.22 0.02
70_A 356_S 0.84 0.22 0.02
13_I 369_L 0.84 0.22 0.02
46_F 138_M 0.84 0.22 0.02
46_F 328_A 0.83 0.22 0.02
28_L 308_F 0.83 0.22 0.02
33_I 140_M 0.83 0.21 0.01
65_A 105_F 0.82 0.21 0.01
47_V 376_V 0.82 0.21 0.01
47_V 349_L 0.82 0.21 0.01
11_A 338_G 0.81 0.20 0.01
73_A 214_W 0.81 0.20 0.01
34_G 23_L 0.81 0.20 0.01
50_G 77_F 0.81 0.20 0.01
47_V 397_S 0.81 0.20 0.01
85_R 131_V 0.81 0.20 0.01
59_Q 345_L 0.81 0.20 0.01
79_L 300_P 0.80 0.20 0.01
61_M 61_T 0.80 0.20 0.01
3_P 64_V 0.80 0.20 0.01
46_F 131_V 0.80 0.20 0.01
26_R 246_P 0.80 0.20 0.01
13_I 250_I 0.80 0.20 0.01
80_L 192_N 0.80 0.20 0.01
48_V 22_R 0.80 0.20 0.01
68_L 44_W 0.79 0.19 0.01
18_G 183_G 0.78 0.19 0.01
60_V 186_V 0.78 0.18 0.01
47_V 239_K 0.78 0.18 0.01
30_F 341_L 0.77 0.18 0.01
58_G 71_P 0.77 0.18 0.01
2_I 385_A 0.77 0.18 0.01
54_G 290_A 0.77 0.18 0.01
33_I 358_Q 0.77 0.18 0.01
4_L 79_S 0.77 0.18 0.01
79_L 400_W 0.77 0.18 0.01
12_A 414_I 0.77 0.18 0.01
87_R 201_L 0.77 0.18 0.01
11_A 59_I 0.77 0.18 0.01
35_L 227_V 0.77 0.18 0.01
50_G 252_D 0.77 0.18 0.01
29_L 300_P 0.76 0.18 0.01
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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