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OPENSEQ.org
cI_F_cIII_cytb
Genes: A B A+B
Length: 184 440 595
Sequences: 2037 3168 678
Seq/Len: 11.07 7.2 1.14
MirrorTree (Pazo et al. 2001) 0.63
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 0.04
2 0.00 0.00 0.08
5 0.00 0.00 0.22
10 0.00 0.00 0.32
20 0.00 0.00 0.37
100 0.01 0.00 0.45
∞ 0.02 0.01 1.09
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
13_I 204_V 1.49 0.80 0.04
40_S 414_I 1.42 0.74 0.03
63_I 331_F 1.30 0.65 0.02
130_G 121_Y 1.27 0.62 0.02
20_I 29_V 1.18 0.54 0.01
37_L 42_N 1.18 0.54 0.01
71_V 113_F 1.17 0.53 0.01
3_F 267_V 1.16 0.52 0.01
106_V 242_L 1.15 0.51 0.01
73_M 356_S 1.13 0.49 0.01
99_L 269_F 1.13 0.49 0.01
54_L 189_P 1.05 0.42 0.01
96_P 186_V 1.02 0.39 0.01
129_V 61_T 1.02 0.39 0.01
56_I 308_F 1.01 0.38 0.01
120_D 372_V 1.01 0.38 0.01
31_Y 286_L 1.01 0.38 0.01
151_G 361_P 1.00 0.38 0.01
35_S 394_L 1.00 0.37 0.01
25_P 396_G 1.00 0.37 0.01
153_V 258_V 0.99 0.37 0.01
154_V 200_L 0.99 0.36 0.01
53_A 374_F 0.99 0.36 0.01
134_F 216_F 0.99 0.36 0.01
51_A 207_A 0.98 0.36 0.01
72_M 150_P 0.98 0.35 0.01
56_I 143_A 0.98 0.35 0.01
30_L 266_I 0.98 0.35 0.01
56_I 392_I 0.97 0.35 0.01
40_S 122_K 0.97 0.35 0.01
63_I 75_L 0.97 0.34 0.01
55_E 367_F 0.96 0.34 0.01
147_L 307_A 0.96 0.33 0.01
79_S 243_P 0.95 0.33 0.01
51_A 376_V 0.95 0.33 0.01
103_M 364_K 0.95 0.33 0.01
133_L 110_I 0.94 0.32 0.01
91_Q 138_M 0.94 0.32 0.01
16_T 59_I 0.93 0.31 0.01
63_I 215_A 0.93 0.31 0.01
153_V 110_I 0.93 0.31 0.01
9_G 176_I 0.92 0.30 0.01
167_V 277_P 0.92 0.30 0.01
157_H 418_D 0.92 0.30 0.01
13_I 179_W 0.91 0.30 0.01
65_V 284_N 0.91 0.30 0.01
104_L 334_I 0.91 0.29 0.01
137_Y 121_Y 0.91 0.29 0.01
132_T 392_I 0.91 0.29 0.01
65_V 172_V 0.90 0.28 0.01
46_L 71_P 0.89 0.28 0.01
141_V 251_K 0.89 0.28 0.01
36_L 224_P 0.89 0.28 0.01
40_S 39_K 0.89 0.27 0.01
4_A 64_V 0.88 0.27 0.01
12_A 282_E 0.88 0.27 0.01
65_V 171_G 0.87 0.26 0.01
71_V 396_G 0.86 0.26 0.01
2_E 290_A 0.86 0.26 0.01
80_E 138_M 0.86 0.26 0.01
128_A 61_T 0.86 0.26 0.01
21_T 96_L 0.86 0.26 0.01
45_S 84_M 0.86 0.26 0.01
65_V 72_H 0.86 0.25 0.01
83_Q 282_E 0.85 0.25 0.01
7_I 14_G 0.85 0.25 0.01
141_V 399_Y 0.85 0.25 0.01
129_V 388_I 0.85 0.25 0.01
16_T 237_A 0.85 0.25 0.01
23_T 246_P 0.84 0.24 0.01
13_I 244_F 0.84 0.24 0.01
44_F 214_W 0.84 0.24 0.01
153_V 60_A 0.84 0.24 0.01
106_V 371_A 0.84 0.24 0.01
64_M 280_Y 0.84 0.24 0.01
31_Y 32_T 0.84 0.24 0.01
28_A 204_V 0.84 0.24 0.01
111_I 136_Y 0.84 0.24 0.01
28_A 56_V 0.83 0.24 0.01
173_D 392_I 0.83 0.24 0.01
10_L 172_V 0.83 0.23 0.01
100_S 380_V 0.83 0.23 0.01
143_L 63_I 0.83 0.23 0.01
147_L 258_V 0.82 0.23 0.01
20_I 200_L 0.82 0.23 0.01
51_A 343_M 0.82 0.23 0.01
47_G 407_I 0.82 0.23 0.01
100_S 57_L 0.82 0.23 0.01
73_M 139_M 0.81 0.22 0.01
29_L 380_V 0.81 0.22 0.01
52_G 248_F 0.81 0.22 0.01
58_V 402_A 0.81 0.22 0.01
36_L 271_P 0.81 0.22 0.01
38_A 167_G 0.81 0.22 0.01
151_G 397_S 0.81 0.22 0.01
54_L 175_A 0.81 0.22 0.01
18_R 395_A 0.81 0.22 0.01
87_W 363_F 0.80 0.22 0.01
15_A 364_K 0.80 0.21 0.00
170_N 383_M 0.80 0.21 0.00
129_V 238_K 0.80 0.21 0.00
136_P 164_G 0.80 0.21 0.00
29_L 139_M 0.80 0.21 0.00
49_Y 151_W 0.80 0.21 0.00
71_V 276_H 0.80 0.21 0.00
50_F 372_V 0.79 0.21 0.00
22_H 284_N 0.79 0.21 0.00
3_F 135_I 0.79 0.21 0.00
75_N 277_P 0.79 0.21 0.00
19_V 59_I 0.79 0.21 0.00
49_Y 400_W 0.79 0.21 0.00
48_A 39_K 0.79 0.21 0.00
102_I 197_L 0.79 0.21 0.00
140_A 46_I 0.79 0.21 0.00
142_E 23_L 0.79 0.21 0.00
65_V 20_H 0.79 0.20 0.00
46_L 369_L 0.78 0.20 0.00
42_V 337_F 0.78 0.20 0.00
31_Y 300_P 0.78 0.20 0.00
113_G 180_L 0.78 0.20 0.00
31_Y 35_I 0.78 0.20 0.00
113_G 19_L 0.78 0.20 0.00
91_Q 375_V 0.77 0.20 0.00
45_S 344_A 0.77 0.20 0.00
19_V 392_I 0.77 0.20 0.00
153_V 331_F 0.77 0.20 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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