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OPENSEQ.org
isp_cytb
Genes: A B A+B
Length: 195 440 605
Sequences: 974 3168 532
Seq/Len: 4.99 7.2 0.88
MirrorTree (Pazo et al. 2001) 0.90
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 0.83
2 0.00 0.00 0.84
5 0.01 0.00 0.84
10 0.01 0.00 0.84
20 0.01 0.00 0.84
100 0.01 0.00 0.84
∞ 0.02 0.01 0.85
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
46_Q 64_V 1.83 0.90 0.33
47_M 197_L 1.71 0.85 0.26
20_R 415_E 1.36 0.62 0.10
132_V 137_L 1.35 0.61 0.10
43_L 96_L 1.33 0.59 0.09
47_M 88_N 1.24 0.52 0.07
47_M 64_V 1.18 0.47 0.06
85_R 156_F 1.17 0.46 0.05
77_L 184_P 1.17 0.45 0.05
20_R 197_L 1.14 0.43 0.05
36_A 60_A 1.13 0.42 0.05
38_A 207_A 1.13 0.42 0.04
109_N 327_D 1.10 0.40 0.04
50_S 82_H 1.09 0.39 0.04
147_D 148_V 1.09 0.39 0.04
43_L 383_M 1.08 0.38 0.04
47_M 180_L 1.06 0.36 0.04
52_D 51_L 1.04 0.34 0.03
37_G 106_L 1.03 0.34 0.03
47_M 281_I 1.02 0.33 0.03
194_L 277_P 1.01 0.32 0.03
46_Q 221_N 0.99 0.31 0.03
67_E 242_L 0.98 0.30 0.03
39_A 395_A 0.98 0.30 0.03
33_T 364_K 0.97 0.29 0.03
54_Q 184_P 0.97 0.29 0.03
110_S 304_I 0.97 0.29 0.03
19_T 180_L 0.97 0.29 0.03
172_R 171_G 0.96 0.28 0.02
120_E 256_L 0.95 0.28 0.02
40_A 345_L 0.95 0.28 0.02
183_V 370_L 0.95 0.28 0.02
20_R 75_L 0.94 0.27 0.02
88_E 169_I 0.94 0.27 0.02
71_Q 136_Y 0.94 0.27 0.02
151_D 36_P 0.94 0.27 0.02
60_Q 264_F 0.94 0.27 0.02
67_E 334_I 0.94 0.27 0.02
38_A 138_M 0.93 0.26 0.02
136_V 148_V 0.93 0.26 0.02
28_T 344_A 0.92 0.26 0.02
118_T 78_A 0.92 0.26 0.02
33_T 342_V 0.92 0.25 0.02
148_G 361_P 0.91 0.25 0.02
172_R 352_S 0.91 0.25 0.02
181_I 270_M 0.91 0.25 0.02
81_V 136_Y 0.91 0.24 0.02
52_D 82_H 0.89 0.23 0.02
110_S 335_A 0.89 0.23 0.02
38_A 188_N 0.89 0.23 0.02
50_S 50_V 0.89 0.23 0.02
56_L 184_P 0.88 0.23 0.02
23_F 122_K 0.88 0.23 0.02
47_M 133_M 0.88 0.23 0.02
193_K 59_I 0.88 0.23 0.02
63_V 44_W 0.88 0.23 0.02
73_T 409_P 0.88 0.23 0.02
169_R 271_P 0.88 0.23 0.02
186_F 63_I 0.87 0.22 0.02
183_V 284_N 0.87 0.22 0.02
36_A 256_L 0.87 0.22 0.02
50_S 58_Q 0.86 0.22 0.02
40_A 378_M 0.86 0.22 0.02
51_A 413_I 0.86 0.22 0.02
132_V 413_I 0.86 0.21 0.02
186_F 301_F 0.86 0.21 0.02
136_V 262_V 0.86 0.21 0.01
145_I 408_L 0.86 0.21 0.01
61_V 118_Y 0.85 0.21 0.01
78_G 39_K 0.85 0.21 0.01
34_V 419_A 0.85 0.21 0.01
120_E 74_D 0.85 0.21 0.01
39_A 402_A 0.85 0.21 0.01
79_K 234_K 0.85 0.21 0.01
155_W 412_G 0.84 0.20 0.01
103_I 327_D 0.84 0.20 0.01
33_T 397_S 0.84 0.20 0.01
27_A 419_A 0.84 0.20 0.01
173_G 213_I 0.84 0.20 0.01
86_R 71_P 0.83 0.20 0.01
35_A 343_M 0.83 0.20 0.01
50_S 51_L 0.83 0.20 0.01
178_N 271_P 0.83 0.20 0.01
60_Q 364_K 0.83 0.20 0.01
63_V 71_P 0.83 0.20 0.01
161_G 263_F 0.83 0.20 0.01
40_A 341_L 0.83 0.20 0.01
112_K 367_F 0.83 0.20 0.01
40_A 209_V 0.83 0.20 0.01
36_A 304_I 0.83 0.20 0.01
33_T 178_T 0.82 0.20 0.01
131_L 405_L 0.82 0.20 0.01
82_F 285_P 0.82 0.19 0.01
81_V 286_L 0.82 0.19 0.01
83_I 295_E 0.82 0.19 0.01
35_A 177_Q 0.82 0.19 0.01
132_V 369_L 0.82 0.19 0.01
62_D 384_P 0.81 0.19 0.01
88_E 213_I 0.81 0.19 0.01
194_L 103_L 0.81 0.19 0.01
73_T 30_Y 0.81 0.19 0.01
167_S 339_A 0.81 0.19 0.01
73_T 363_F 0.81 0.19 0.01
109_N 379_W 0.81 0.19 0.01
73_T 186_V 0.81 0.19 0.01
187_L 419_A 0.81 0.18 0.01
17_G 128_T 0.80 0.18 0.01
121_N 189_P 0.80 0.18 0.01
88_E 393_A 0.80 0.18 0.01
79_K 39_K 0.80 0.18 0.01
47_M 186_V 0.80 0.18 0.01
190_T 116_L 0.80 0.18 0.01
178_N 114_R 0.79 0.18 0.01
40_A 351_T 0.79 0.18 0.01
79_K 19_L 0.79 0.18 0.01
94_G 367_F 0.79 0.18 0.01
173_G 363_F 0.79 0.18 0.01
63_V 355_R 0.79 0.18 0.01
60_Q 403_Y 0.79 0.18 0.01
81_V 131_V 0.79 0.17 0.01
150_G 408_L 0.79 0.17 0.01
85_R 133_M 0.79 0.17 0.01
150_G 36_P 0.79 0.17 0.01
143_V 35_I 0.79 0.17 0.01
188_D 235_E 0.79 0.17 0.01
133_M 364_K 0.79 0.17 0.01
88_E 391_Y 0.79 0.17 0.01
74_V 228_E 0.78 0.17 0.01
161_G 181_L 0.78 0.17 0.01
178_N 85_R 0.78 0.17 0.01
16_H 422_Q 0.78 0.17 0.01
25_Y 360_R 0.78 0.17 0.01
92_Q 266_I 0.78 0.17 0.01
156_F 86_D 0.78 0.17 0.01
169_R 114_R 0.78 0.17 0.01
192_I 342_V 0.78 0.17 0.01
181_I 334_I 0.78 0.17 0.01
82_F 278_D 0.77 0.17 0.01
23_F 96_L 0.77 0.17 0.01
86_R 37_T 0.77 0.17 0.01
100_G 267_V 0.77 0.17 0.01
173_G 353_R 0.77 0.17 0.01
44_V 207_A 0.77 0.17 0.01
56_L 176_I 0.77 0.17 0.01
162_S 271_P 0.77 0.17 0.01
191_T 164_G 0.77 0.16 0.01
26_Y 64_V 0.76 0.16 0.01
135_G 179_W 0.76 0.16 0.01
156_F 308_F 0.76 0.16 0.01
38_A 264_F 0.76 0.16 0.01
27_A 344_A 0.76 0.16 0.01
28_T 375_V 0.76 0.16 0.01
87_T 399_Y 0.76 0.16 0.01
169_R 85_R 0.76 0.16 0.01
29_A 308_F 0.76 0.16 0.01
27_A 207_A 0.76 0.16 0.01
47_M 284_N 0.76 0.16 0.01
183_V 131_V 0.76 0.16 0.01
179_L 269_F 0.76 0.16 0.01
91_I 192_N 0.76 0.16 0.01
73_T 249_V 0.76 0.16 0.01
52_D 251_K 0.76 0.16 0.01
184_A 400_W 0.76 0.16 0.01
50_S 208_L 0.75 0.16 0.01
53_V 140_M 0.75 0.16 0.01
97_V 339_A 0.75 0.16 0.01
180_H 376_V 0.75 0.16 0.01
14_G 25_I 0.75 0.16 0.01
44_V 265_A 0.75 0.16 0.01
46_Q 410_L 0.75 0.16 0.01
60_Q 363_F 0.75 0.16 0.01
75_K 142_T 0.75 0.16 0.01
75_K 203_F 0.75 0.15 0.01
189_D 196_S 0.75 0.15 0.01
83_I 186_V 0.75 0.15 0.01
62_D 25_I 0.75 0.15 0.01
172_R 307_A 0.74 0.15 0.01
64_S 169_I 0.74 0.15 0.01
51_A 135_I 0.74 0.15 0.01
119_D 299_L 0.74 0.15 0.01
20_R 72_H 0.74 0.15 0.01
24_L 276_H 0.74 0.15 0.01
119_D 25_I 0.74 0.15 0.01
147_D 27_S 0.74 0.15 0.01
103_I 164_G 0.74 0.15 0.01
129_E 66_V 0.74 0.15 0.01
147_D 36_P 0.74 0.15 0.01
44_V 227_V 0.74 0.15 0.01
191_T 235_E 0.73 0.15 0.01
147_D 341_L 0.73 0.15 0.01
67_E 57_L 0.73 0.15 0.01
191_T 172_V 0.73 0.15 0.01
36_A 205_I 0.73 0.15 0.01
53_V 82_H 0.73 0.15 0.01
72_L 237_A 0.73 0.15 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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