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OPENSEQ.org
cI_Bcterm_cIII_cytb
Genes: A B A+B
Length: 170 440 550
Sequences: 4897 3168 2023
Seq/Len: 28.81 7.2 3.68
MirrorTree (Pazo et al. 2001) 0.79
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 0.29
2 0.00 0.00 2.13
5 0.01 0.00 2.23
10 0.01 0.00 2.37
20 0.01 0.00 2.49
100 0.01 0.00 2.57
∞ 0.03 0.01 3.32
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
128_I 207_A 1.37 0.94 0.55
145_N 293_V 1.21 0.88 0.41
151_Y 59_I 1.20 0.87 0.40
161_V 375_V 1.17 0.85 0.37
146_G 213_I 1.13 0.83 0.34
161_V 395_A 1.11 0.82 0.32
148_L 356_S 1.02 0.73 0.25
99_D 88_N 1.02 0.73 0.24
60_V 53_F 1.00 0.71 0.23
145_N 106_L 1.00 0.71 0.23
66_A 26_V 0.97 0.68 0.21
22_T 171_G 0.97 0.67 0.21
64_L 342_V 0.96 0.66 0.20
125_M 172_V 0.96 0.66 0.20
21_S 407_I 0.96 0.66 0.20
15_I 88_N 0.94 0.64 0.19
99_D 81_E 0.93 0.63 0.18
11_S 352_S 0.93 0.62 0.18
154_S 172_V 0.93 0.62 0.18
66_A 395_A 0.92 0.61 0.18
57_V 189_P 0.91 0.60 0.17
42_L 342_V 0.91 0.60 0.17
32_L 327_D 0.90 0.58 0.16
159_A 186_V 0.88 0.56 0.15
145_N 174_E 0.88 0.56 0.15
141_L 131_V 0.88 0.56 0.15
125_M 213_I 0.86 0.54 0.14
143_S 108_V 0.86 0.54 0.14
113_I 41_L 0.86 0.54 0.14
86_R 29_V 0.86 0.54 0.14
105_V 398_A 0.86 0.53 0.14
9_T 93_L 0.85 0.53 0.14
24_V 243_P 0.85 0.53 0.14
21_S 58_Q 0.85 0.52 0.13
158_G 22_R 0.85 0.52 0.13
36_L 344_A 0.84 0.51 0.13
160_V 180_L 0.84 0.51 0.13
60_V 258_V 0.83 0.50 0.13
148_L 364_K 0.83 0.50 0.12
78_S 376_V 0.83 0.50 0.12
122_L 103_L 0.83 0.50 0.12
126_M 272_N 0.83 0.50 0.12
141_L 256_L 0.82 0.49 0.12
58_A 54_C 0.82 0.49 0.12
143_S 404_F 0.82 0.48 0.12
50_L 411_L 0.82 0.48 0.12
156_S 50_V 0.82 0.48 0.12
27_L 362_L 0.81 0.47 0.12
66_A 218_T 0.81 0.47 0.12
69_W 268_G 0.81 0.47 0.12
26_A 95_Y 0.81 0.47 0.11
26_A 264_F 0.81 0.47 0.11
8_V 172_V 0.81 0.46 0.11
138_K 278_D 0.80 0.46 0.11
159_A 207_A 0.80 0.46 0.11
59_V 389_Y 0.80 0.46 0.11
36_L 389_Y 0.80 0.45 0.11
51_E 21_R 0.79 0.45 0.11
60_V 405_L 0.79 0.44 0.10
99_D 124_P 0.79 0.44 0.10
95_A 246_P 0.79 0.44 0.10
141_L 383_M 0.78 0.44 0.10
152_V 95_Y 0.78 0.44 0.10
165_L 406_I 0.78 0.44 0.10
19_I 174_E 0.78 0.43 0.10
89_S 356_S 0.78 0.43 0.10
96_W 93_L 0.78 0.43 0.10
104_K 205_I 0.78 0.43 0.10
20_L 255_A 0.78 0.43 0.10
160_V 103_L 0.78 0.43 0.10
8_V 345_L 0.77 0.42 0.10
45_G 176_I 0.77 0.42 0.10
124_S 211_V 0.77 0.42 0.10
8_V 171_G 0.77 0.41 0.10
65_A 38_P 0.76 0.41 0.09
10_H 364_K 0.76 0.40 0.09
38_Q 51_L 0.76 0.40 0.09
74_T 375_V 0.76 0.40 0.09
101_L 369_L 0.76 0.40 0.09
116_L 334_I 0.76 0.40 0.09
72_K 392_I 0.76 0.40 0.09
3_H 145_M 0.76 0.40 0.09
2_A 64_V 0.75 0.40 0.09
153_A 287_V 0.75 0.40 0.09
145_N 344_A 0.75 0.40 0.09
153_A 108_V 0.75 0.40 0.09
154_S 25_I 0.75 0.40 0.09
133_S 207_A 0.75 0.40 0.09
123_N 22_R 0.75 0.40 0.09
46_S 136_Y 0.75 0.39 0.09
67_W 75_L 0.75 0.39 0.09
147_Y 207_A 0.75 0.39 0.09
63_L 345_L 0.75 0.39 0.09
16_V 345_L 0.75 0.39 0.09
23_F 341_L 0.75 0.39 0.09
97_G 361_P 0.74 0.39 0.09
95_A 93_L 0.74 0.39 0.09
122_L 363_F 0.74 0.39 0.09
122_L 222_N 0.74 0.39 0.09
59_V 237_A 0.74 0.39 0.09
102_Y 43_W 0.74 0.38 0.09
49_T 265_A 0.74 0.38 0.09
99_D 276_H 0.74 0.38 0.09
155_M 204_V 0.74 0.38 0.09
134_R 209_V 0.74 0.38 0.08
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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