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OPENSEQ.org
cI_G_cIII_cyt1_10
Genes: A B A+B
Length: 100 263 344
Sequences: 1241 884 265
Seq/Len: 12.41 3.36 0.77
MirrorTree (Pazo et al. 2001) 0.39
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.01 0.01 0.05
∞ 0.02 0.01 0.73
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
41_A 82_E 1.68 0.81 0.04
87_R 214_A 1.39 0.61 0.02
17_L 236_I 1.38 0.59 0.02
17_L 196_T 1.26 0.49 0.01
17_L 187_A 1.24 0.48 0.01
16_V 131_A 1.24 0.48 0.01
46_F 237_F 1.24 0.48 0.01
89_N 158_L 1.18 0.43 0.01
89_N 249_N 1.18 0.43 0.01
7_G 214_A 1.17 0.42 0.01
28_L 59_S 1.17 0.42 0.01
80_L 84_Q 1.15 0.40 0.01
11_A 205_V 1.14 0.39 0.01
12_A 73_A 1.14 0.39 0.01
96_S 158_L 1.13 0.38 0.01
89_N 33_F 1.08 0.35 0.01
65_A 81_P 1.08 0.35 0.01
20_T 213_A 1.08 0.34 0.01
1_M 49_R 1.06 0.33 0.01
23_V 38_P 1.04 0.32 0.01
56_T 108_T 1.04 0.32 0.01
5_Q 240_V 1.03 0.31 0.01
34_G 86_R 1.03 0.31 0.01
96_S 188_A 1.03 0.31 0.01
38_M 22_S 1.01 0.30 0.01
60_V 254_Q 1.00 0.28 0.01
13_I 243_A 0.99 0.28 0.01
26_R 246_Y 0.99 0.28 0.01
32_L 111_F 0.98 0.28 0.01
46_F 25_A 0.97 0.27 0.01
93_D 101_E 0.97 0.27 0.01
87_R 37_G 0.97 0.27 0.01
52_Y 206_D 0.97 0.27 0.01
61_M 221_E 0.97 0.26 0.01
2_I 65_R 0.96 0.26 0.01
65_A 59_S 0.96 0.26 0.01
47_V 83_D 0.94 0.25 0.01
3_P 195_V 0.94 0.24 0.01
47_V 45_H 0.94 0.24 0.01
13_I 206_D 0.93 0.24 0.01
7_G 243_A 0.93 0.24 0.01
95_V 250_K 0.93 0.24 0.01
34_G 236_I 0.92 0.23 0.01
34_G 178_A 0.92 0.23 0.01
38_M 213_A 0.92 0.23 0.01
47_V 217_M 0.92 0.23 0.01
83_L 42_F 0.90 0.22 0.00
41_A 54_Y 0.90 0.22 0.00
54_G 244_L 0.90 0.22 0.00
11_A 30_D 0.90 0.22 0.00
54_G 223_K 0.89 0.22 0.00
29_L 118_G 0.89 0.22 0.00
10_L 219_T 0.89 0.21 0.00
83_L 55_T 0.88 0.21 0.00
1_M 241_L 0.88 0.21 0.00
35_L 168_E 0.88 0.21 0.00
14_L 141_L 0.87 0.20 0.00
38_M 151_P 0.87 0.20 0.00
6_H 206_D 0.87 0.20 0.00
52_Y 256_I 0.87 0.20 0.00
13_I 16_A 0.87 0.20 0.00
47_V 126_M 0.86 0.20 0.00
35_L 16_A 0.86 0.20 0.00
75_I 182_N 0.86 0.20 0.00
22_L 60_A 0.86 0.20 0.00
87_R 129_A 0.85 0.19 0.00
16_V 76_G 0.85 0.19 0.00
26_R 146_N 0.85 0.19 0.00
83_L 154_I 0.85 0.19 0.00
56_T 229_Q 0.85 0.19 0.00
89_N 137_Y 0.84 0.19 0.00
64_L 235_V 0.84 0.19 0.00
31_M 53_V 0.84 0.19 0.00
12_A 36_E 0.84 0.19 0.00
19_L 229_Q 0.84 0.19 0.00
41_A 215_F 0.84 0.18 0.00
93_D 81_P 0.83 0.18 0.00
6_H 74_D 0.83 0.18 0.00
87_R 35_F 0.83 0.18 0.00
75_I 249_N 0.83 0.18 0.00
65_A 194_Q 0.83 0.18 0.00
60_V 84_Q 0.83 0.18 0.00
11_A 77_G 0.83 0.18 0.00
60_V 216_L 0.82 0.18 0.00
89_N 167_E 0.82 0.18 0.00
54_G 41_K 0.82 0.18 0.00
8_L 240_V 0.82 0.18 0.00
54_G 233_V 0.82 0.17 0.00
75_I 79_Q 0.81 0.17 0.00
46_F 20_G 0.81 0.17 0.00
18_G 200_G 0.81 0.17 0.00
93_D 163_G 0.81 0.17 0.00
99_R 237_F 0.81 0.17 0.00
96_S 177_A 0.81 0.17 0.00
23_V 104_P 0.81 0.17 0.00
29_L 124_S 0.81 0.17 0.00
10_L 73_A 0.81 0.17 0.00
28_L 131_A 0.81 0.17 0.00
88_Q 97_P 0.80 0.17 0.00
34_G 60_A 0.80 0.17 0.00
33_I 256_I 0.80 0.17 0.00
11_A 75_E 0.80 0.17 0.00
82_Q 90_A 0.80 0.17 0.00
34_G 72_L 0.80 0.17 0.00
44_L 184_I 0.80 0.17 0.00
84_H 237_F 0.80 0.17 0.00
17_L 137_Y 0.79 0.16 0.00
46_F 83_D 0.79 0.16 0.00
98_M 140_G 0.79 0.16 0.00
87_R 49_R 0.79 0.16 0.00
82_Q 230_V 0.79 0.16 0.00
73_A 73_A 0.79 0.16 0.00
46_F 164_E 0.79 0.16 0.00
93_D 174_Y 0.79 0.16 0.00
10_L 67_V 0.79 0.16 0.00
98_M 254_Q 0.79 0.16 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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