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OPENSEQ.org
ccmCD
Genes: A B A+B
Length: 69 245 308
Sequences: 208 5196 145
Seq/Len: 3.01 21.21 0.47
MirrorTree (Pazo et al. 2001) 0.17
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 0.45
2 0.00 0.02 0.46
5 0.00 0.50 0.46
10 0.00 0.51 0.46
20 0.00 0.51 0.46
100 0.00 0.51 0.46
∞ 0.04 0.53 0.47
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
47_L 239_I 2.56 0.97 0.92
46_I 221_M 1.73 0.70 0.45
25_V 200_S 1.56 0.59 0.31
46_I 212_L 1.39 0.46 0.19
35_L 121_T 1.36 0.44 0.17
25_V 41_F 1.34 0.42 0.16
50_V 87_K 1.32 0.41 0.15
4_A 152_R 1.28 0.38 0.13
24_A 150_D 1.28 0.38 0.13
31_P 105_F 1.25 0.35 0.11
61_R 59_L 1.17 0.30 0.08
17_Y 118_M 1.17 0.30 0.08
23_L 113_A 1.14 0.28 0.07
55_A 196_P 1.14 0.28 0.07
60_L 231_R 1.11 0.27 0.07
46_I 223_N 1.08 0.25 0.06
18_A 81_G 1.08 0.25 0.06
59_R 40_G 1.07 0.24 0.06
35_L 216_L 1.07 0.24 0.06
43_H 144_A 1.06 0.24 0.06
4_A 228_M 1.06 0.24 0.05
31_P 170_L 1.06 0.24 0.05
4_A 52_N 1.05 0.23 0.05
1_M 210_L 1.05 0.23 0.05
18_A 13_R 1.05 0.23 0.05
57_E 162_L 1.05 0.23 0.05
39_S 219_M 1.04 0.23 0.05
50_V 93_V 1.04 0.23 0.05
62_A 239_I 1.03 0.22 0.05
4_A 8_L 1.03 0.22 0.05
53_Q 161_I 1.02 0.22 0.05
38_H 155_A 1.02 0.22 0.04
26_V 210_L 1.02 0.22 0.04
57_E 226_L 1.02 0.22 0.04
42_Q 87_K 1.01 0.21 0.04
26_V 8_L 1.01 0.21 0.04
46_I 90_N 1.01 0.21 0.04
18_A 150_D 1.00 0.21 0.04
38_H 11_P 1.00 0.21 0.04
57_E 236_S 1.00 0.21 0.04
39_S 154_L 0.99 0.20 0.04
51_A 230_K 0.99 0.20 0.04
18_A 225_I 0.99 0.20 0.04
18_A 160_G 0.98 0.20 0.04
35_L 63_A 0.97 0.19 0.04
36_V 121_T 0.97 0.19 0.04
8_W 99_I 0.96 0.19 0.04
39_S 157_R 0.96 0.19 0.04
40_V 237_E 0.96 0.19 0.04
60_L 59_L 0.96 0.19 0.03
64_Q 29_S 0.96 0.19 0.03
62_A 227_L 0.95 0.18 0.03
34_V 157_R 0.95 0.18 0.03
27_M 113_A 0.95 0.18 0.03
50_V 208_G 0.95 0.18 0.03
59_R 202_L 0.95 0.18 0.03
12_F 207_F 0.94 0.18 0.03
62_A 81_G 0.94 0.18 0.03
24_A 92_A 0.94 0.18 0.03
65_Q 87_K 0.94 0.18 0.03
48_R 99_I 0.94 0.18 0.03
61_R 204_W 0.93 0.17 0.03
28_T 80_I 0.93 0.17 0.03
53_Q 90_N 0.92 0.17 0.03
63_A 148_A 0.92 0.17 0.03
43_H 25_L 0.91 0.17 0.03
26_V 236_S 0.91 0.17 0.03
20_F 168_V 0.90 0.16 0.03
53_Q 195_D 0.89 0.16 0.02
46_I 174_H 0.88 0.15 0.02
8_W 205_S 0.88 0.15 0.02
52_Q 57_I 0.88 0.15 0.02
52_Q 189_R 0.87 0.15 0.02
28_T 193_S 0.86 0.15 0.02
27_M 105_F 0.85 0.14 0.02
32_L 212_L 0.85 0.14 0.02
43_H 82_L 0.85 0.14 0.02
61_R 168_V 0.85 0.14 0.02
42_Q 8_L 0.85 0.14 0.02
53_Q 93_V 0.84 0.14 0.02
1_M 33_L 0.84 0.14 0.02
43_H 238_L 0.84 0.14 0.02
50_V 46_A 0.83 0.14 0.02
9_N 92_A 0.83 0.14 0.02
61_R 13_R 0.83 0.14 0.02
60_L 10_I 0.83 0.14 0.02
43_H 153_R 0.83 0.14 0.02
63_A 25_L 0.83 0.14 0.02
64_Q 10_I 0.83 0.14 0.02
36_V 154_L 0.83 0.13 0.02
9_N 27_I 0.83 0.13 0.02
44_R 157_R 0.82 0.13 0.02
19_F 82_L 0.82 0.13 0.02
54_R 160_G 0.82 0.13 0.02
26_V 41_F 0.82 0.13 0.02
52_Q 80_I 0.82 0.13 0.02
57_E 227_L 0.81 0.13 0.02
35_L 155_A 0.81 0.13 0.02
67_E 160_G 0.81 0.13 0.02
29_V 38_I 0.81 0.13 0.02
36_V 212_L 0.80 0.13 0.02
64_Q 65_I 0.80 0.13 0.02
45_A 80_I 0.80 0.12 0.02
49_G 22_I 0.80 0.12 0.02
18_A 208_G 0.80 0.12 0.02
62_A 8_L 0.80 0.12 0.02
2_T 170_L 0.80 0.12 0.01
54_R 144_A 0.80 0.12 0.01
25_V 210_L 0.79 0.12 0.01
6_A 206_I 0.79 0.12 0.01
27_M 73_S 0.79 0.12 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.51 > 0.4) of paralogs.
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