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OPENSEQ.org
ntran ccmCD
Genes: A B A+B
Length: 37 208 243
Sequences: 765 903 529
Seq/Len: 20.68 4.34 2.18
MirrorTree (Pazo et al. 2001) 0.56
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 2.16
2 0.00 0.00 2.16
5 0.00 0.00 2.16
10 0.00 0.00 2.16
20 0.01 0.01 2.16
100 0.01 0.01 2.16
∞ 0.02 0.02 2.20
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
18_P 83_V 2.90 1.00 1.00
4_Y 99_M 2.63 1.00 1.00
22_L 83_V 1.61 0.95 0.90
10_L 94_A 1.47 0.91 0.84
7_F 103_W 1.33 0.85 0.75
4_Y 33_N 1.33 0.85 0.74
14_M 90_V 1.32 0.84 0.73
33_I 204_N 1.30 0.83 0.72
15_T 40_L 1.24 0.78 0.66
11_A 91_T 1.17 0.72 0.58
12_V 181_S 1.16 0.72 0.58
14_M 59_A 1.14 0.70 0.56
23_V 12_V 1.00 0.55 0.39
12_V 40_L 0.98 0.53 0.38
36_G 66_Q 0.93 0.46 0.31
1_M 179_M 0.92 0.46 0.30
34_L 86_F 0.92 0.46 0.30
12_V 22_F 0.92 0.46 0.30
28_M 185_W 0.92 0.46 0.30
4_Y 155_H 0.91 0.45 0.30
22_L 80_I 0.89 0.42 0.27
18_P 27_A 0.89 0.42 0.27
15_T 190_F 0.86 0.40 0.25
13_V 205_L 0.85 0.38 0.23
19_L 193_L 0.85 0.38 0.23
30_H 86_F 0.85 0.38 0.23
14_M 86_F 0.85 0.38 0.23
8_V 132_D 0.84 0.38 0.23
6_F 87_I 0.84 0.37 0.22
23_V 197_L 0.84 0.37 0.22
4_Y 51_I 0.83 0.36 0.22
24_V 9_A 0.80 0.33 0.19
13_V 93_S 0.79 0.32 0.18
35_R 9_A 0.78 0.31 0.17
11_A 94_A 0.78 0.31 0.17
22_L 66_Q 0.78 0.31 0.17
32_A 138_R 0.78 0.30 0.17
26_S 197_L 0.77 0.30 0.17
7_F 202_M 0.77 0.29 0.16
11_A 131_D 0.77 0.29 0.16
7_F 134_R 0.76 0.29 0.16
31_R 6_L 0.75 0.28 0.15
26_S 204_N 0.75 0.28 0.15
15_T 85_T 0.75 0.28 0.15
7_F 40_L 0.74 0.27 0.14
2_G 146_I 0.74 0.27 0.14
1_M 108_A 0.74 0.27 0.14
24_V 115_V 0.73 0.26 0.14
29_Q 128_H 0.72 0.26 0.13
26_S 87_I 0.72 0.25 0.13
9_W 52_Y 0.72 0.25 0.13
26_S 22_F 0.72 0.25 0.13
18_P 77_M 0.72 0.25 0.13
30_H 117_L 0.71 0.25 0.13
27_V 207_L 0.71 0.25 0.13
20_V 129_A 0.71 0.24 0.12
2_G 110_L 0.70 0.24 0.12
4_Y 167_G 0.70 0.24 0.12
3_G 179_M 0.70 0.24 0.12
1_M 61_I 0.70 0.23 0.12
12_V 72_L 0.69 0.23 0.11
34_L 102_T 0.69 0.23 0.11
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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