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OPENSEQ.org
4487
Genes: A B A+B
Length: 93 109 191
Sequences: 4027 2221 925
Seq/Len: 43.3 20.38 4.84
MirrorTree (Pazo et al. 2001) 0.70
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 0.01 0.01 4.58
2 0.02 0.02 4.61
5 0.02 0.03 4.65
10 0.03 0.03 4.65
20 0.04 0.04 4.74
100 0.05 0.06 5.01
∞ 0.11 0.11 6.07
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
19_Y 23_V 2.23 1.00 0.99
10_H 30_G 1.96 1.00 0.98
7_K 33_E 1.94 1.00 0.98
22_A 23_V 1.82 1.00 0.97
16_D 19_V 1.46 0.98 0.91
6_H 29_I 1.45 0.98 0.90
12_E 11_R 1.34 0.96 0.86
79_Y 52_F 1.32 0.96 0.85
16_D 22_R 1.25 0.94 0.81
27_E 27_R 1.19 0.91 0.76
30_E 27_R 1.19 0.91 0.76
19_Y 26_D 1.12 0.88 0.70
58_P 66_W 1.11 0.87 0.69
23_W 30_G 1.01 0.79 0.58
19_Y 22_R 1.00 0.79 0.57
13_W 22_R 0.97 0.76 0.53
46_T 83_K 0.95 0.73 0.51
34_A 34_Y 0.92 0.70 0.47
22_A 40_R 0.91 0.69 0.46
6_H 26_D 0.88 0.65 0.42
53_R 29_I 0.87 0.63 0.40
60_V 10_A 0.85 0.60 0.38
6_H 76_M 0.83 0.58 0.36
12_E 15_T 0.81 0.56 0.34
27_E 30_G 0.81 0.56 0.34
53_R 104_N 0.80 0.54 0.32
40_R 53_E 0.80 0.54 0.32
10_H 33_E 0.80 0.54 0.32
67_N 44_T 0.78 0.52 0.30
40_R 55_R 0.78 0.51 0.29
22_A 93_N 0.78 0.50 0.29
65_E 55_R 0.78 0.50 0.29
23_W 23_V 0.78 0.50 0.29
52_E 34_Y 0.76 0.48 0.27
55_G 21_I 0.75 0.47 0.27
9_L 14_A 0.75 0.46 0.26
34_A 31_K 0.75 0.46 0.26
26_E 24_K 0.75 0.46 0.26
39_W 84_S 0.74 0.46 0.26
6_H 30_G 0.74 0.46 0.26
36_L 66_W 0.74 0.45 0.25
14_M 26_D 0.74 0.45 0.25
55_G 18_P 0.74 0.45 0.25
34_A 35_D 0.72 0.43 0.23
65_E 53_E 0.72 0.42 0.23
38_E 76_M 0.71 0.41 0.22
81_H 16_A 0.71 0.41 0.22
75_T 65_I 0.71 0.41 0.22
21_T 97_K 0.70 0.40 0.21
84_G 61_I 0.70 0.40 0.21
73_I 89_A 0.70 0.40 0.21
13_W 15_T 0.70 0.39 0.21
50_V 12_E 0.69 0.39 0.21
61_I 49_D 0.69 0.38 0.20
31_K 36_A 0.69 0.38 0.20
57_T 76_M 0.69 0.38 0.20
62_S 97_K 0.68 0.38 0.20
48_A 62_A 0.68 0.38 0.20
61_I 20_K 0.68 0.37 0.19
60_V 43_D 0.67 0.36 0.19
64_L 43_D 0.67 0.36 0.19
79_Y 13_E 0.67 0.36 0.18
71_A 66_W 0.67 0.36 0.18
84_G 87_T 0.66 0.34 0.17
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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