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OPENSEQ.org
6180
Genes: A B A+B
Length: 96 103 197
Sequences: 2766 804 391
Seq/Len: 28.81 7.81 1.98
MirrorTree (Pazo et al. 2001) 0.61
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 0.00 1.96
2 0.01 0.00 1.98
5 0.02 0.01 1.99
10 0.03 0.01 2.00
20 0.03 0.01 2.01
100 0.04 0.03 2.07
∞ 0.10 0.07 2.39
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
10_T 99_L 2.00 0.99 0.96
15_Q 7_E 1.61 0.94 0.85
3_K 92_E 1.48 0.90 0.77
12_S 78_L 1.44 0.88 0.74
47_S 45_L 1.39 0.86 0.70
63_R 46_R 1.36 0.84 0.67
13_M 100_N 1.24 0.76 0.55
61_T 46_R 1.23 0.75 0.54
8_R 11_E 1.20 0.73 0.52
47_S 70_K 1.19 0.71 0.50
26_P 89_S 1.15 0.68 0.46
12_S 8_I 1.15 0.68 0.46
39_E 51_V 1.14 0.67 0.45
5_L 80_Y 1.13 0.66 0.44
20_I 73_E 1.12 0.65 0.42
61_T 45_L 1.09 0.62 0.40
64_N 65_Y 1.08 0.61 0.39
70_R 74_I 1.07 0.60 0.37
10_T 95_M 1.07 0.60 0.37
45_G 29_L 1.06 0.58 0.36
79_L 87_D 1.04 0.56 0.34
19_I 14_Q 1.00 0.53 0.30
67_Q 46_R 0.99 0.51 0.29
49_S 27_F 0.98 0.50 0.28
2_D 84_I 0.98 0.49 0.28
68_G 78_L 0.97 0.49 0.28
19_I 4_I 0.95 0.46 0.25
47_S 19_D 0.95 0.46 0.25
51_F 24_R 0.93 0.45 0.24
61_T 33_P 0.93 0.44 0.23
31_E 2_L 0.92 0.44 0.23
31_E 10_T 0.91 0.42 0.22
62_L 65_Y 0.91 0.42 0.22
90_V 14_Q 0.91 0.42 0.22
7_E 88_L 0.90 0.41 0.21
10_T 40_P 0.89 0.40 0.20
77_K 17_L 0.88 0.39 0.20
14_A 34_D 0.88 0.39 0.19
11_H 11_E 0.88 0.39 0.19
9_L 89_S 0.87 0.38 0.19
6_F 64_I 0.87 0.38 0.18
70_R 77_L 0.87 0.38 0.18
11_H 7_E 0.86 0.36 0.17
48_Q 40_P 0.85 0.36 0.17
78_A 96_L 0.85 0.35 0.17
87_P 96_L 0.84 0.35 0.17
38_K 53_G 0.84 0.35 0.16
64_N 45_L 0.84 0.35 0.16
70_R 13_V 0.84 0.34 0.16
15_Q 90_P 0.83 0.34 0.16
14_A 7_E 0.83 0.34 0.16
58_S 75_R 0.83 0.34 0.16
61_T 38_V 0.82 0.33 0.15
39_E 20_D 0.82 0.32 0.15
67_Q 67_H 0.81 0.32 0.15
25_Q 83_G 0.81 0.32 0.14
2_D 58_R 0.81 0.32 0.14
8_R 99_L 0.81 0.31 0.14
62_L 22_F 0.81 0.31 0.14
63_R 29_L 0.80 0.31 0.14
73_T 30_A 0.80 0.31 0.14
74_G 8_I 0.79 0.30 0.13
23_T 58_R 0.79 0.30 0.13
19_I 75_R 0.79 0.30 0.13
59_V 37_E 0.79 0.30 0.13
15_Q 75_R 0.79 0.29 0.13
78_A 9_F 0.79 0.29 0.13
21_E 41_E 0.79 0.29 0.13
8_R 83_G 0.79 0.29 0.13
75_P 58_R 0.78 0.29 0.12
31_E 57_K 0.77 0.28 0.12
47_S 9_F 0.77 0.28 0.12
86_D 19_D 0.77 0.28 0.12
45_G 61_V 0.77 0.28 0.12
48_Q 93_K 0.77 0.28 0.12
45_G 55_K 0.76 0.28 0.12
11_H 27_F 0.76 0.27 0.12
16_M 18_T 0.76 0.27 0.11
54_L 97_R 0.76 0.27 0.11
8_R 12_D 0.76 0.27 0.11
45_G 7_E 0.76 0.27 0.11
25_Q 14_Q 0.76 0.27 0.11
13_M 85_K 0.75 0.27 0.11
50_K 96_L 0.75 0.26 0.11
22_G 46_R 0.75 0.26 0.11
20_I 75_R 0.75 0.26 0.11
47_S 23_S 0.75 0.26 0.11
26_P 45_L 0.74 0.26 0.10
11_H 87_D 0.74 0.25 0.10
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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