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OPENSEQ.org
Ftype_a_trunc_c_trunc
Genes: A B A+B
Length: 79 31 108
Sequences: 2973 95 150
Seq/Len: 37.63 3.06 1.39
MirrorTree (Pazo et al. 2001) 0.62
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 0.25
2 0.00 0.01 0.45
5 0.00 0.01 0.80
10 0.00 0.01 1.18
20 0.00 0.01 1.36
100 0.00 0.01 1.45
∞ 0.00 0.01 1.44
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
22_L 22_C 1.78 0.94 0.69
73_L 18_M 1.47 0.83 0.42
68_T 26_A 1.22 0.64 0.22
29_G 31_F 1.21 0.63 0.21
76_H 29_I 1.20 0.62 0.21
51_L 6_S 1.20 0.61 0.21
5_Q 1_K 1.19 0.61 0.20
11_V 3_Q 1.11 0.54 0.16
75_L 31_F 1.11 0.54 0.16
76_H 15_S 1.09 0.51 0.15
68_T 25_V 1.09 0.51 0.14
37_I 8_A 1.06 0.48 0.13
69_L 2_Q 1.06 0.48 0.13
22_L 19_G 1.05 0.47 0.13
52_L 22_C 1.05 0.47 0.13
71_V 6_S 1.05 0.47 0.12
26_L 3_Q 1.04 0.46 0.12
19_A 8_A 1.02 0.44 0.11
34_L 25_V 1.02 0.44 0.11
49_L 1_K 1.01 0.43 0.11
8_A 8_A 0.99 0.41 0.10
36_S 25_V 0.98 0.40 0.10
18_T 31_F 0.96 0.38 0.09
73_L 31_F 0.95 0.37 0.09
28_G 31_F 0.92 0.35 0.08
65_Y 14_L 0.92 0.34 0.07
23_L 24_M 0.92 0.34 0.07
59_V 19_G 0.91 0.34 0.07
55_L 24_M 0.91 0.33 0.07
47_T 4_L 0.91 0.33 0.07
55_L 4_L 0.90 0.32 0.07
66_V 27_F 0.88 0.31 0.06
28_G 19_G 0.85 0.28 0.06
48_I 7_Y 0.85 0.28 0.05
4_I 24_M 0.84 0.28 0.05
13_L 27_F 0.84 0.27 0.05
62_I 15_S 0.83 0.27 0.05
7_M 4_L 0.82 0.26 0.05
72_S 14_L 0.82 0.26 0.05
23_L 4_L 0.82 0.26 0.05
43_L 22_C 0.81 0.25 0.05
70_L 27_F 0.81 0.25 0.05
39_T 31_F 0.79 0.23 0.04
75_L 25_V 0.78 0.23 0.04
38_S 14_L 0.78 0.23 0.04
58_A 15_S 0.78 0.23 0.04
26_L 7_Y 0.77 0.22 0.04
27_I 24_M 0.77 0.22 0.04
4_I 18_M 0.76 0.22 0.04
23_L 30_L 0.76 0.22 0.04
61_M 25_V 0.76 0.21 0.04
67_F 7_Y 0.76 0.21 0.04
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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