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OPENSEQ.org
fdxisca
Genes: A B A+B
Length: 111 107 217
Sequences: 5163 3152 332
Seq/Len: 46.51 29.46 1.53
MirrorTree (Pazo et al. 2001) 0.87
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 0.02 0.00 0.22
2 0.04 0.00 0.34
5 0.05 0.01 1.52
10 0.05 0.01 1.68
20 0.06 0.02 1.87
100 0.08 0.03 2.79
∞ 0.13 0.08 6.58
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
31_A 41_V 1.41 0.82 0.07
100_I 71_F 1.37 0.79 0.06
6_I 41_V 1.35 0.78 0.06
2_P 17_L 1.28 0.72 0.05
65_S 3_I 1.26 0.71 0.05
97_V 103_E 1.26 0.70 0.05
35_G 27_R 1.11 0.56 0.03
67_E 26_L 1.09 0.54 0.03
21_A 75_T 1.08 0.53 0.03
12_L 79_F 1.07 0.52 0.03
35_G 11_A 1.07 0.52 0.03
55_V 62_V 1.07 0.52 0.03
109_R 5_L 1.05 0.50 0.02
45_S 26_L 1.04 0.49 0.02
45_S 33_S 1.04 0.49 0.02
3_K 63_V 1.02 0.47 0.02
27_I 7_D 1.01 0.45 0.02
91_V 44_F 1.00 0.44 0.02
80_E 28_L 0.99 0.44 0.02
66_S 51_E 0.99 0.43 0.02
94_E 63_V 0.98 0.43 0.02
20_E 106_H 0.98 0.42 0.02
29_D 95_V 0.96 0.41 0.02
90_R 58_K 0.95 0.40 0.02
24_G 82_E 0.94 0.39 0.02
19_L 70_Q 0.94 0.38 0.02
36_I 64_V 0.93 0.38 0.02
44_K 12_R 0.92 0.37 0.02
3_K 91_T 0.92 0.36 0.01
68_Q 97_D 0.92 0.36 0.01
88_Q 71_F 0.91 0.36 0.01
67_E 64_V 0.89 0.34 0.01
63_P 49_T 0.89 0.34 0.01
5_V 89_K 0.88 0.32 0.01
37_E 106_H 0.88 0.32 0.01
60_D 6_S 0.87 0.32 0.01
25_E 59_G 0.87 0.32 0.01
62_L 64_V 0.86 0.31 0.01
31_A 58_K 0.86 0.31 0.01
46_C 77_L 0.85 0.30 0.01
11_D 73_D 0.85 0.30 0.01
90_R 26_L 0.84 0.29 0.01
31_A 63_V 0.83 0.29 0.01
5_V 80_V 0.83 0.29 0.01
28_L 66_G 0.83 0.28 0.01
72_M 14_N 0.83 0.28 0.01
107_H 63_V 0.83 0.28 0.01
53_C 58_K 0.82 0.28 0.01
64_E 63_V 0.82 0.28 0.01
18_V 106_H 0.82 0.28 0.01
31_A 42_L 0.82 0.28 0.01
11_D 18_A 0.82 0.27 0.01
54_I 31_R 0.81 0.27 0.01
41_A 46_D 0.81 0.27 0.01
31_A 57_D 0.81 0.27 0.01
102_R 72_L 0.81 0.27 0.01
54_I 95_V 0.81 0.27 0.01
107_H 56_E 0.81 0.27 0.01
75_K 106_H 0.81 0.26 0.01
55_V 100_G 0.80 0.26 0.01
77_W 86_E 0.80 0.26 0.01
28_L 30_V 0.79 0.25 0.01
29_D 12_R 0.79 0.25 0.01
37_E 62_V 0.78 0.25 0.01
68_Q 98_E 0.78 0.25 0.01
57_E 1_M 0.78 0.25 0.01
3_K 31_R 0.78 0.24 0.01
63_P 18_A 0.78 0.24 0.01
11_D 13_V 0.78 0.24 0.01
80_E 95_V 0.77 0.24 0.01
43_E 39_A 0.77 0.24 0.01
21_A 12_R 0.77 0.24 0.01
105_I 16_F 0.76 0.23 0.01
64_E 45_V 0.76 0.23 0.01
56_R 44_F 0.76 0.23 0.01
8_P 83_G 0.76 0.23 0.01
30_V 15_T 0.76 0.23 0.01
26_T 39_A 0.76 0.23 0.01
28_L 63_V 0.75 0.22 0.01
80_E 98_E 0.75 0.22 0.01
17_A 4_T 0.75 0.22 0.01
10_Q 24_F 0.74 0.22 0.01
3_K 81_K 0.74 0.22 0.01
25_E 47_E 0.74 0.22 0.01
29_D 51_E 0.74 0.21 0.01
12_L 70_Q 0.74 0.21 0.01
55_V 4_T 0.74 0.21 0.01
67_E 97_D 0.74 0.21 0.01
108_A 56_E 0.73 0.21 0.01
10_Q 48_P 0.73 0.21 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)
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