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OPENSEQ.org
frxiscR
Genes: A B A+B
Length: 111 162 263
Sequences: 1735 5205 271
Seq/Len: 15.63 32.13 1.03
MirrorTree (Pazo et al. 2001) 0.83
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 0.01
2 0.01 0.01 0.03
5 0.01 0.01 0.10
10 0.01 0.02 0.99
20 0.01 0.02 1.03
100 0.01 0.03 1.28
∞ 0.03 0.10 2.60
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 9_Y 2.31 0.99 0.95
31_A 79_V 1.70 0.88 0.72
68_Q 86_S 1.48 0.76 0.53
6_I 9_Y 1.46 0.75 0.52
5_V 54_L 1.40 0.70 0.45
68_Q 124_I 1.32 0.64 0.38
22_N 22_E 1.32 0.64 0.37
28_L 5_S 1.32 0.64 0.37
64_E 141_R 1.32 0.63 0.37
59_F 76_V 1.32 0.63 0.37
22_N 69_K 1.25 0.57 0.31
31_A 91_R 1.23 0.56 0.29
21_A 94_G 1.20 0.53 0.26
98_V 137_D 1.13 0.46 0.21
31_A 30_D 1.12 0.45 0.20
2_P 136_L 1.10 0.44 0.19
28_L 108_A 1.09 0.43 0.18
28_L 91_R 1.06 0.40 0.17
70_D 78_E 1.06 0.40 0.16
63_P 138_V 1.05 0.39 0.15
29_D 115_D 1.04 0.38 0.15
31_A 68_G 1.02 0.37 0.14
66_S 119_G 1.01 0.35 0.13
108_A 134_E 1.00 0.35 0.13
92_T 51_K 1.00 0.34 0.13
97_V 140_G 0.98 0.33 0.12
54_I 95_K 0.98 0.33 0.12
34_N 135_V 0.97 0.32 0.11
54_I 72_S 0.97 0.32 0.11
66_S 108_A 0.96 0.32 0.11
25_E 53_G 0.96 0.31 0.11
70_D 32_S 0.95 0.31 0.10
109_R 135_V 0.95 0.30 0.10
5_V 125_T 0.94 0.30 0.10
35_G 23_A 0.94 0.30 0.10
4_I 144_T 0.94 0.29 0.10
17_A 78_E 0.93 0.29 0.09
23_S 73_S 0.92 0.28 0.09
28_L 9_Y 0.92 0.28 0.09
6_I 114_S 0.92 0.28 0.09
26_T 96_G 0.92 0.28 0.09
13_C 94_G 0.91 0.28 0.09
22_N 141_R 0.91 0.28 0.09
66_S 138_V 0.90 0.27 0.08
68_Q 78_E 0.90 0.27 0.08
3_K 101_G 0.89 0.26 0.08
43_E 14_M 0.89 0.26 0.08
6_I 68_G 0.89 0.26 0.08
6_I 79_V 0.88 0.25 0.08
66_S 142_Q 0.87 0.25 0.07
66_S 86_S 0.86 0.24 0.07
105_I 97_G 0.86 0.24 0.07
65_S 73_S 0.86 0.24 0.07
39_E 48_R 0.86 0.24 0.07
64_E 99_Q 0.86 0.24 0.07
28_L 93_Q 0.85 0.23 0.07
28_L 97_G 0.85 0.23 0.06
45_S 48_R 0.85 0.23 0.06
18_V 53_G 0.84 0.23 0.06
76_A 65_Y 0.84 0.22 0.06
60_D 74_I 0.83 0.22 0.06
27_I 69_K 0.82 0.21 0.06
54_I 71_A 0.82 0.21 0.06
1_M 33_E 0.82 0.21 0.06
4_I 87_V 0.82 0.21 0.06
64_E 144_T 0.82 0.21 0.06
90_R 145_H 0.82 0.21 0.06
56_R 94_G 0.81 0.21 0.05
82_E 99_Q 0.81 0.21 0.05
56_R 100_G 0.81 0.20 0.05
28_L 128_E 0.80 0.20 0.05
31_A 114_S 0.80 0.20 0.05
78_G 110_W 0.80 0.20 0.05
28_L 120_F 0.80 0.20 0.05
97_V 80_I 0.79 0.20 0.05
27_I 125_T 0.79 0.20 0.05
29_D 137_D 0.78 0.19 0.05
109_R 9_Y 0.78 0.19 0.05
75_K 58_V 0.78 0.19 0.04
55_V 20_N 0.78 0.19 0.04
18_V 19_L 0.78 0.19 0.04
96_L 45_L 0.77 0.19 0.04
109_R 132_N 0.77 0.18 0.04
20_E 132_N 0.77 0.18 0.04
63_P 143_H 0.77 0.18 0.04
104_T 95_K 0.77 0.18 0.04
33_R 22_E 0.77 0.18 0.04
44_K 33_E 0.77 0.18 0.04
5_V 81_S 0.76 0.18 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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