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OPENSEQ.org
IscUfdx
Genes: A B A+B
Length: 128 106 226
Sequences: 2384 1717 237
Seq/Len: 18.62 16.2 1.05
MirrorTree (Pazo et al. 2001) 0.44
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 0.00 0.01
2 0.00 0.00 0.03
5 0.00 0.01 1.00
10 0.00 0.01 1.01
20 0.01 0.01 1.05
100 0.01 0.01 1.18
∞ 0.02 0.03 2.04
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
52_I 22_S 1.65 0.86 0.14
61_Y 36_I 1.52 0.79 0.10
57_R 53_V 1.37 0.68 0.07
52_I 3_K 1.33 0.65 0.06
57_R 74_F 1.33 0.65 0.06
61_Y 76_Y 1.32 0.64 0.06
20_F 17_D 1.25 0.58 0.05
98_E 53_V 1.15 0.49 0.03
81_S 71_M 1.15 0.49 0.03
19_S 23_T 1.14 0.48 0.03
31_M 25_M 1.13 0.47 0.03
5_E 32_S 1.11 0.46 0.03
8_I 25_M 1.10 0.44 0.03
61_Y 42_G 1.08 0.43 0.03
31_M 85_S 1.06 0.40 0.02
89_K 42_G 1.04 0.39 0.02
91_T 67_M 1.04 0.39 0.02
23_N 6_I 1.04 0.38 0.02
124_K 87_Q 1.00 0.35 0.02
5_E 97_L 0.98 0.34 0.02
21_D 53_V 0.98 0.34 0.02
46_K 3_K 0.97 0.33 0.02
57_R 32_S 0.96 0.31 0.02
108_I 28_A 0.95 0.31 0.02
98_E 28_A 0.95 0.31 0.02
121_Y 37_E 0.95 0.31 0.02
124_K 74_F 0.95 0.31 0.02
19_S 24_V 0.94 0.30 0.02
24_D 18_V 0.94 0.30 0.01
125_R 51_V 0.92 0.29 0.01
119_A 19_E 0.92 0.28 0.01
98_E 25_M 0.92 0.28 0.01
36_A 80_P 0.91 0.28 0.01
92_D 98_V 0.90 0.27 0.01
73_V 6_I 0.90 0.27 0.01
118_I 32_S 0.90 0.27 0.01
104_I 17_D 0.90 0.27 0.01
118_I 34_P 0.89 0.27 0.01
119_A 59_A 0.89 0.26 0.01
91_T 99_V 0.87 0.25 0.01
61_Y 60_Q 0.86 0.24 0.01
84_E 28_A 0.86 0.24 0.01
52_I 55_D 0.86 0.24 0.01
78_K 87_Q 0.86 0.24 0.01
118_I 64_P 0.86 0.24 0.01
48_N 52_Y 0.86 0.24 0.01
115_K 20_N 0.85 0.24 0.01
95_E 7_V 0.85 0.24 0.01
81_S 3_K 0.85 0.24 0.01
20_F 95_D 0.85 0.24 0.01
31_M 47_A 0.85 0.24 0.01
84_E 95_D 0.85 0.24 0.01
22_N 87_Q 0.85 0.23 0.01
31_M 76_Y 0.85 0.23 0.01
78_K 44_C 0.85 0.23 0.01
73_V 16_L 0.84 0.23 0.01
73_V 28_A 0.83 0.22 0.01
8_I 31_N 0.83 0.22 0.01
24_D 89_K 0.83 0.22 0.01
45_I 39_E 0.82 0.22 0.01
13_N 33_V 0.82 0.22 0.01
51_G 77_D 0.81 0.21 0.01
94_A 80_P 0.80 0.20 0.01
108_I 16_L 0.80 0.20 0.01
95_E 16_L 0.80 0.20 0.01
61_Y 103_E 0.80 0.20 0.01
4_S 5_T 0.79 0.20 0.01
61_Y 13_R 0.79 0.20 0.01
73_V 25_M 0.79 0.20 0.01
25_E 59_A 0.79 0.20 0.01
52_I 30_R 0.79 0.20 0.01
4_S 17_D 0.79 0.20 0.01
86_Q 19_E 0.78 0.19 0.01
80_K 59_A 0.78 0.19 0.01
61_Y 104_R 0.78 0.19 0.01
78_K 101_V 0.78 0.19 0.01
61_Y 99_V 0.78 0.19 0.01
88_I 66_A 0.78 0.19 0.01
125_R 20_N 0.78 0.19 0.01
81_S 27_N 0.77 0.19 0.01
124_K 80_P 0.77 0.19 0.01
61_Y 85_S 0.77 0.19 0.01
22_N 65_E 0.77 0.19 0.01
22_N 67_M 0.77 0.18 0.01
124_K 18_V 0.77 0.18 0.01
76_W 26_E 0.77 0.18 0.01
122_K 71_M 0.76 0.18 0.01
116_A 43_A 0.76 0.18 0.01
36_A 92_E 0.75 0.18 0.01
31_M 36_I 0.75 0.18 0.01
86_Q 51_V 0.75 0.17 0.01
26_N 97_L 0.75 0.17 0.01
118_I 78_V 0.75 0.17 0.01
23_N 22_S 0.75 0.17 0.01
55_D 41_G 0.74 0.17 0.01
47_V 81_T 0.74 0.17 0.01
82_L 22_S 0.74 0.17 0.01
123_S 63_T 0.74 0.17 0.01
29_S 51_V 0.74 0.17 0.01
31_M 104_R 0.73 0.17 0.01
61_Y 16_L 0.73 0.17 0.01
116_A 41_G 0.73 0.16 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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