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OPENSEQ.org
EutV vs Rv1626
Genes: A B A+B
Length: 205 190 369
Sequences: 12927 5252 134
Seq/Len: 63.06 27.64 0.36
MirrorTree (Pazo et al. 2001) 0.27
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 0.02
2 0.01 0.00 0.03
5 0.02 0.01 0.07
10 0.03 0.02 0.16
20 0.05 0.05 0.34
100 0.11 0.09 1.24
∞ 0.19 0.18 2.98
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
46_D 52_L 1.65 0.57 0.00
88_I 7_I 1.57 0.51 0.00
18_I 23_I 1.29 0.32 0.00
24_L 33_A 1.28 0.32 0.00
190_R 43_C 1.27 0.31 0.00
88_I 26_G 1.24 0.29 0.00
169_T 33_A 1.20 0.27 0.00
111_Y 38_E 1.16 0.25 0.00
46_D 67_K 1.15 0.24 0.00
44_A 113_P 1.14 0.24 0.00
91_L 152_L 1.14 0.24 0.00
89_V 100_G 1.13 0.23 0.00
56_L 101_Y 1.11 0.23 0.00
86_A 7_I 1.05 0.20 0.00
130_S 9_D 1.04 0.19 0.00
176_W 35_D 1.03 0.19 0.00
105_D 30_V 1.03 0.19 0.00
29_L 102_L 1.03 0.19 0.00
29_L 50_L 1.02 0.18 0.00
80_I 69_I 1.02 0.18 0.00
58_K 43_C 1.01 0.18 0.00
112_L 107_D 0.99 0.17 0.00
40_I 102_L 0.98 0.17 0.00
18_I 98_A 0.98 0.17 0.00
55_E 19_R 0.97 0.16 0.00
88_I 78_I 0.97 0.16 0.00
19_A 113_P 0.96 0.16 0.00
19_A 96_L 0.95 0.16 0.00
80_I 6_V 0.95 0.16 0.00
53_L 7_I 0.95 0.16 0.00
120_D 96_L 0.95 0.15 0.00
44_A 123_K 0.95 0.15 0.00
29_L 109_K 0.94 0.15 0.00
185_R 29_V 0.94 0.15 0.00
176_W 16_L 0.93 0.15 0.00
62_V 9_D 0.93 0.15 0.00
132_F 94_K 0.92 0.14 0.00
170_E 52_L 0.92 0.14 0.00
172_D 27_Y 0.91 0.14 0.00
29_L 69_I 0.91 0.14 0.00
89_V 136_S 0.90 0.14 0.00
18_I 121_R 0.90 0.14 0.00
45_G 115_I 0.89 0.14 0.00
172_D 47_Q 0.89 0.13 0.00
64_M 61_D 0.89 0.13 0.00
145_L 22_V 0.89 0.13 0.00
111_Y 48_P 0.89 0.13 0.00
140_G 152_L 0.89 0.13 0.00
194_V 163_A 0.89 0.13 0.00
61_L 7_I 0.88 0.13 0.00
81_A 182_A 0.88 0.13 0.00
103_A 177_R 0.88 0.13 0.00
145_L 50_L 0.87 0.13 0.00
169_T 59_I 0.87 0.13 0.00
149_L 66_G 0.87 0.13 0.00
89_V 155_E 0.87 0.13 0.00
178_Q 81_L 0.86 0.13 0.00
92_T 167_L 0.86 0.13 0.00
195_V 163_A 0.86 0.13 0.00
42_G 102_L 0.86 0.12 0.00
20_E 120_E 0.86 0.12 0.00
79_E 41_E 0.85 0.12 0.00
30_A 39_A 0.85 0.12 0.00
37_G 71_Q 0.85 0.12 0.00
89_V 109_K 0.85 0.12 0.00
59_P 20_D 0.85 0.12 0.00
98_D 98_A 0.84 0.12 0.00
176_W 151_I 0.84 0.12 0.00
127_L 40_I 0.84 0.12 0.00
127_L 48_P 0.83 0.12 0.00
180_A 94_K 0.83 0.12 0.00
72_D 9_D 0.81 0.11 0.00
89_V 144_I 0.81 0.11 0.00
92_T 151_I 0.81 0.11 0.00
80_I 50_L 0.81 0.11 0.00
47_G 64_K 0.81 0.11 0.00
153_K 22_V 0.81 0.11 0.00
61_L 106_L 0.81 0.11 0.00
119_S 98_A 0.80 0.11 0.00
72_D 37_F 0.80 0.11 0.00
95_S 26_G 0.80 0.11 0.00
90_V 40_I 0.79 0.11 0.00
144_T 127_L 0.79 0.10 0.00
125_I 105_P 0.79 0.10 0.00
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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