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OPENSEQ.org
TsaB-vs-L20
Genes: A B A+B
Length: 231 118 342
Sequences: 3108 1984 1344
Seq/Len: 13.45 16.81 3.93
MirrorTree (Pazo et al. 2001) 0.67
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 0.00 0.10 0.00
2 0.00 0.10 0.00
5 0.00 0.10 0.04
10 0.00 0.10 0.06
20 0.00 0.10 0.11
100 0.00 0.10 0.55
∞ 0.00 0.10 3.85
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
71_V 36_F 1.08 0.80 0.04
80_G 38_A 1.04 0.77 0.04
73_I 41_K 0.96 0.69 0.03
170_W 17_I 0.93 0.64 0.03
197_I 73_G 0.92 0.63 0.03
66_G 93_K 0.90 0.60 0.03
88_P 78_K 0.85 0.54 0.02
36_Q 27_A 0.82 0.51 0.02
96_M 79_F 0.82 0.51 0.02
19_N 53_R 0.81 0.48 0.02
68_F 14_H 0.80 0.48 0.02
124_W 91_D 0.80 0.47 0.02
76_G 40_I 0.79 0.47 0.02
84_G 68_A 0.79 0.46 0.02
219_R 25_Y 0.79 0.46 0.02
76_G 22_K 0.79 0.46 0.02
68_F 6_R 0.79 0.46 0.02
16_A 93_K 0.77 0.44 0.02
75_I 40_I 0.77 0.43 0.02
80_G 40_I 0.75 0.41 0.02
10_T 11_R 0.75 0.41 0.02
211_E 75_S 0.75 0.41 0.02
118_R 45_Y 0.75 0.41 0.02
93_S 25_Y 0.75 0.41 0.02
35_T 40_I 0.74 0.39 0.01
125_A 75_S 0.73 0.38 0.01
227_L 91_D 0.72 0.38 0.01
93_S 75_S 0.72 0.38 0.01
201_M 37_Q 0.72 0.37 0.01
166_G 8_V 0.72 0.37 0.01
150_H 53_R 0.71 0.36 0.01
26_H 32_Y 0.71 0.36 0.01
81_L 84_K 0.71 0.36 0.01
51_T 38_A 0.70 0.34 0.01
147_E 105_A 0.70 0.34 0.01
59_L 42_A 0.69 0.34 0.01
10_T 2_A 0.69 0.34 0.01
49_S 88_V 0.69 0.34 0.01
186_V 88_V 0.69 0.34 0.01
79_Q 10_A 0.69 0.33 0.01
47_T 53_R 0.68 0.33 0.01
84_G 53_R 0.68 0.33 0.01
80_G 27_A 0.68 0.33 0.01
16_A 97_D 0.68 0.32 0.01
3_I 109_L 0.68 0.32 0.01
10_T 32_Y 0.68 0.32 0.01
94_T 56_Q 0.68 0.32 0.01
62_G 30_R 0.68 0.32 0.01
77_I 21_A 0.67 0.32 0.01
118_R 38_A 0.67 0.31 0.01
74_G 36_F 0.67 0.31 0.01
23_V 51_R 0.67 0.31 0.01
166_G 14_H 0.67 0.31 0.01
98_M 86_A 0.67 0.31 0.01
9_A 19_K 0.66 0.30 0.01
189_P 97_D 0.66 0.30 0.01
41_M 37_Q 0.66 0.30 0.01
39_L 39_V 0.66 0.30 0.01
67_S 55_R 0.66 0.30 0.01
176_E 110_V 0.66 0.30 0.01
119_M 43_G 0.66 0.30 0.01
228_P 94_I 0.66 0.29 0.01
89_M 103_K 0.65 0.29 0.01
82_A 48_R 0.65 0.29 0.01
211_E 80_I 0.65 0.28 0.01
38_I 110_V 0.64 0.28 0.01
226_K 63_A 0.64 0.28 0.01
14_S 85_K 0.64 0.28 0.01
94_T 79_F 0.64 0.28 0.01
222_V 6_R 0.64 0.27 0.01
219_R 82_G 0.64 0.27 0.01
120_G 15_K 0.64 0.27 0.01
43_Q 41_K 0.63 0.27 0.01
36_Q 9_I 0.63 0.27 0.01
112_L 11_R 0.63 0.27 0.01
83_L 31_V 0.63 0.27 0.01
6_I 81_N 0.62 0.26 0.01
23_V 104_V 0.62 0.26 0.01
41_M 34_V 0.62 0.26 0.01
218_L 108_A 0.62 0.26 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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