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OPENSEQ.org
TsaB-vs-RsfS
Genes: A B A+B
Length: 231 105 331
Sequences: 3108 2682 1320
Seq/Len: 13.45 25.54 3.99
MirrorTree (Pazo et al. 2001) 0.66
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 0.01 0.03
2 0.00 0.01 0.03
5 0.00 0.01 0.05
10 0.00 0.01 0.07
20 0.00 0.01 0.12
100 0.00 0.01 0.40
∞ 0.00 0.01 3.93
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
218_L 26_D 1.36 0.95 0.57
68_F 41_T 1.07 0.80 0.31
38_I 3_G 1.04 0.77 0.28
94_T 66_P 1.02 0.76 0.27
193_D 86_I 0.97 0.69 0.22
68_F 18_K 0.96 0.69 0.22
61_Y 54_H 0.94 0.67 0.21
71_V 10_V 0.91 0.62 0.18
197_I 44_S 0.90 0.61 0.18
67_S 90_M 0.89 0.60 0.17
14_S 31_S 0.88 0.59 0.16
96_M 48_V 0.87 0.57 0.16
219_R 46_R 0.85 0.55 0.15
7_D 19_G 0.85 0.54 0.14
92_V 63_G 0.83 0.53 0.14
85_A 51_I 0.83 0.52 0.14
80_G 14_I 0.83 0.52 0.14
118_R 47_H 0.83 0.52 0.13
221_N 75_A 0.82 0.51 0.13
136_H 89_V 0.81 0.49 0.12
61_Y 90_M 0.81 0.49 0.12
67_S 31_S 0.80 0.48 0.12
74_G 105_S 0.80 0.47 0.12
57_N 19_G 0.80 0.47 0.12
71_V 80_V 0.79 0.47 0.11
34_H 78_I 0.79 0.47 0.11
92_V 57_Q 0.78 0.46 0.11
80_G 94_S 0.78 0.45 0.11
93_S 34_T 0.78 0.45 0.11
59_L 31_S 0.77 0.44 0.10
71_V 68_G 0.77 0.44 0.10
74_G 12_D 0.76 0.43 0.10
68_F 86_I 0.76 0.42 0.10
70_G 52_A 0.75 0.41 0.10
213_A 101_E 0.75 0.41 0.10
219_R 40_C 0.75 0.41 0.10
83_L 30_K 0.74 0.41 0.09
5_A 104_W 0.74 0.41 0.09
157_S 38_I 0.74 0.40 0.09
197_I 72_E 0.74 0.40 0.09
119_M 44_S 0.74 0.40 0.09
221_N 59_S 0.73 0.39 0.09
79_Q 36_C 0.72 0.38 0.09
91_G 37_M 0.72 0.38 0.09
213_A 37_M 0.72 0.38 0.09
83_L 49_M 0.72 0.37 0.08
56_I 87_V 0.72 0.37 0.08
167_W 80_V 0.71 0.36 0.08
219_R 83_G 0.71 0.36 0.08
51_T 92_E 0.71 0.36 0.08
73_I 36_C 0.71 0.36 0.08
40_P 57_Q 0.70 0.35 0.08
21_G 89_V 0.70 0.35 0.08
38_I 99_E 0.69 0.34 0.07
119_M 47_H 0.69 0.34 0.07
89_M 22_I 0.69 0.34 0.07
34_H 48_V 0.69 0.34 0.07
213_A 24_A 0.69 0.34 0.07
212_H 7_Q 0.69 0.34 0.07
94_T 37_M 0.69 0.33 0.07
78_A 93_E 0.69 0.33 0.07
78_A 50_S 0.68 0.33 0.07
11_E 92_E 0.68 0.33 0.07
99_A 55_V 0.68 0.33 0.07
179_L 39_I 0.68 0.32 0.07
119_M 27_V 0.68 0.32 0.07
151_E 39_I 0.67 0.32 0.07
13_C 42_G 0.67 0.31 0.07
52_S 55_V 0.67 0.31 0.07
119_M 90_M 0.67 0.31 0.07
123_Y 89_V 0.67 0.31 0.07
215_P 44_S 0.67 0.31 0.07
114_A 6_L 0.67 0.31 0.07
209_A 63_G 0.66 0.31 0.07
17_L 51_I 0.66 0.31 0.07
79_Q 90_M 0.66 0.30 0.06
200_Q 89_V 0.66 0.30 0.06
213_A 96_R 0.66 0.30 0.06
220_N 47_H 0.66 0.30 0.06
108_A 63_G 0.66 0.30 0.06
43_Q 39_I 0.66 0.30 0.06
94_T 23_I 0.65 0.29 0.06
94_T 45_S 0.65 0.29 0.06
195_L 31_S 0.65 0.29 0.06
57_N 89_V 0.65 0.29 0.06
198_A 89_V 0.65 0.29 0.06
28_E 78_I 0.65 0.29 0.06
36_Q 57_Q 0.65 0.29 0.06
38_I 38_I 0.64 0.28 0.06
7_D 102_K 0.64 0.28 0.06
116_D 90_M 0.64 0.28 0.06
57_N 62_A 0.64 0.28 0.06
213_A 90_M 0.64 0.28 0.06
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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