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OPENSEQ.org
TsaB-vs-S4
Genes: A B A+B
Length: 231 206 432
Sequences: 3108 1236 643
Seq/Len: 13.45 6 1.49
MirrorTree (Pazo et al. 2001) 0.63
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 0.09 0.00
2 0.00 0.09 0.00
5 0.00 0.09 0.00
10 0.00 0.09 0.01
20 0.00 0.09 0.03
100 0.00 0.09 0.20
∞ 0.00 0.09 1.47
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
76_G 123_I 1.53 0.87 0.21
167_W 62_R 1.03 0.47 0.05
91_G 105_M 1.01 0.45 0.04
88_P 171_L 1.00 0.44 0.04
38_I 45_K 1.00 0.44 0.04
83_L 50_D 0.99 0.43 0.04
7_D 184_R 0.95 0.39 0.04
2_R 10_K 0.95 0.39 0.04
44_D 138_S 0.94 0.38 0.03
69_T 130_V 0.94 0.38 0.03
80_G 180_G 0.94 0.37 0.03
89_M 146_R 0.91 0.35 0.03
40_P 137_V 0.91 0.35 0.03
124_W 76_Y 0.91 0.35 0.03
163_V 200_I 0.90 0.34 0.03
127_Y 106_G 0.88 0.33 0.03
59_L 157_A 0.88 0.32 0.03
68_F 90_L 0.88 0.32 0.03
82_A 146_R 0.88 0.32 0.03
215_P 135_Y 0.87 0.32 0.03
100_Q 70_R 0.86 0.30 0.03
73_I 121_K 0.85 0.30 0.02
75_I 11_L 0.85 0.30 0.02
118_R 158_A 0.85 0.29 0.02
127_Y 160_E 0.84 0.29 0.02
80_G 83_K 0.84 0.29 0.02
226_K 76_Y 0.84 0.29 0.02
94_T 131_N 0.84 0.29 0.02
221_N 122_A 0.83 0.28 0.02
33_E 20_F 0.83 0.28 0.02
48_T 113_E 0.83 0.28 0.02
35_T 128_R 0.83 0.28 0.02
170_W 96_G 0.83 0.28 0.02
191_A 206_K 0.83 0.28 0.02
197_I 128_R 0.82 0.27 0.02
116_D 159_L 0.81 0.27 0.02
84_G 37_A 0.81 0.27 0.02
80_G 170_W 0.80 0.26 0.02
167_W 147_E 0.80 0.26 0.02
9_A 133_A 0.80 0.25 0.02
15_V 146_R 0.80 0.25 0.02
81_L 157_A 0.79 0.24 0.02
88_P 205_S 0.79 0.24 0.02
17_L 179_E 0.78 0.24 0.02
7_D 56_R 0.78 0.24 0.02
140_T 156_K 0.78 0.24 0.02
123_Y 152_Q 0.78 0.24 0.02
107_G 78_E 0.78 0.24 0.02
162_T 62_R 0.78 0.24 0.02
15_V 159_L 0.77 0.23 0.02
190_A 206_K 0.77 0.23 0.02
74_G 198_H 0.77 0.23 0.02
148_I 5_L 0.77 0.23 0.02
223_A 157_A 0.77 0.23 0.02
145_K 161_L 0.77 0.23 0.02
80_G 131_N 0.76 0.23 0.02
118_R 130_V 0.76 0.22 0.02
68_F 15_E 0.76 0.22 0.02
207_T 131_N 0.76 0.22 0.02
59_L 153_S 0.75 0.22 0.02
63_R 143_V 0.75 0.22 0.02
214_E 145_I 0.75 0.22 0.01
5_A 196_N 0.75 0.22 0.01
61_Y 122_A 0.75 0.22 0.01
41_M 91_L 0.75 0.22 0.01
216_V 50_D 0.75 0.22 0.01
118_R 12_S 0.75 0.22 0.01
74_G 158_A 0.75 0.21 0.01
122_V 130_V 0.74 0.21 0.01
10_T 159_L 0.74 0.21 0.01
10_T 142_V 0.74 0.21 0.01
127_Y 178_M 0.74 0.21 0.01
221_N 24_G 0.74 0.21 0.01
60_A 49_S 0.73 0.21 0.01
62_G 205_S 0.73 0.21 0.01
99_A 106_G 0.73 0.21 0.01
216_V 78_E 0.73 0.20 0.01
79_Q 85_N 0.73 0.20 0.01
189_P 101_V 0.73 0.20 0.01
13_C 121_K 0.73 0.20 0.01
123_Y 73_R 0.73 0.20 0.01
109_T 148_K 0.73 0.20 0.01
57_N 167_K 0.73 0.20 0.01
91_G 94_L 0.73 0.20 0.01
70_G 52_G 0.73 0.20 0.01
118_R 111_R 0.72 0.20 0.01
46_L 57_E 0.72 0.20 0.01
92_V 203_L 0.72 0.20 0.01
67_S 102_V 0.72 0.20 0.01
218_L 179_E 0.72 0.20 0.01
125_A 50_D 0.72 0.20 0.01
88_P 74_N 0.72 0.20 0.01
208_V 155_V 0.72 0.20 0.01
2_R 143_V 0.72 0.20 0.01
39_L 52_G 0.72 0.20 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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