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OPENSEQ.org
BamB-BamD
Genes: A B A+B
Length: 392 245 620
Sequences: 3152 1309 552
Seq/Len: 8.04 5.34 0.89
MirrorTree (Pazo et al. 2001) 0.55
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 0.02 0.01 0.00
2 0.02 0.01 0.01
5 0.04 0.01 0.02
10 0.05 0.01 0.03
20 0.05 0.01 0.07
100 0.07 0.01 0.19
∞ 0.13 0.01 0.87
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
380_I 224_Q 1.25 0.53 0.00
175_N 115_T 1.22 0.51 0.00
178_D 160_T 1.20 0.48 0.00
44_P 202_L 1.15 0.44 0.00
12_L 127_F 1.14 0.43 0.00
76_D 208_T 1.14 0.43 0.00
300_D 143_A 1.05 0.36 0.00
350_N 194_V 1.05 0.35 0.00
221_M 108_V 1.04 0.35 0.00
174_L 33_N 1.04 0.34 0.00
154_R 77_Y 1.03 0.34 0.00
72_V 49_R 1.03 0.34 0.00
96_S 156_N 1.02 0.33 0.00
196_G 117_M 1.02 0.33 0.00
210_G 81_K 1.01 0.33 0.00
124_I 95_F 1.01 0.32 0.00
131_V 101_T 1.00 0.32 0.00
45_T 14_S 0.97 0.29 0.00
274_S 32_P 0.97 0.29 0.00
76_D 225_M 0.96 0.28 0.00
379_L 199_E 0.95 0.28 0.00
81_V 210_A 0.95 0.28 0.00
7_L 239_A 0.94 0.27 0.00
335_G 221_A 0.94 0.27 0.00
116_T 43_L 0.93 0.27 0.00
10_G 220_N 0.92 0.26 0.00
274_S 242_S 0.92 0.26 0.00
11_L 176_K 0.92 0.25 0.00
171_L 17_L 0.91 0.25 0.00
87_D 154_Y 0.91 0.25 0.00
350_N 221_A 0.91 0.25 0.00
335_G 19_G 0.91 0.25 0.00
155_P 80_Y 0.90 0.24 0.00
318_T 160_T 0.90 0.24 0.00
159_D 9_A 0.90 0.24 0.00
255_N 48_W 0.90 0.24 0.00
52_V 224_Q 0.90 0.24 0.00
371_P 35_I 0.90 0.24 0.00
309_T 15_L 0.89 0.24 0.00
173_A 187_E 0.89 0.24 0.00
274_S 203_R 0.89 0.24 0.00
140_T 86_P 0.89 0.24 0.00
313_G 214_A 0.89 0.23 0.00
49_S 39_A 0.88 0.23 0.00
53_G 195_V 0.88 0.23 0.00
43_T 195_V 0.87 0.23 0.00
142_A 53_T 0.87 0.23 0.00
140_T 161_T 0.87 0.23 0.00
173_A 194_V 0.87 0.22 0.00
220_L 99_N 0.87 0.22 0.00
126_S 10_A 0.86 0.22 0.00
142_A 113_G 0.86 0.22 0.00
272_L 76_I 0.86 0.22 0.00
85_N 48_W 0.86 0.22 0.00
146_K 21_S 0.86 0.22 0.00
255_N 201_M 0.86 0.22 0.00
140_T 225_M 0.85 0.21 0.00
15_T 127_F 0.85 0.21 0.00
185_V 243_S 0.85 0.21 0.00
343_E 113_G 0.85 0.21 0.00
339_V 205_Y 0.85 0.21 0.00
13_S 205_Y 0.85 0.21 0.00
233_S 112_R 0.84 0.21 0.00
73_Y 16_F 0.84 0.21 0.00
118_S 111_M 0.84 0.21 0.00
173_A 51_A 0.84 0.21 0.00
298_L 21_S 0.84 0.21 0.00
67_L 12_T 0.84 0.21 0.00
346_L 13_L 0.84 0.20 0.00
265_G 63_P 0.84 0.20 0.00
123_Y 19_G 0.83 0.20 0.00
73_Y 234_V 0.83 0.20 0.00
115_V 18_A 0.82 0.20 0.00
298_L 22_G 0.82 0.20 0.00
164_I 183_E 0.82 0.19 0.00
303_D 226_Q 0.82 0.19 0.00
46_T 32_P 0.82 0.19 0.00
114_G 159_Y 0.81 0.19 0.00
356_F 151_V 0.81 0.19 0.00
382_A 231_A 0.81 0.19 0.00
249_T 46_G 0.81 0.19 0.00
337_L 145_S 0.81 0.19 0.00
10_G 124_L 0.81 0.19 0.00
380_I 23_S 0.81 0.19 0.00
180_A 84_D 0.80 0.18 0.00
207_A 140_A 0.80 0.18 0.00
290_I 168_V 0.80 0.18 0.00
94_S 13_L 0.79 0.18 0.00
380_I 242_S 0.79 0.18 0.00
119_G 179_Y 0.79 0.18 0.00
202_T 15_L 0.79 0.18 0.00
346_L 79_Y 0.79 0.18 0.00
164_I 194_V 0.79 0.18 0.00
221_M 79_Y 0.79 0.18 0.00
18_S 128_F 0.79 0.18 0.00
90_K 124_L 0.79 0.17 0.00
15_T 220_N 0.79 0.17 0.00
195_R 65_G 0.78 0.17 0.00
345_Y 191_W 0.78 0.17 0.00
305_V 52_I 0.78 0.17 0.00
355_R 83_A 0.78 0.17 0.00
169_G 205_Y 0.78 0.17 0.00
296_I 55_L 0.78 0.17 0.00
318_T 154_Y 0.78 0.17 0.00
138_D 194_V 0.78 0.17 0.00
309_T 104_N 0.78 0.17 0.00
171_L 196_N 0.78 0.17 0.00
238_S 171_K 0.78 0.17 0.00
296_I 209_Q 0.77 0.17 0.00
155_P 159_Y 0.77 0.17 0.00
140_T 10_A 0.77 0.17 0.00
293_G 167_L 0.77 0.17 0.00
199_A 148_S 0.77 0.17 0.00
292_D 202_L 0.76 0.16 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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