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OPENSEQ.org
BamB-BamD
Genes: A B A+B
Length: 392 113 486
Sequences: 3152 575 325
Seq/Len: 8.04 5.09 0.67
MirrorTree (Pazo et al. 2001) 0.45
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 0.00
5 0.04 0.01 0.00
10 0.05 0.01 0.00
20 0.05 0.01 0.02
100 0.07 0.01 0.19
∞ 0.13 0.01 0.64
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
244_L 66_D 1.85 0.86 0.14
94_S 71_N 1.81 0.84 0.13
138_D 61_T 1.33 0.52 0.04
297_Y 101_L 1.28 0.47 0.03
119_G 64_M 1.20 0.41 0.02
334_N 52_Q 1.20 0.41 0.02
298_L 42_D 1.18 0.39 0.02
186_N 59_L 1.18 0.39 0.02
133_A 66_D 1.17 0.39 0.02
299_V 32_I 1.15 0.37 0.02
162_V 72_T 1.14 0.36 0.02
84_L 61_T 1.11 0.34 0.02
193_S 89_Q 1.09 0.32 0.01
245_S 59_L 1.08 0.31 0.01
305_V 41_N 1.08 0.31 0.01
288_D 69_G 1.06 0.30 0.01
340_G 28_Y 1.05 0.30 0.01
156_V 38_L 1.05 0.30 0.01
381_Q 51_T 1.05 0.29 0.01
212_D 57_Y 1.04 0.29 0.01
340_G 82_G 1.03 0.28 0.01
135_N 56_A 1.03 0.28 0.01
210_G 48_V 1.03 0.28 0.01
253_V 91_L 1.03 0.28 0.01
162_V 74_F 1.02 0.27 0.01
89_G 36_N 1.01 0.27 0.01
41_Q 45_K 1.01 0.27 0.01
198_S 83_H 1.00 0.26 0.01
174_L 19_G 1.00 0.26 0.01
265_G 57_Y 0.99 0.26 0.01
353_D 11_A 0.99 0.25 0.01
147_V 88_Q 0.99 0.25 0.01
218_A 47_R 0.98 0.25 0.01
380_I 99_G 0.98 0.25 0.01
294_N 106_N 0.98 0.25 0.01
18_S 99_G 0.96 0.24 0.01
158_S 58_A 0.96 0.23 0.01
216_V 46_I 0.95 0.23 0.01
311_D 91_L 0.95 0.23 0.01
178_D 41_N 0.95 0.23 0.01
65_P 43_V 0.95 0.23 0.01
185_V 28_Y 0.95 0.23 0.01
34_P 19_G 0.95 0.23 0.01
241_I 32_I 0.95 0.23 0.01
274_S 96_N 0.94 0.23 0.01
72_V 86_V 0.94 0.23 0.01
331_V 48_V 0.94 0.23 0.01
356_F 51_T 0.94 0.23 0.01
255_N 107_K 0.94 0.23 0.01
19_G 55_V 0.94 0.23 0.01
387_V 57_Y 0.94 0.22 0.01
163_L 84_E 0.94 0.22 0.01
207_A 99_G 0.93 0.22 0.01
48_W 36_N 0.93 0.22 0.01
307_A 59_L 0.93 0.22 0.01
85_N 84_E 0.93 0.22 0.01
125_G 83_H 0.93 0.22 0.01
313_G 95_F 0.92 0.21 0.01
349_I 99_G 0.92 0.21 0.01
266_N 61_T 0.91 0.21 0.01
255_N 106_N 0.91 0.21 0.01
153_S 84_E 0.91 0.21 0.01
122_V 66_D 0.91 0.21 0.01
134_L 51_T 0.91 0.21 0.01
90_K 59_L 0.91 0.21 0.01
248_D 27_V 0.91 0.20 0.01
348_W 67_P 0.90 0.20 0.01
69_D 19_G 0.90 0.20 0.01
120_G 32_I 0.90 0.20 0.01
264_N 72_T 0.90 0.20 0.01
172_Q 32_I 0.89 0.20 0.01
181_V 92_T 0.89 0.20 0.01
245_S 30_P 0.89 0.20 0.01
113_G 27_V 0.89 0.20 0.01
366_G 27_V 0.89 0.20 0.01
248_D 90_T 0.89 0.20 0.01
129_A 45_K 0.89 0.19 0.01
126_S 38_L 0.88 0.19 0.01
84_L 32_I 0.88 0.19 0.01
176_E 40_A 0.88 0.19 0.01
181_V 76_V 0.88 0.19 0.01
337_L 86_V 0.88 0.19 0.01
300_D 64_M 0.88 0.19 0.01
47_A 96_N 0.87 0.19 0.01
359_Q 74_F 0.87 0.19 0.01
390_I 39_T 0.87 0.19 0.01
141_V 71_N 0.87 0.18 0.01
196_G 67_P 0.87 0.18 0.01
323_L 45_K 0.86 0.18 0.01
262_A 90_T 0.86 0.18 0.01
39_E 32_I 0.86 0.18 0.01
141_V 21_S 0.86 0.18 0.01
149_G 33_N 0.86 0.18 0.01
247_V 21_S 0.86 0.18 0.01
272_L 47_R 0.86 0.18 0.01
267_L 69_G 0.85 0.18 0.01
141_V 97_S 0.85 0.17 0.01
268_T 39_T 0.85 0.17 0.01
356_F 63_L 0.84 0.17 0.01
96_S 112_G 0.84 0.17 0.01
168_N 33_N 0.84 0.17 0.01
353_D 103_N 0.84 0.17 0.01
216_V 40_A 0.84 0.17 0.01
346_L 32_I 0.84 0.17 0.01
173_A 78_R 0.84 0.17 0.01
369_T 105_D 0.84 0.17 0.01
186_N 56_A 0.83 0.17 0.01
230_Q 90_T 0.83 0.17 0.01
39_E 14_L 0.83 0.17 0.01
299_V 16_L 0.83 0.17 0.01
199_A 98_S 0.83 0.17 0.01
200_P 27_V 0.83 0.17 0.01
218_A 18_A 0.83 0.17 0.01
303_D 83_H 0.83 0.17 0.01
247_V 40_A 0.83 0.17 0.01
380_I 41_N 0.82 0.17 0.01
13_S 100_V 0.82 0.16 0.01
177_A 102_T 0.82 0.16 0.01
372_V 32_I 0.82 0.16 0.01
123_Y 103_N 0.82 0.16 0.01
131_V 94_T 0.82 0.16 0.01
274_S 41_N 0.81 0.16 0.01
223_Q 46_I 0.81 0.16 0.01
133_A 38_L 0.81 0.16 0.01
212_D 70_T 0.81 0.16 0.01
337_L 52_Q 0.81 0.16 0.01
338_V 42_D 0.81 0.16 0.01
297_Y 99_G 0.81 0.16 0.01
12_L 61_T 0.81 0.16 0.01
297_Y 59_L 0.81 0.16 0.01
239_T 42_D 0.81 0.16 0.01
134_L 59_L 0.80 0.15 0.01
357_V 96_N 0.80 0.15 0.01
177_A 18_A 0.80 0.15 0.01
85_N 97_S 0.80 0.15 0.01
292_D 43_V 0.79 0.15 0.01
96_S 43_V 0.79 0.15 0.01
362_V 30_P 0.79 0.15 0.01
85_N 12_V 0.79 0.15 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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