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OPENSEQ.org
AtmxE
Genes: A B A+B
Length: 339 98 408
Sequences: 1350 888 477
Seq/Len: 3.98 9.06 1.17
MirrorTree (Pazo et al. 2001) 0.64
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.02
10 0.01 0.00 0.09
20 0.02 0.00 0.59
100 0.03 0.01 1.09
∞ 0.07 0.01 1.35
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
252_I 54_I 1.65 0.88 0.23
331_Y 85_K 1.49 0.80 0.16
70_I 80_L 1.47 0.79 0.15
70_I 81_E 1.45 0.78 0.14
264_I 36_E 1.37 0.72 0.11
276_A 81_E 1.27 0.63 0.08
42_V 61_D 1.27 0.63 0.08
270_A 78_F 1.25 0.62 0.08
86_I 81_E 1.24 0.61 0.07
202_A 39_D 1.23 0.59 0.07
69_Y 94_T 1.20 0.57 0.07
150_S 96_T 1.19 0.56 0.06
148_K 94_T 1.18 0.55 0.06
235_Q 62_L 1.17 0.54 0.06
193_V 86_A 1.14 0.51 0.05
132_V 36_E 1.11 0.48 0.05
65_L 67_I 1.11 0.48 0.05
260_I 73_E 1.11 0.48 0.05
284_A 96_T 1.11 0.48 0.05
63_I 93_I 1.10 0.47 0.05
225_I 80_L 1.10 0.47 0.04
136_C 93_I 1.08 0.45 0.04
310_L 30_A 1.07 0.44 0.04
151_T 71_K 1.07 0.44 0.04
117_A 60_K 1.07 0.44 0.04
308_F 85_K 1.06 0.43 0.04
67_S 88_S 1.06 0.43 0.04
227_G 74_S 1.05 0.42 0.04
226_I 47_G 1.04 0.41 0.04
154_S 47_G 1.03 0.41 0.04
309_A 82_V 1.03 0.41 0.04
218_I 94_T 1.02 0.40 0.04
140_L 44_Q 1.02 0.39 0.03
237_D 56_T 1.01 0.39 0.03
274_T 85_K 1.01 0.39 0.03
235_Q 98_I 1.00 0.38 0.03
86_I 97_Q 0.99 0.37 0.03
140_L 31_K 0.99 0.37 0.03
89_F 54_I 0.99 0.37 0.03
96_A 76_M 0.99 0.37 0.03
56_S 94_T 0.99 0.37 0.03
302_G 48_E 0.98 0.36 0.03
41_I 72_A 0.98 0.36 0.03
97_T 76_M 0.98 0.36 0.03
185_T 91_K 0.97 0.35 0.03
286_G 86_A 0.97 0.35 0.03
182_D 93_I 0.97 0.35 0.03
272_I 80_L 0.97 0.35 0.03
260_I 71_K 0.96 0.34 0.03
32_F 71_K 0.96 0.34 0.03
252_I 53_D 0.96 0.34 0.03
42_V 41_N 0.96 0.34 0.03
270_A 63_H 0.95 0.33 0.03
134_V 36_E 0.95 0.33 0.03
153_V 65_A 0.94 0.32 0.03
164_A 93_I 0.94 0.32 0.03
249_I 87_I 0.94 0.32 0.03
153_V 54_I 0.94 0.32 0.03
118_A 51_M 0.93 0.32 0.03
281_E 54_I 0.93 0.31 0.02
81_T 28_E 0.93 0.31 0.02
60_S 98_I 0.93 0.31 0.02
154_S 81_E 0.92 0.31 0.02
146_V 78_F 0.92 0.30 0.02
248_T 64_Q 0.92 0.30 0.02
247_Y 37_I 0.91 0.30 0.02
47_P 87_I 0.91 0.30 0.02
264_I 61_D 0.91 0.30 0.02
246_T 61_D 0.91 0.30 0.02
52_F 95_R 0.91 0.29 0.02
127_N 44_Q 0.90 0.29 0.02
42_V 56_T 0.90 0.29 0.02
273_I 65_A 0.89 0.29 0.02
59_L 70_T 0.89 0.28 0.02
53_L 62_L 0.89 0.28 0.02
192_E 47_G 0.89 0.28 0.02
148_K 71_K 0.89 0.28 0.02
187_R 28_E 0.89 0.28 0.02
95_I 98_I 0.88 0.28 0.02
292_L 63_H 0.88 0.28 0.02
40_I 81_E 0.88 0.28 0.02
42_V 63_H 0.88 0.28 0.02
193_V 94_T 0.88 0.28 0.02
157_Q 48_E 0.88 0.27 0.02
65_L 87_I 0.88 0.27 0.02
296_R 98_I 0.88 0.27 0.02
126_G 82_V 0.88 0.27 0.02
136_C 88_S 0.87 0.27 0.02
56_S 81_E 0.87 0.27 0.02
211_K 79_M 0.87 0.27 0.02
64_I 41_N 0.87 0.27 0.02
231_I 67_I 0.86 0.26 0.02
29_I 58_Q 0.86 0.26 0.02
133_I 96_T 0.86 0.26 0.02
62_L 54_I 0.86 0.26 0.02
121_E 77_K 0.86 0.26 0.02
267_T 95_R 0.85 0.25 0.02
269_T 75_S 0.85 0.25 0.02
118_A 61_D 0.85 0.25 0.02
307_I 33_L 0.84 0.25 0.02
222_I 61_D 0.84 0.25 0.02
117_A 96_T 0.83 0.24 0.02
211_K 69_I 0.82 0.23 0.02
129_V 86_A 0.82 0.23 0.02
297_T 86_A 0.82 0.23 0.02
89_F 72_A 0.82 0.23 0.02
193_V 87_I 0.82 0.23 0.02
44_L 70_T 0.82 0.23 0.01
323_A 40_L 0.82 0.23 0.01
176_L 94_T 0.82 0.23 0.01
264_I 79_M 0.81 0.23 0.01
215_V 39_D 0.81 0.23 0.01
124_V 72_A 0.81 0.23 0.01
41_I 73_E 0.81 0.22 0.01
38_A 37_I 0.81 0.22 0.01
126_G 91_K 0.81 0.22 0.01
188_A 82_V 0.81 0.22 0.01
271_I 58_Q 0.81 0.22 0.01
223_I 26_G 0.81 0.22 0.01
142_N 78_F 0.81 0.22 0.01
322_M 61_D 0.81 0.22 0.01
96_A 61_D 0.80 0.22 0.01
85_I 30_A 0.80 0.22 0.01
99_R 44_Q 0.80 0.22 0.01
75_D 67_I 0.80 0.22 0.01
51_F 50_A 0.80 0.22 0.01
180_L 85_K 0.80 0.21 0.01
187_R 32_M 0.79 0.21 0.01
234_F 36_E 0.79 0.21 0.01
183_E 63_H 0.79 0.21 0.01
258_S 97_Q 0.79 0.21 0.01
269_T 71_K 0.79 0.21 0.01
260_I 50_A 0.79 0.21 0.01
89_F 70_T 0.78 0.21 0.01
252_I 62_L 0.78 0.21 0.01
154_S 87_I 0.78 0.21 0.01
139_V 54_I 0.78 0.20 0.01
182_D 47_G 0.78 0.20 0.01
53_L 98_I 0.78 0.20 0.01
81_T 53_D 0.78 0.20 0.01
295_Y 81_E 0.78 0.20 0.01
322_M 40_L 0.78 0.20 0.01
327_L 37_I 0.78 0.20 0.01
330_G 87_I 0.78 0.20 0.01
229_F 52_T 0.77 0.20 0.01
77_T 63_H 0.77 0.20 0.01
141_I 87_I 0.77 0.20 0.01
270_A 91_K 0.76 0.20 0.01
285_E 38_N 0.76 0.19 0.01
142_N 70_T 0.76 0.19 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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