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OPENSEQ.org
AtmxP
Genes: A B A+B
Length: 339 244 549
Sequences: 1350 1471 1102
Seq/Len: 3.98 6.03 2.01
MirrorTree (Pazo et al. 2001) 0.71
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 0.01
2 0.01 0.00 0.03
5 0.01 0.01 1.20
10 0.01 0.01 1.44
20 0.02 0.02 1.65
100 0.03 0.03 1.89
∞ 0.07 0.07 2.15
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
29_I 190_L 1.52 0.92 0.49
33_L 87_I 1.34 0.84 0.34
284_A 224_I 1.31 0.82 0.32
292_L 222_L 1.26 0.78 0.28
193_V 209_M 1.22 0.74 0.24
122_F 79_T 1.21 0.73 0.24
86_I 215_M 1.18 0.71 0.22
32_F 103_V 1.17 0.70 0.21
42_V 205_A 1.16 0.69 0.20
269_T 174_M 1.10 0.63 0.17
67_S 68_V 1.07 0.61 0.16
54_A 179_K 1.07 0.61 0.16
183_E 212_P 1.07 0.60 0.15
223_I 67_I 1.05 0.58 0.15
252_I 44_V 1.04 0.57 0.14
248_T 97_F 1.03 0.56 0.13
25_K 134_K 1.03 0.55 0.13
97_T 200_S 1.01 0.54 0.13
267_T 216_I 1.01 0.54 0.13
86_I 80_Q 1.00 0.52 0.12
52_F 133_F 0.99 0.52 0.12
264_I 90_T 0.98 0.51 0.11
182_D 172_A 0.98 0.51 0.11
37_L 228_V 0.98 0.50 0.11
307_I 160_T 0.98 0.50 0.11
65_L 214_T 0.98 0.50 0.11
171_A 204_M 0.98 0.50 0.11
226_I 134_K 0.97 0.50 0.11
113_S 236_Q 0.97 0.49 0.11
123_V 206_M 0.97 0.49 0.11
153_V 223_L 0.95 0.47 0.10
65_L 193_L 0.95 0.47 0.10
54_A 188_I 0.94 0.46 0.10
183_E 72_F 0.94 0.46 0.10
34_V 239_V 0.94 0.45 0.10
56_S 178_L 0.94 0.45 0.10
270_A 215_M 0.94 0.45 0.10
140_L 168_V 0.93 0.45 0.09
288_L 222_L 0.92 0.44 0.09
57_I 44_V 0.92 0.44 0.09
320_G 129_G 0.92 0.43 0.09
171_A 211_L 0.91 0.42 0.09
251_T 223_L 0.91 0.42 0.08
193_V 40_T 0.90 0.42 0.08
141_I 37_L 0.90 0.41 0.08
194_I 202_V 0.90 0.41 0.08
230_L 120_I 0.90 0.41 0.08
297_T 173_F 0.90 0.41 0.08
125_G 202_V 0.90 0.41 0.08
244_A 202_V 0.89 0.41 0.08
218_I 214_T 0.89 0.40 0.08
202_A 123_E 0.89 0.40 0.08
97_T 172_A 0.89 0.40 0.08
150_S 224_I 0.89 0.40 0.08
283_F 56_I 0.88 0.40 0.08
76_L 214_T 0.88 0.39 0.08
267_T 212_P 0.88 0.39 0.08
148_K 209_M 0.88 0.39 0.07
77_T 139_K 0.87 0.39 0.07
322_M 134_K 0.87 0.38 0.07
217_G 222_L 0.87 0.38 0.07
324_L 110_E 0.87 0.38 0.07
304_V 212_P 0.87 0.38 0.07
29_I 204_M 0.86 0.38 0.07
270_A 75_Q 0.86 0.38 0.07
265_T 47_L 0.86 0.37 0.07
128_M 82_M 0.86 0.37 0.07
203_M 178_L 0.86 0.37 0.07
157_Q 37_L 0.86 0.37 0.07
329_L 202_V 0.86 0.37 0.07
255_G 218_L 0.86 0.37 0.07
67_S 209_M 0.86 0.37 0.07
308_F 79_T 0.86 0.37 0.07
76_L 74_R 0.86 0.37 0.07
115_I 188_I 0.85 0.36 0.07
272_I 216_I 0.85 0.36 0.07
276_A 212_P 0.85 0.36 0.07
83_I 59_V 0.85 0.36 0.07
79_F 100_M 0.84 0.35 0.07
153_V 204_M 0.84 0.35 0.07
154_S 201_S 0.84 0.35 0.07
28_T 163_D 0.84 0.35 0.07
182_D 135_D 0.84 0.35 0.06
247_Y 33_T 0.84 0.35 0.06
211_K 80_Q 0.84 0.35 0.06
221_T 212_P 0.84 0.35 0.06
236_H 197_M 0.83 0.34 0.06
270_A 47_L 0.83 0.34 0.06
82_L 140_N 0.83 0.34 0.06
199_F 137_M 0.83 0.34 0.06
247_Y 106_K 0.82 0.33 0.06
65_L 198_V 0.82 0.33 0.06
130_I 179_K 0.82 0.33 0.06
233_S 121_G 0.82 0.33 0.06
29_I 58_F 0.82 0.33 0.06
262_G 212_P 0.82 0.33 0.06
276_A 53_A 0.82 0.33 0.06
234_F 103_V 0.81 0.33 0.06
141_I 237_R 0.81 0.32 0.06
82_L 232_N 0.81 0.32 0.06
115_I 57_V 0.81 0.32 0.06
291_L 133_F 0.81 0.32 0.06
176_L 44_V 0.81 0.32 0.06
86_I 59_V 0.81 0.32 0.06
42_V 73_L 0.81 0.32 0.06
193_V 205_A 0.81 0.32 0.06
63_I 187_L 0.81 0.32 0.06
199_F 48_T 0.80 0.32 0.06
314_L 138_L 0.80 0.32 0.06
142_N 75_Q 0.80 0.32 0.06
82_L 49_I 0.80 0.31 0.05
335_Q 117_A 0.80 0.31 0.05
171_A 236_Q 0.80 0.31 0.05
200_Y 188_I 0.79 0.30 0.05
67_S 106_K 0.79 0.30 0.05
218_I 168_V 0.79 0.30 0.05
89_F 68_V 0.79 0.30 0.05
165_M 99_I 0.79 0.30 0.05
242_D 119_K 0.79 0.30 0.05
124_V 22_P 0.78 0.30 0.05
210_I 178_L 0.78 0.29 0.05
146_V 228_V 0.78 0.29 0.05
251_T 217_S 0.78 0.29 0.05
147_T 191_P 0.78 0.29 0.05
104_E 218_L 0.78 0.29 0.05
97_T 220_F 0.78 0.29 0.05
286_G 190_L 0.78 0.29 0.05
56_S 224_I 0.78 0.29 0.05
302_G 41_L 0.78 0.29 0.05
33_L 209_M 0.77 0.28 0.05
240_L 84_P 0.77 0.28 0.05
185_T 133_F 0.77 0.28 0.05
269_T 55_S 0.77 0.28 0.05
252_I 78_G 0.77 0.28 0.05
62_L 131_K 0.77 0.28 0.05
146_V 212_P 0.77 0.28 0.05
298_L 77_M 0.77 0.28 0.05
108_G 186_F 0.77 0.28 0.05
72_K 92_A 0.76 0.28 0.05
177_N 48_T 0.76 0.28 0.05
42_V 108_Y 0.76 0.28 0.05
55_L 131_K 0.76 0.28 0.05
306_F 199_V 0.76 0.27 0.04
191_Q 99_I 0.76 0.27 0.04
333_T 120_I 0.76 0.27 0.04
218_I 88_L 0.76 0.27 0.04
237_D 70_F 0.76 0.27 0.04
78_T 126_F 0.76 0.27 0.04
142_N 236_Q 0.76 0.27 0.04
297_T 93_L 0.76 0.27 0.04
245_S 128_K 0.76 0.27 0.04
324_L 124_E 0.75 0.27 0.04
64_I 52_L 0.75 0.27 0.04
202_A 119_K 0.75 0.27 0.04
100_M 181_A 0.75 0.27 0.04
266_S 190_L 0.75 0.27 0.04
331_Y 236_Q 0.75 0.27 0.04
95_I 89_V 0.75 0.27 0.04
219_I 64_L 0.75 0.27 0.04
51_F 109_N 0.75 0.27 0.04
37_L 106_K 0.75 0.26 0.04
134_V 70_F 0.75 0.26 0.04
87_T 65_R 0.75 0.26 0.04
268_A 99_I 0.75 0.26 0.04
279_D 87_I 0.75 0.26 0.04
132_V 173_F 0.75 0.26 0.04
218_I 197_M 0.75 0.26 0.04
240_L 205_A 0.75 0.26 0.04
30_V 43_I 0.75 0.26 0.04
108_G 209_M 0.75 0.26 0.04
187_R 66_L 0.74 0.26 0.04
48_I 45_I 0.74 0.26 0.04
121_E 87_I 0.74 0.26 0.04
140_L 163_D 0.74 0.26 0.04
41_I 215_M 0.74 0.25 0.04
82_L 62_S 0.74 0.25 0.04
157_Q 212_P 0.74 0.25 0.04
30_V 58_F 0.74 0.25 0.04
98_T 229_D 0.73 0.25 0.04
35_C 70_F 0.73 0.25 0.04
41_I 188_I 0.73 0.25 0.04
211_K 57_V 0.73 0.25 0.04
184_Q 96_T 0.73 0.25 0.04
32_F 234_L 0.73 0.25 0.04
178_A 47_L 0.73 0.25 0.04
150_S 193_L 0.73 0.25 0.04
140_L 217_S 0.73 0.25 0.04
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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