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OPENSEQ.org
MFD_MYTU_334-651-RPOB_MYTU_1-142
Genes: A B A+B
Length: 318 142 432
Sequences: 5169 584 374
Seq/Len: 16.25 4.11 0.87
MirrorTree (Pazo et al. 2001) 0.92
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 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.04
∞ 0.00 0.00 0.81
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
313_G 130_A 1.71 0.85 0.11
53_S 101_G 1.67 0.83 0.10
187_A 130_A 1.61 0.80 0.09
256_A 114_D 1.47 0.71 0.06
20_A 65_I 1.45 0.69 0.05
198_I 110_P 1.44 0.68 0.05
240_M 55_D 1.43 0.68 0.05
7_S 99_F 1.41 0.66 0.05
111_R 125_K 1.41 0.66 0.05
278_E 33_P 1.41 0.66 0.05
160_T 125_K 1.34 0.60 0.04
315_T 125_K 1.33 0.59 0.04
163_R 90_L 1.30 0.56 0.04
288_A 81_N 1.25 0.53 0.03
138_G 109_D 1.25 0.53 0.03
228_G 110_P 1.24 0.52 0.03
228_G 136_T 1.24 0.51 0.03
86_R 67_S 1.23 0.51 0.03
82_F 120_D 1.22 0.50 0.03
201_F 134_F 1.22 0.49 0.03
108_V 69_R 1.20 0.48 0.03
228_G 113_D 1.19 0.47 0.03
233_T 108_S 1.19 0.47 0.03
288_A 39_V 1.17 0.45 0.02
75_Q 74_A 1.16 0.44 0.02
89_I 74_A 1.15 0.44 0.02
288_A 62_E 1.15 0.43 0.02
234_D 129_Y 1.14 0.42 0.02
255_P 103_M 1.13 0.42 0.02
211_G 100_S 1.12 0.41 0.02
153_V 45_R 1.11 0.40 0.02
7_S 134_F 1.10 0.40 0.02
212_A 112_F 1.10 0.39 0.02
12_A 126_D 1.09 0.38 0.02
140_L 71_R 1.09 0.38 0.02
287_Y 54_L 1.09 0.38 0.02
271_K 67_S 1.08 0.38 0.02
215_E 133_L 1.08 0.38 0.02
228_G 111_R 1.08 0.38 0.02
184_A 52_G 1.08 0.37 0.02
186_T 101_G 1.08 0.37 0.02
130_P 72_E 1.08 0.37 0.02
160_T 115_V 1.07 0.36 0.02
68_A 75_A 1.06 0.36 0.02
164_V 142_N 1.06 0.36 0.02
69_P 68_P 1.06 0.36 0.02
93_G 90_L 1.06 0.36 0.02
246_L 69_R 1.05 0.35 0.01
247_S 67_S 1.05 0.35 0.01
168_E 126_D 1.04 0.34 0.01
106_H 126_D 1.04 0.34 0.01
288_A 58_T 1.04 0.34 0.01
20_A 110_P 1.03 0.34 0.01
88_H 55_D 1.03 0.34 0.01
161_G 135_V 1.03 0.34 0.01
295_G 54_L 1.03 0.33 0.01
125_G 130_A 1.03 0.33 0.01
5_E 68_P 1.02 0.32 0.01
211_G 48_L 1.02 0.32 0.01
10_V 65_I 1.01 0.32 0.01
112_L 77_R 1.00 0.31 0.01
107_R 44_L 1.00 0.31 0.01
13_L 52_G 1.00 0.31 0.01
95_A 118_P 1.00 0.31 0.01
33_V 34_G 1.00 0.31 0.01
267_N 33_P 1.00 0.31 0.01
227_G 39_V 0.99 0.31 0.01
45_T 130_A 0.99 0.31 0.01
313_G 49_E 0.99 0.31 0.01
100_P 90_L 0.99 0.30 0.01
151_L 120_D 0.99 0.30 0.01
215_E 61_F 0.98 0.30 0.01
40_A 118_P 0.98 0.30 0.01
30_S 55_D 0.98 0.30 0.01
212_A 126_D 0.98 0.30 0.01
100_P 67_S 0.98 0.29 0.01
112_L 79_D 0.98 0.29 0.01
182_P 40_S 0.98 0.29 0.01
277_R 71_R 0.98 0.29 0.01
98_V 101_G 0.97 0.29 0.01
298_F 54_L 0.97 0.29 0.01
158_D 99_F 0.96 0.28 0.01
208_T 136_T 0.96 0.28 0.01
291_Q 55_D 0.96 0.28 0.01
217_L 88_E 0.96 0.28 0.01
239_P 53_L 0.95 0.28 0.01
202_V 29_N 0.95 0.27 0.01
304_W 103_M 0.95 0.27 0.01
115_S 114_D 0.95 0.27 0.01
278_E 121_E 0.95 0.27 0.01
160_T 111_R 0.94 0.27 0.01
144_V 93_L 0.94 0.27 0.01
155_T 28_S 0.94 0.27 0.01
106_H 37_N 0.94 0.27 0.01
209_V 39_V 0.94 0.27 0.01
79_D 72_E 0.94 0.27 0.01
307_E 112_F 0.94 0.27 0.01
235_K 126_D 0.94 0.27 0.01
192_V 53_L 0.94 0.26 0.01
273_R 65_I 0.94 0.26 0.01
228_G 69_R 0.94 0.26 0.01
155_T 33_P 0.94 0.26 0.01
32_F 127_M 0.93 0.26 0.01
131_G 75_A 0.93 0.26 0.01
56_S 125_K 0.93 0.26 0.01
48_P 90_L 0.93 0.26 0.01
247_S 65_I 0.93 0.26 0.01
242_S 54_L 0.93 0.26 0.01
107_R 116_K 0.92 0.26 0.01
310_D 59_D 0.92 0.25 0.01
127_A 120_D 0.92 0.25 0.01
147_P 72_E 0.92 0.25 0.01
37_Q 99_F 0.92 0.25 0.01
133_V 76_E 0.91 0.25 0.01
28_G 118_P 0.91 0.25 0.01
198_I 34_G 0.91 0.25 0.01
142_D 72_E 0.91 0.25 0.01
243_L 54_L 0.91 0.25 0.01
138_G 101_G 0.91 0.24 0.01
237_Y 39_V 0.91 0.24 0.01
123_D 59_D 0.90 0.24 0.01
270_T 55_D 0.90 0.24 0.01
224_A 73_S 0.90 0.24 0.01
43_A 68_P 0.90 0.24 0.01
207_R 137_A 0.90 0.24 0.01
137_Q 130_A 0.90 0.24 0.01
150_N 69_R 0.89 0.23 0.01
42_A 101_G 0.89 0.23 0.01
179_I 77_R 0.89 0.23 0.01
238_V 106_S 0.89 0.23 0.01
286_L 40_S 0.89 0.23 0.01
136_L 72_E 0.89 0.23 0.01
19_Q 72_E 0.89 0.23 0.01
90_A 28_S 0.89 0.23 0.01
222_A 131_A 0.89 0.23 0.01
233_T 110_P 0.89 0.23 0.01
37_Q 43_K 0.89 0.23 0.01
237_Y 121_E 0.89 0.23 0.01
202_V 129_Y 0.88 0.23 0.01
308_L 93_L 0.88 0.23 0.01
7_S 100_S 0.88 0.23 0.01
268_T 102_S 0.88 0.23 0.01
69_P 121_E 0.88 0.23 0.01
150_N 65_I 0.88 0.23 0.01
247_S 71_R 0.88 0.23 0.01
277_R 59_D 0.88 0.22 0.01
294_P 35_A 0.88 0.22 0.01
235_K 136_T 0.88 0.22 0.01
32_F 55_D 0.87 0.22 0.01
156_E 101_G 0.87 0.22 0.01
189_D 107_F 0.87 0.22 0.01
51_T 32_V 0.87 0.22 0.01
51_T 125_K 0.87 0.22 0.01
46_G 87_E 0.87 0.22 0.01
116_D 106_S 0.87 0.22 0.01
270_T 52_G 0.87 0.22 0.01
215_E 122_C 0.87 0.22 0.01
97_L 26_S 0.86 0.21 0.01
248_R 100_S 0.86 0.21 0.01
285_S 113_D 0.86 0.21 0.01
18_N 32_V 0.86 0.21 0.01
5_E 125_K 0.86 0.21 0.01
34_E 81_N 0.86 0.21 0.01
198_I 108_S 0.86 0.21 0.01
53_S 102_S 0.86 0.21 0.01
211_G 134_F 0.85 0.21 0.01
89_I 28_S 0.85 0.21 0.01
29_G 142_N 0.85 0.21 0.01
212_A 128_T 0.85 0.21 0.01
282_E 77_R 0.85 0.21 0.01
266_A 62_E 0.85 0.21 0.01
158_D 135_V 0.85 0.21 0.01
141_R 125_K 0.85 0.21 0.01
282_E 106_S 0.84 0.20 0.01
218_V 105_L 0.84 0.20 0.01
170_K 30_N 0.84 0.20 0.01
201_F 76_E 0.84 0.20 0.01
211_G 99_F 0.84 0.20 0.01
195_Q 99_F 0.84 0.20 0.01
141_R 55_D 0.84 0.20 0.01
254_A 87_E 0.84 0.20 0.01
5_E 30_N 0.84 0.20 0.01
251_G 54_L 0.84 0.20 0.01
206_E 90_L 0.84 0.20 0.01
107_R 98_D 0.84 0.20 0.01
181_D 54_L 0.84 0.20 0.01
288_A 71_R 0.84 0.20 0.01
251_G 40_S 0.83 0.20 0.01
296_H 89_V 0.83 0.20 0.01
86_R 36_P 0.83 0.20 0.01
66_R 114_D 0.83 0.20 0.01
85_L 101_G 0.83 0.20 0.01
123_D 28_S 0.83 0.20 0.01
242_S 50_V 0.83 0.20 0.01
208_T 111_R 0.83 0.20 0.01
111_R 90_L 0.83 0.20 0.01
110_E 112_F 0.83 0.20 0.01
48_P 101_G 0.83 0.20 0.01
224_A 140_I 0.83 0.20 0.01
237_Y 46_E 0.83 0.20 0.01
65_V 28_S 0.82 0.19 0.01
211_G 112_F 0.82 0.19 0.01
256_A 73_S 0.82 0.19 0.01
288_A 90_L 0.82 0.19 0.01
215_E 124_D 0.82 0.19 0.01
245_Q 128_T 0.82 0.19 0.01
55_L 109_D 0.82 0.19 0.01
260_L 123_K 0.82 0.19 0.01
203_E 128_T 0.82 0.19 0.01
160_T 126_D 0.82 0.19 0.01
36_D 67_S 0.82 0.19 0.01
228_G 134_F 0.82 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)
ID Seq/Len Name Options I_Prob Status
7376 0.89 MFD_MYTU_334-651-RPOB_MYTU_1-142 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.33 Done - Shared
7350 0.87 MFD_MYTU_334-651-RPOB_MYTU_1-142 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.11 Done - Shared
7349 0 MFD_MYTU_334-651-RPOB_MYTU_1-142 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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