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OPENSEQ.org
MFD_MYTU_334-651-RPOB_MYTU_1-142
Genes: A B A+B
Length: 318 142 434
Sequences: 5959 589 386
Seq/Len: 18.74 4.15 0.89
MirrorTree (Pazo et al. 2001) 0.91
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 0.05
∞ 0.00 0.00 0.84
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
187_A 130_A 1.83 0.90 0.33
313_G 130_A 1.50 0.73 0.15
111_R 125_K 1.45 0.70 0.13
278_E 33_P 1.40 0.66 0.11
315_T 125_K 1.36 0.63 0.10
7_S 99_F 1.33 0.60 0.09
256_A 114_D 1.33 0.60 0.09
130_P 72_E 1.32 0.59 0.09
198_I 110_P 1.30 0.58 0.08
40_A 118_P 1.27 0.55 0.07
240_M 55_D 1.25 0.53 0.07
75_Q 74_A 1.25 0.53 0.07
82_F 120_D 1.23 0.51 0.07
228_G 113_D 1.22 0.50 0.06
79_D 78_G 1.21 0.49 0.06
138_G 109_D 1.20 0.49 0.06
233_T 108_S 1.19 0.48 0.06
228_G 136_T 1.19 0.48 0.06
85_L 129_Y 1.18 0.47 0.06
86_R 67_S 1.18 0.47 0.05
228_G 110_P 1.18 0.47 0.05
163_R 90_L 1.17 0.46 0.05
224_A 73_S 1.16 0.45 0.05
160_T 125_K 1.16 0.45 0.05
12_A 126_D 1.16 0.45 0.05
106_H 126_D 1.14 0.43 0.05
203_E 107_F 1.13 0.42 0.05
313_G 77_R 1.12 0.42 0.04
62_E 72_E 1.12 0.41 0.04
108_V 69_R 1.12 0.41 0.04
247_S 67_S 1.11 0.41 0.04
150_N 65_I 1.11 0.41 0.04
98_V 101_G 1.11 0.40 0.04
125_G 130_A 1.10 0.40 0.04
201_F 134_F 1.10 0.40 0.04
211_G 100_S 1.10 0.39 0.04
228_G 111_R 1.09 0.39 0.04
288_A 62_E 1.08 0.38 0.04
133_V 76_E 1.08 0.38 0.04
211_G 48_L 1.08 0.38 0.04
63_L 68_P 1.07 0.37 0.04
233_T 130_A 1.06 0.36 0.04
153_V 45_R 1.05 0.36 0.03
140_L 71_R 1.05 0.35 0.03
89_I 74_A 1.04 0.35 0.03
170_K 113_D 1.04 0.35 0.03
310_D 59_D 1.04 0.34 0.03
201_F 43_K 1.04 0.34 0.03
160_T 111_R 1.03 0.34 0.03
215_E 124_D 1.03 0.34 0.03
273_R 65_I 1.02 0.34 0.03
93_G 90_L 1.02 0.34 0.03
288_A 39_V 1.02 0.33 0.03
246_L 69_R 1.02 0.33 0.03
5_E 68_P 1.02 0.33 0.03
59_S 80_V 1.00 0.32 0.03
235_K 126_D 1.00 0.32 0.03
95_A 118_P 1.00 0.32 0.03
123_D 59_D 1.00 0.31 0.03
288_A 58_T 0.99 0.31 0.03
160_T 115_V 0.99 0.31 0.03
271_K 67_S 0.99 0.31 0.03
294_P 35_A 0.99 0.31 0.03
201_F 76_E 0.99 0.31 0.03
212_A 112_F 0.99 0.30 0.03
202_V 29_N 0.98 0.30 0.03
211_G 127_M 0.98 0.30 0.03
13_L 52_G 0.98 0.30 0.03
255_P 103_M 0.97 0.29 0.03
281_G 101_G 0.97 0.29 0.03
184_A 52_G 0.97 0.29 0.03
33_V 34_G 0.97 0.29 0.03
119_A 120_D 0.97 0.29 0.03
153_V 87_E 0.96 0.29 0.02
88_H 55_D 0.96 0.28 0.02
106_H 37_N 0.96 0.28 0.02
164_V 142_N 0.96 0.28 0.02
209_V 130_A 0.95 0.28 0.02
287_Y 54_L 0.95 0.28 0.02
144_V 93_L 0.95 0.28 0.02
208_T 136_T 0.94 0.27 0.02
285_S 113_D 0.94 0.27 0.02
62_E 28_S 0.94 0.27 0.02
170_K 101_G 0.94 0.27 0.02
288_A 71_R 0.94 0.27 0.02
206_E 133_L 0.94 0.27 0.02
198_I 34_G 0.94 0.27 0.02
113_S 101_G 0.94 0.27 0.02
7_S 134_F 0.94 0.27 0.02
63_L 120_D 0.93 0.27 0.02
142_D 72_E 0.93 0.27 0.02
267_N 33_P 0.93 0.27 0.02
234_D 129_Y 0.93 0.27 0.02
278_E 121_E 0.93 0.27 0.02
237_Y 78_G 0.93 0.27 0.02
220_E 66_G 0.93 0.26 0.02
32_F 55_D 0.93 0.26 0.02
161_G 135_V 0.93 0.26 0.02
284_V 37_N 0.92 0.26 0.02
270_T 52_G 0.92 0.26 0.02
150_N 127_M 0.92 0.26 0.02
215_E 122_C 0.92 0.25 0.02
234_D 103_M 0.92 0.25 0.02
179_I 77_R 0.91 0.25 0.02
150_N 69_R 0.91 0.25 0.02
32_F 140_I 0.91 0.25 0.02
227_G 39_V 0.91 0.25 0.02
246_L 33_P 0.91 0.25 0.02
28_G 118_P 0.91 0.25 0.02
274_R 107_F 0.91 0.25 0.02
239_P 53_L 0.90 0.24 0.02
79_D 72_E 0.90 0.24 0.02
92_G 120_D 0.90 0.24 0.02
156_E 101_G 0.89 0.24 0.02
131_G 75_A 0.89 0.23 0.02
212_A 128_T 0.89 0.23 0.02
195_Q 99_F 0.89 0.23 0.02
34_E 72_E 0.88 0.23 0.02
206_E 90_L 0.88 0.23 0.02
286_L 40_S 0.88 0.23 0.02
215_E 61_F 0.88 0.23 0.02
295_G 54_L 0.88 0.23 0.02
207_R 137_A 0.88 0.23 0.02
137_Q 130_A 0.88 0.23 0.02
91_T 30_N 0.88 0.23 0.02
151_L 35_A 0.88 0.23 0.02
228_G 69_R 0.88 0.23 0.02
105_A 126_D 0.87 0.23 0.02
100_P 67_S 0.87 0.23 0.02
242_S 50_V 0.87 0.23 0.02
5_E 125_K 0.87 0.23 0.02
247_S 65_I 0.87 0.22 0.02
138_G 101_G 0.87 0.22 0.02
182_P 40_S 0.87 0.22 0.02
141_R 125_K 0.87 0.22 0.02
272_A 66_G 0.87 0.22 0.02
108_V 130_A 0.86 0.22 0.02
36_D 67_S 0.86 0.22 0.02
237_Y 69_R 0.86 0.22 0.02
215_E 133_L 0.85 0.21 0.01
307_E 112_F 0.85 0.21 0.01
211_G 99_F 0.85 0.21 0.01
291_Q 55_D 0.85 0.21 0.01
156_E 73_S 0.85 0.21 0.01
245_Q 128_T 0.85 0.21 0.01
228_G 23_R 0.85 0.21 0.01
213_R 68_P 0.85 0.21 0.01
174_A 68_P 0.85 0.21 0.01
32_F 58_T 0.84 0.21 0.01
247_S 71_R 0.84 0.21 0.01
208_T 111_R 0.84 0.21 0.01
314_F 72_E 0.84 0.21 0.01
240_M 52_G 0.84 0.21 0.01
158_D 99_F 0.84 0.21 0.01
262_G 135_V 0.84 0.21 0.01
106_H 35_A 0.84 0.20 0.01
233_T 110_P 0.84 0.20 0.01
224_A 140_I 0.84 0.20 0.01
268_T 102_S 0.84 0.20 0.01
47_H 114_D 0.84 0.20 0.01
48_P 101_G 0.84 0.20 0.01
238_V 106_S 0.84 0.20 0.01
53_S 101_G 0.83 0.20 0.01
217_L 88_E 0.83 0.20 0.01
190_L 75_A 0.83 0.20 0.01
177_R 104_S 0.83 0.20 0.01
32_F 127_M 0.83 0.20 0.01
110_E 43_K 0.83 0.20 0.01
56_S 126_D 0.83 0.20 0.01
163_R 71_R 0.83 0.20 0.01
159_L 29_N 0.83 0.20 0.01
96_A 27_S 0.83 0.20 0.01
111_R 52_G 0.83 0.20 0.01
158_D 126_D 0.83 0.20 0.01
111_R 90_L 0.83 0.20 0.01
272_A 54_L 0.83 0.20 0.01
68_A 75_A 0.83 0.20 0.01
235_K 107_F 0.83 0.20 0.01
107_R 44_L 0.82 0.20 0.01
44_R 72_E 0.82 0.20 0.01
220_E 48_L 0.82 0.20 0.01
67_A 71_R 0.82 0.19 0.01
277_R 71_R 0.82 0.19 0.01
58_E 58_T 0.82 0.19 0.01
251_G 54_L 0.82 0.19 0.01
305_Q 120_D 0.82 0.19 0.01
155_T 100_S 0.82 0.19 0.01
112_L 109_D 0.81 0.19 0.01
37_Q 76_E 0.81 0.19 0.01
99_A 126_D 0.81 0.19 0.01
275_A 65_I 0.81 0.19 0.01
207_R 94_S 0.81 0.19 0.01
144_V 88_E 0.81 0.19 0.01
235_K 128_T 0.81 0.19 0.01
70_S 59_D 0.81 0.19 0.01
304_W 103_M 0.81 0.19 0.01
242_S 54_L 0.81 0.19 0.01
213_R 67_S 0.81 0.19 0.01
97_L 107_F 0.81 0.19 0.01
285_S 102_S 0.81 0.19 0.01
309_E 88_E 0.81 0.19 0.01
158_D 135_V 0.81 0.19 0.01
45_T 29_N 0.80 0.18 0.01
42_A 101_G 0.80 0.18 0.01
107_R 116_K 0.80 0.18 0.01
160_T 126_D 0.80 0.18 0.01
118_P 47_P 0.80 0.18 0.01
127_A 82_P 0.80 0.18 0.01
32_F 62_E 0.80 0.18 0.01
271_K 68_P 0.80 0.18 0.01
29_G 121_E 0.80 0.18 0.01
308_L 93_L 0.80 0.18 0.01
314_F 120_D 0.80 0.18 0.01
207_R 139_F 0.79 0.18 0.01
177_R 112_F 0.79 0.18 0.01
68_A 29_N 0.79 0.18 0.01
69_P 121_E 0.79 0.18 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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