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OPENSEQ.org
MFD_MYCTU_334_651-RPOB_MYCTU_1_176 V2
Genes: A B A+B
Length: 318 176 460
Sequences: 5169 2044 1178
Seq/Len: 16.25 11.61 2.56
MirrorTree (Pazo et al. 2001) 0.82
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 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.03
100 0.00 0.00 0.15
∞ 0.00 0.00 2.38
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
234_D 150_Q 1.81 0.99 0.93
313_G 135_V 1.43 0.92 0.78
215_E 54_L 1.36 0.89 0.72
100_P 167_I 1.30 0.86 0.67
297_A 168_I 1.25 0.83 0.63
314_F 119_V 1.25 0.83 0.62
258_S 54_L 1.25 0.83 0.62
207_R 147_I 1.24 0.82 0.62
278_E 33_P 1.23 0.82 0.61
161_G 146_E 1.22 0.81 0.60
187_A 49_E 1.22 0.81 0.59
310_D 93_L 1.21 0.80 0.58
198_I 93_L 1.19 0.79 0.56
243_L 126_D 1.18 0.78 0.56
133_V 157_F 1.13 0.73 0.50
243_L 54_L 1.12 0.73 0.49
246_L 107_F 1.10 0.71 0.47
236_L 148_K 1.09 0.70 0.46
110_E 48_L 1.08 0.69 0.45
97_L 61_F 1.08 0.69 0.45
228_G 110_P 1.07 0.68 0.44
234_D 97_E 1.07 0.67 0.43
252_G 46_E 1.05 0.66 0.41
196_H 132_P 1.05 0.66 0.41
307_E 112_F 1.04 0.64 0.40
20_A 65_I 1.04 0.64 0.40
32_F 129_Y 1.01 0.61 0.36
196_H 148_K 1.01 0.60 0.36
272_A 151_T 1.01 0.60 0.36
198_I 87_E 1.00 0.60 0.36
239_P 148_K 1.00 0.60 0.35
158_D 112_F 1.00 0.59 0.35
33_V 175_V 0.99 0.59 0.35
106_H 37_N 0.99 0.58 0.34
5_E 68_P 0.99 0.58 0.34
262_G 131_A 0.98 0.58 0.34
161_G 147_I 0.98 0.58 0.34
314_F 126_D 0.98 0.57 0.34
242_S 146_E 0.98 0.57 0.33
219_L 43_K 0.97 0.56 0.32
237_Y 39_V 0.97 0.56 0.32
207_R 138_E 0.96 0.55 0.31
123_D 168_I 0.95 0.54 0.31
156_E 101_G 0.95 0.54 0.31
189_D 100_S 0.95 0.54 0.31
263_S 42_A 0.95 0.54 0.30
100_P 54_L 0.95 0.54 0.30
305_Q 144_T 0.95 0.54 0.30
212_A 93_L 0.94 0.53 0.30
133_V 109_D 0.94 0.53 0.30
273_R 107_F 0.94 0.53 0.30
276_V 83_V 0.94 0.53 0.29
111_R 90_L 0.94 0.53 0.29
97_L 107_F 0.94 0.53 0.29
315_T 136_T 0.93 0.52 0.29
182_P 126_D 0.93 0.52 0.28
222_A 131_A 0.93 0.51 0.28
204_M 140_I 0.92 0.51 0.28
298_F 42_A 0.92 0.51 0.28
44_R 168_I 0.92 0.51 0.28
215_E 133_L 0.92 0.50 0.27
272_A 136_T 0.91 0.49 0.27
201_F 31_S 0.91 0.49 0.27
198_I 49_E 0.89 0.47 0.25
276_V 48_L 0.89 0.46 0.24
172_L 129_Y 0.89 0.46 0.24
313_G 130_A 0.88 0.46 0.24
249_Y 56_V 0.88 0.46 0.24
237_Y 160_M 0.87 0.45 0.23
216_Y 48_L 0.87 0.45 0.23
247_S 54_L 0.87 0.44 0.23
272_A 54_L 0.87 0.44 0.23
168_E 101_G 0.87 0.44 0.22
181_D 165_T 0.87 0.44 0.22
145_I 61_F 0.87 0.44 0.22
285_S 117_A 0.86 0.44 0.22
192_V 165_T 0.86 0.43 0.22
211_G 141_N 0.86 0.43 0.22
287_Y 90_L 0.86 0.43 0.22
182_P 54_L 0.86 0.43 0.22
217_L 168_I 0.86 0.43 0.22
266_A 165_T 0.86 0.43 0.22
203_E 121_E 0.85 0.43 0.21
160_T 111_R 0.85 0.43 0.21
301_D 129_Y 0.85 0.43 0.21
234_D 100_S 0.85 0.42 0.21
228_G 69_R 0.85 0.42 0.21
285_S 168_I 0.85 0.42 0.21
5_E 26_S 0.85 0.42 0.21
86_R 80_V 0.85 0.42 0.21
79_D 74_A 0.85 0.42 0.21
153_V 49_E 0.84 0.41 0.20
269_K 175_V 0.84 0.41 0.20
207_R 131_A 0.84 0.41 0.20
198_I 34_G 0.84 0.41 0.20
170_K 79_D 0.84 0.41 0.20
107_R 89_V 0.83 0.40 0.20
308_L 93_L 0.83 0.40 0.19
224_A 73_S 0.83 0.40 0.19
179_I 110_P 0.83 0.39 0.19
50_W 119_V 0.83 0.39 0.19
48_P 101_G 0.82 0.39 0.19
308_L 92_E 0.82 0.39 0.19
262_G 136_T 0.82 0.39 0.18
241_D 112_F 0.82 0.39 0.18
126_Q 78_G 0.82 0.38 0.18
251_G 156_D 0.81 0.38 0.18
265_W 174_V 0.81 0.38 0.18
235_K 144_T 0.81 0.38 0.18
311_A 61_F 0.81 0.38 0.18
5_E 71_R 0.81 0.38 0.18
239_P 159_M 0.81 0.37 0.18
147_P 167_I 0.81 0.37 0.17
79_D 80_V 0.81 0.37 0.17
242_S 145_G 0.80 0.37 0.17
175_K 62_E 0.80 0.37 0.17
138_G 43_K 0.80 0.37 0.17
5_E 69_R 0.80 0.37 0.17
214_R 137_A 0.80 0.37 0.17
50_W 123_K 0.80 0.37 0.17
70_S 80_V 0.80 0.36 0.17
161_G 165_T 0.80 0.36 0.17
239_P 53_L 0.80 0.36 0.17
315_T 125_K 0.80 0.36 0.17
253_Q 144_T 0.80 0.36 0.17
195_Q 146_E 0.80 0.36 0.17
255_P 123_K 0.79 0.36 0.17
269_K 116_K 0.79 0.35 0.17
210_G 175_V 0.79 0.35 0.16
86_R 129_Y 0.79 0.35 0.16
107_R 44_L 0.79 0.35 0.16
180_V 54_L 0.79 0.35 0.16
179_I 45_R 0.79 0.35 0.16
201_F 88_E 0.79 0.35 0.16
195_Q 165_T 0.79 0.35 0.16
214_R 147_I 0.79 0.35 0.16
217_L 150_Q 0.79 0.35 0.16
55_L 34_G 0.79 0.35 0.16
19_Q 72_E 0.79 0.35 0.16
239_P 147_I 0.79 0.35 0.16
131_G 157_F 0.79 0.35 0.16
214_R 52_G 0.78 0.35 0.16
189_D 124_D 0.78 0.34 0.16
19_Q 69_R 0.78 0.34 0.16
160_T 125_K 0.78 0.34 0.16
95_A 93_L 0.78 0.34 0.16
5_E 30_N 0.78 0.34 0.16
96_A 30_N 0.78 0.34 0.16
228_G 134_F 0.78 0.34 0.15
278_E 133_L 0.78 0.34 0.15
236_L 43_K 0.78 0.34 0.15
41_A 83_V 0.78 0.34 0.15
298_F 146_E 0.77 0.34 0.15
259_R 135_V 0.77 0.34 0.15
279_I 54_L 0.77 0.34 0.15
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
8461 2.56 MFD_MYCTU_334_651-RPOB_MYCTU_1_176 V2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.93 Done - Shared
8460 0.04 MFD_MYCTU_334_651-RPOB_MYCTU_1_176 V2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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