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OPENSEQ.org
MFD_BACSU_1_450-UVRA_BACSU_121_263
Genes: A B A+B
Length: 450 143 573
Sequences: 9935 7073 1659
Seq/Len: 22.08 49.46 2.9
MirrorTree (Pazo et al. 2001) 0.45
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 0.04 1.76
2 0.00 0.04 2.09
5 0.00 0.04 2.51
10 0.00 0.04 2.80
20 0.00 0.04 3.00
100 0.01 0.04 3.61
∞ 0.09 0.04 6.16
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
180_I 57_V 1.36 0.91 0.41
252_K 29_K 1.18 0.81 0.27
179_G 88_R 1.08 0.73 0.20
147_D 92_K 1.04 0.68 0.17
197_F 58_R 1.02 0.66 0.16
426_V 13_T 1.01 0.64 0.15
197_F 88_R 0.98 0.61 0.14
202_D 58_R 0.95 0.58 0.13
274_L 129_H 0.95 0.58 0.13
187_T 17_M 0.93 0.55 0.12
202_D 88_R 0.89 0.51 0.10
412_F 52_R 0.89 0.51 0.10
396_L 138_S 0.88 0.49 0.10
130_P 40_R 0.87 0.48 0.09
229_L 36_I 0.85 0.46 0.09
324_K 1_H 0.85 0.46 0.09
263_L 10_T 0.84 0.45 0.09
108_N 1_H 0.84 0.44 0.08
106_V 85_V 0.82 0.42 0.08
150_P 101_D 0.80 0.40 0.07
334_L 15_E 0.78 0.38 0.07
153_L 130_H 0.78 0.38 0.07
173_E 81_S 0.77 0.36 0.06
242_K 64_E 0.77 0.36 0.06
412_F 56_Y 0.77 0.36 0.06
363_Y 135_C 0.76 0.35 0.06
179_G 58_R 0.76 0.34 0.06
427_L 125_M 0.76 0.34 0.06
199_T 88_R 0.75 0.34 0.06
233_P 13_T 0.74 0.33 0.06
67_T 130_H 0.74 0.33 0.06
248_A 23_E 0.74 0.33 0.06
117_I 59_V 0.72 0.31 0.05
335_E 86_I 0.72 0.31 0.05
36_S 5_H 0.72 0.30 0.05
321_Q 37_V 0.72 0.30 0.05
71_T 56_Y 0.72 0.30 0.05
18_I 17_M 0.71 0.30 0.05
418_E 29_K 0.71 0.30 0.05
177_R 105_T 0.71 0.30 0.05
263_L 135_C 0.71 0.29 0.05
327_A 70_D 0.71 0.29 0.05
289_Y 15_E 0.70 0.29 0.05
408_F 21_I 0.70 0.29 0.05
162_Y 17_M 0.69 0.28 0.04
151_D 101_D 0.69 0.27 0.04
324_K 135_C 0.69 0.27 0.04
97_P 61_I 0.68 0.27 0.04
198_D 90_V 0.67 0.26 0.04
403_F 105_T 0.67 0.25 0.04
376_Q 56_Y 0.66 0.25 0.04
146_H 8_E 0.66 0.24 0.04
211_D 59_V 0.65 0.24 0.04
191_P 128_E 0.65 0.24 0.04
409_T 131_A 0.65 0.24 0.04
64_Q 60_R 0.65 0.24 0.04
148_I 56_Y 0.65 0.23 0.04
159_E 47_V 0.65 0.23 0.04
403_F 60_R 0.65 0.23 0.04
67_T 54_Q 0.64 0.23 0.04
210_D 52_R 0.64 0.23 0.03
434_A 101_D 0.64 0.23 0.03
274_L 52_R 0.64 0.23 0.03
307_L 49_E 0.64 0.23 0.03
369_H 86_I 0.64 0.22 0.03
433_E 38_S 0.64 0.22 0.03
219_T 61_I 0.63 0.22 0.03
93_A 125_M 0.63 0.22 0.03
57_T 16_Q 0.63 0.22 0.03
240_M 73_E 0.63 0.22 0.03
192_V 48_L 0.63 0.22 0.03
349_F 19_D 0.62 0.21 0.03
420_T 62_D 0.62 0.21 0.03
78_S 76_K 0.62 0.21 0.03
172_G 11_S 0.62 0.21 0.03
355_E 36_I 0.62 0.21 0.03
198_D 88_R 0.61 0.21 0.03
269_H 59_V 0.61 0.21 0.03
229_L 128_E 0.61 0.20 0.03
440_K 131_A 0.61 0.20 0.03
265_A 131_A 0.61 0.20 0.03
43_S 5_H 0.61 0.20 0.03
418_E 21_I 0.61 0.20 0.03
247_L 15_E 0.61 0.20 0.03
101_A 50_Q 0.61 0.20 0.03
387_Q 29_K 0.60 0.20 0.03
168_V 143_E 0.60 0.20 0.03
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
7103 2.9 MFD_BACSU_1_450-UVRA_BACSU_121_263 Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.41 Done - Shared
7102 1.81 MFD_BACSU_1_450-UVRA_BACSU_121_263 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
7091 6.35 MFD_BACSU_1_450-UVRA_BACSU_121_263 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.90 Done - Shared
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