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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 1037
Seq/Len: 22.08 49.46 1.81
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 0.04 1.75
2 0.00 0.04 2.08
5 0.00 0.04 2.51
10 0.00 0.04 2.79
20 0.00 0.04 2.98
100 0.01 0.04 3.60
∞ 0.09 0.04 6.14
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
183_I 13_T 1.14 0.64 0.01
281_Q 135_C 1.13 0.64 0.01
229_L 36_I 1.13 0.63 0.01
153_L 130_H 1.12 0.62 0.01
263_L 135_C 1.08 0.58 0.00
180_I 57_V 1.07 0.57 0.00
187_T 17_M 1.06 0.55 0.00
269_H 142_L 1.05 0.55 0.00
162_Y 17_M 1.03 0.53 0.00
418_E 29_K 1.03 0.52 0.00
281_Q 4_E 1.02 0.52 0.00
179_G 88_R 1.02 0.51 0.00
36_S 5_H 1.02 0.51 0.00
252_K 29_K 1.01 0.50 0.00
33_L 5_H 0.99 0.49 0.00
409_T 131_A 0.98 0.47 0.00
108_N 1_H 0.96 0.46 0.00
427_L 125_M 0.96 0.46 0.00
289_Y 15_E 0.94 0.43 0.00
300_Y 40_R 0.94 0.43 0.00
64_Q 60_R 0.93 0.41 0.00
293_K 135_C 0.91 0.40 0.00
387_Q 29_K 0.91 0.39 0.00
222_N 52_R 0.91 0.39 0.00
197_F 58_R 0.91 0.39 0.00
197_F 88_R 0.90 0.38 0.00
148_I 56_Y 0.88 0.36 0.00
208_N 4_E 0.85 0.34 0.00
334_L 15_E 0.85 0.34 0.00
418_E 21_I 0.85 0.34 0.00
403_F 60_R 0.85 0.33 0.00
308_I 56_Y 0.84 0.33 0.00
437_T 18_V 0.83 0.32 0.00
159_E 37_V 0.83 0.32 0.00
85_N 60_R 0.83 0.32 0.00
202_D 27_R 0.83 0.32 0.00
440_K 131_A 0.83 0.32 0.00
234_E 21_I 0.83 0.32 0.00
101_A 50_Q 0.82 0.31 0.00
314_R 129_H 0.81 0.30 0.00
426_V 13_T 0.81 0.30 0.00
58_H 129_H 0.81 0.30 0.00
67_T 130_H 0.81 0.30 0.00
269_H 59_V 0.80 0.29 0.00
179_G 58_R 0.80 0.29 0.00
200_E 58_R 0.79 0.28 0.00
189_E 15_E 0.79 0.28 0.00
320_E 142_L 0.79 0.28 0.00
215_I 84_V 0.79 0.28 0.00
238_R 32_V 0.79 0.28 0.00
420_T 62_D 0.79 0.28 0.00
293_K 128_E 0.78 0.28 0.00
21_L 74_L 0.77 0.27 0.00
93_A 125_M 0.77 0.27 0.00
424_S 19_D 0.77 0.26 0.00
374_S 103_L 0.77 0.26 0.00
172_G 47_V 0.77 0.26 0.00
363_Y 116_I 0.77 0.26 0.00
43_S 5_H 0.76 0.26 0.00
159_E 47_V 0.76 0.26 0.00
360_L 56_Y 0.76 0.26 0.00
316_H 61_I 0.76 0.25 0.00
254_L 10_T 0.76 0.25 0.00
210_D 104_E 0.76 0.25 0.00
251_L 139_I 0.76 0.25 0.00
429_D 120_G 0.75 0.25 0.00
263_L 76_K 0.75 0.24 0.00
274_L 129_H 0.75 0.24 0.00
332_N 5_H 0.74 0.24 0.00
401_E 142_L 0.74 0.24 0.00
203_S 95_V 0.74 0.24 0.00
227_K 95_V 0.74 0.24 0.00
263_L 113_R 0.74 0.24 0.00
229_L 128_E 0.73 0.23 0.00
110_L 12_Q 0.73 0.23 0.00
118_V 131_A 0.73 0.23 0.00
146_H 139_I 0.73 0.23 0.00
363_Y 135_C 0.73 0.23 0.00
248_A 23_E 0.73 0.23 0.00
58_H 143_E 0.73 0.23 0.00
382_S 56_Y 0.73 0.23 0.00
237_A 37_V 0.73 0.23 0.00
412_F 56_Y 0.72 0.23 0.00
64_Q 1_H 0.72 0.23 0.00
209_S 21_I 0.72 0.23 0.00
211_D 83_E 0.72 0.23 0.00
202_D 58_R 0.72 0.22 0.00
155_S 39_G 0.72 0.22 0.00
275_S 48_L 0.72 0.22 0.00
85_N 127_S 0.72 0.22 0.00
186_L 68_L 0.71 0.22 0.00
321_Q 133_P 0.71 0.21 0.00
202_D 88_R 0.71 0.21 0.00
56_I 116_I 0.70 0.21 0.00
118_V 4_E 0.70 0.21 0.00
288_S 5_H 0.70 0.21 0.00
265_A 131_A 0.70 0.21 0.00
51_K 30_L 0.70 0.21 0.00
68_D 93_E 0.70 0.21 0.00
71_T 56_Y 0.70 0.21 0.00
418_E 40_R 0.70 0.21 0.00
319_E 56_Y 0.70 0.21 0.00
418_E 129_H 0.69 0.20 0.00
173_E 108_R 0.69 0.20 0.00
118_V 62_D 0.69 0.20 0.00
397_A 84_V 0.69 0.20 0.00
328_E 130_H 0.69 0.20 0.00
48_E 116_I 0.69 0.20 0.00
230_I 59_V 0.69 0.20 0.00
321_Q 37_V 0.69 0.20 0.00
133_E 110_G 0.69 0.20 0.00
133_E 39_G 0.68 0.20 0.00
106_V 85_V 0.68 0.20 0.00
378_I 43_A 0.68 0.20 0.00
188_S 21_I 0.68 0.20 0.00
324_K 135_C 0.68 0.20 0.00
195_E 101_D 0.68 0.19 0.00
67_T 123_E 0.68 0.19 0.00
439_S 47_V 0.68 0.19 0.00
189_E 76_K 0.67 0.19 0.00
250_S 30_L 0.67 0.19 0.00
204_I 142_L 0.67 0.19 0.00
221_I 86_I 0.67 0.19 0.00
210_D 52_R 0.67 0.19 0.00
395_V 118_V 0.67 0.19 0.00
92_I 139_I 0.67 0.19 0.00
33_L 15_E 0.67 0.19 0.00
172_G 11_S 0.66 0.18 0.00
374_S 100_S 0.66 0.18 0.00
83_P 128_E 0.66 0.18 0.00
130_P 10_T 0.66 0.18 0.00
404_K 85_V 0.66 0.18 0.00
45_L 27_R 0.66 0.18 0.00
93_A 84_V 0.66 0.18 0.00
136_K 39_G 0.66 0.18 0.00
378_I 32_V 0.66 0.18 0.00
408_F 86_I 0.66 0.18 0.00
343_I 127_S 0.66 0.18 0.00
50_N 139_I 0.66 0.18 0.00
136_K 67_E 0.66 0.18 0.00
150_P 101_D 0.66 0.18 0.00
410_V 82_I 0.66 0.18 0.00
200_E 88_R 0.66 0.18 0.00
374_S 17_M 0.66 0.18 0.00
251_L 99_L 0.66 0.18 0.00
83_P 90_V 0.66 0.18 0.00
375_P 60_R 0.66 0.18 0.00
402_R 32_V 0.65 0.18 0.00
349_F 113_R 0.65 0.18 0.00
389_F 11_S 0.65 0.18 0.00
76_D 111_E 0.65 0.18 0.00
57_T 78_K 0.65 0.18 0.00
134_V 140_G 0.65 0.18 0.00
321_Q 100_S 0.65 0.18 0.00
129_L 5_H 0.65 0.18 0.00
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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