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OPENSEQ.org
BamB_SurA
Genes: A B A+B
Length: 392 428 790
Sequences: 3152 2689 747
Seq/Len: 8.04 6.28 0.95
MirrorTree (Pazo et al. 2001) 0.33
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.02 0.00
2 0.02 0.04 0.00
5 0.04 0.04 0.00
10 0.05 0.04 0.01
20 0.05 0.04 0.03
100 0.07 0.06 0.19
∞ 0.13 0.20 0.91
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
131_V 37_V 1.85 0.92 0.44
207_A 287_A 1.15 0.46 0.07
122_V 255_I 1.15 0.46 0.07
159_D 92_S 1.02 0.34 0.04
171_L 404_R 0.99 0.32 0.04
202_T 48_S 0.97 0.30 0.03
353_D 205_Q 0.94 0.28 0.03
372_V 123_L 0.93 0.28 0.03
126_S 190_D 0.93 0.28 0.03
298_L 259_I 0.91 0.26 0.03
276_Q 255_I 0.91 0.26 0.03
296_I 419_A 0.90 0.26 0.03
178_D 210_A 0.90 0.26 0.03
323_L 75_I 0.90 0.25 0.03
138_D 296_P 0.89 0.24 0.02
258_V 274_R 0.88 0.24 0.02
162_V 323_A 0.88 0.24 0.02
134_L 35_G 0.88 0.24 0.02
81_V 301_E 0.87 0.23 0.02
164_I 376_H 0.87 0.23 0.02
157_V 42_V 0.87 0.23 0.02
66_A 310_I 0.86 0.23 0.02
219_V 29_A 0.86 0.23 0.02
380_I 35_G 0.85 0.22 0.02
91_E 310_I 0.85 0.22 0.02
122_V 93_D 0.84 0.22 0.02
134_L 132_I 0.84 0.22 0.02
67_L 405_K 0.84 0.21 0.02
19_G 72_E 0.84 0.21 0.02
366_G 357_L 0.83 0.21 0.02
270_L 133_R 0.83 0.21 0.02
162_V 72_E 0.83 0.21 0.02
87_D 401_L 0.83 0.21 0.02
21_S 422_Y 0.82 0.20 0.02
148_A 380_L 0.82 0.20 0.02
135_N 416_E 0.81 0.20 0.02
349_I 93_D 0.81 0.20 0.02
314_V 368_P 0.81 0.19 0.02
350_N 250_A 0.81 0.19 0.02
71_V 191_Q 0.81 0.19 0.02
290_I 68_H 0.80 0.19 0.02
256_G 116_S 0.80 0.19 0.02
325_R 74_L 0.80 0.19 0.02
175_N 259_I 0.80 0.19 0.02
81_V 211_D 0.79 0.19 0.02
254_V 409_E 0.79 0.18 0.01
138_D 215_L 0.79 0.18 0.01
69_D 139_S 0.79 0.18 0.01
343_E 189_S 0.78 0.18 0.01
378_L 401_L 0.78 0.18 0.01
135_N 119_A 0.78 0.18 0.01
297_Y 123_L 0.77 0.17 0.01
126_S 118_L 0.77 0.17 0.01
94_S 70_I 0.77 0.17 0.01
335_G 198_Q 0.77 0.17 0.01
335_G 90_K 0.77 0.17 0.01
273_R 351_P 0.77 0.17 0.01
290_I 153_L 0.77 0.17 0.01
268_T 402_M 0.77 0.17 0.01
67_L 154_P 0.76 0.17 0.01
364_S 365_M 0.76 0.17 0.01
219_V 314_I 0.76 0.17 0.01
372_V 99_A 0.76 0.17 0.01
69_D 73_R 0.75 0.17 0.01
182_K 416_E 0.75 0.16 0.01
312_G 250_A 0.75 0.16 0.01
156_V 75_I 0.75 0.16 0.01
332_L 309_Q 0.75 0.16 0.01
66_A 29_A 0.75 0.16 0.01
273_R 85_Q 0.75 0.16 0.01
98_A 245_Q 0.75 0.16 0.01
334_N 65_T 0.75 0.16 0.01
135_N 345_T 0.74 0.16 0.01
178_D 314_I 0.74 0.16 0.01
247_V 55_Q 0.74 0.16 0.01
180_A 92_S 0.74 0.16 0.01
81_V 96_L 0.74 0.16 0.01
253_V 181_I 0.74 0.16 0.01
51_S 96_L 0.74 0.16 0.01
316_L 98_Q 0.74 0.16 0.01
270_L 185_E 0.74 0.16 0.01
360_Q 181_I 0.73 0.16 0.01
365_S 314_I 0.73 0.16 0.01
349_I 409_E 0.73 0.16 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
13889 0.03 BamB-SurA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
12000 0.95 BamB_SurA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.44 Done
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