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OPENSEQ.org
BamA-BamB (A, 210-810)
Genes: A B A+B
Length: 601 392 940
Sequences: 4403 3152 952
Seq/Len: 7.33 8.04 1.01
MirrorTree (Pazo et al. 2001) 0.16
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 0.01 0.02 0.00
2 0.01 0.02 0.00
5 0.01 0.04 0.02
10 0.01 0.05 0.02
20 0.02 0.05 0.04
100 0.04 0.07 0.25
∞ 0.19 0.13 0.96
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
251_G 375_D 1.36 0.67 0.00
180_L 160_G 1.13 0.46 0.00
507_L 305_V 1.04 0.38 0.00
156_L 138_D 1.01 0.35 0.00
298_K 73_Y 1.00 0.34 0.00
561_A 81_V 1.00 0.34 0.00
156_L 382_A 0.98 0.33 0.00
55_D 346_L 0.98 0.33 0.00
420_V 359_Q 0.98 0.32 0.00
385_N 84_L 0.97 0.32 0.00
105_R 174_L 0.97 0.32 0.00
263_S 207_A 0.96 0.31 0.00
508_E 296_I 0.94 0.30 0.00
62_V 142_A 0.94 0.30 0.00
133_D 163_L 0.94 0.29 0.00
511_T 135_N 0.91 0.27 0.00
450_T 86_A 0.89 0.26 0.00
49_V 131_V 0.88 0.25 0.00
326_S 175_N 0.88 0.25 0.00
52_T 72_V 0.87 0.24 0.00
168_L 348_W 0.87 0.24 0.00
99_I 353_D 0.87 0.24 0.00
232_Q 247_V 0.86 0.24 0.00
443_F 310_I 0.85 0.23 0.00
173_V 316_L 0.85 0.23 0.00
249_I 123_Y 0.85 0.23 0.00
241_L 164_I 0.84 0.22 0.00
450_T 350_N 0.84 0.22 0.00
124_K 209_V 0.83 0.22 0.00
443_F 305_V 0.83 0.22 0.00
399_Y 162_V 0.83 0.22 0.00
127_K 74_A 0.82 0.21 0.00
221_I 375_D 0.82 0.21 0.00
280_L 160_G 0.82 0.21 0.00
59_L 85_N 0.81 0.21 0.00
233_A 217_S 0.81 0.20 0.00
52_T 157_V 0.81 0.20 0.00
223_Y 38_V 0.81 0.20 0.00
281_F 223_Q 0.81 0.20 0.00
419_V 356_F 0.81 0.20 0.00
302_T 312_G 0.81 0.20 0.00
406_T 375_D 0.81 0.20 0.00
213_N 380_I 0.80 0.20 0.00
571_L 88_D 0.80 0.20 0.00
601_W 357_V 0.80 0.20 0.00
399_Y 380_I 0.80 0.20 0.00
364_N 362_V 0.79 0.19 0.00
92_V 178_D 0.79 0.19 0.00
433_G 320_S 0.79 0.19 0.00
412_I 122_V 0.79 0.19 0.00
208_K 331_V 0.78 0.19 0.00
363_F 118_S 0.78 0.19 0.00
79_T 258_V 0.78 0.18 0.00
304_V 185_V 0.77 0.18 0.00
112_R 308_L 0.77 0.18 0.00
436_E 138_D 0.77 0.18 0.00
249_I 117_V 0.77 0.18 0.00
582_F 332_L 0.77 0.18 0.00
61_G 258_V 0.77 0.18 0.00
401_K 73_Y 0.77 0.18 0.00
73_A 176_E 0.76 0.18 0.00
54_G 274_S 0.76 0.18 0.00
171_D 174_L 0.76 0.18 0.00
262_L 379_L 0.76 0.17 0.00
528_F 73_Y 0.75 0.17 0.00
265_T 297_Y 0.75 0.17 0.00
278_G 202_T 0.75 0.17 0.00
497_V 43_T 0.75 0.17 0.00
156_L 244_L 0.75 0.17 0.00
233_A 115_V 0.75 0.17 0.00
573_P 293_G 0.75 0.17 0.00
26_Y 373_A 0.75 0.17 0.00
99_I 72_V 0.74 0.17 0.00
426_W 134_L 0.74 0.17 0.00
451_V 353_D 0.74 0.17 0.00
77_Q 85_N 0.74 0.17 0.00
143_I 140_T 0.74 0.17 0.00
368_T 178_D 0.74 0.16 0.00
507_L 307_A 0.74 0.16 0.00
132_V 216_V 0.74 0.16 0.00
499_G 96_S 0.74 0.16 0.00
417_K 140_T 0.73 0.16 0.00
173_V 138_D 0.73 0.16 0.00
156_L 81_V 0.73 0.16 0.00
218_N 390_I 0.73 0.16 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)
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