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OPENSEQ.org
wspAwspR
Genes: A B A+B
Length: 542 347 873
Sequences: 16042 3627 469
Seq/Len: 29.6 10.45 0.54
MirrorTree (Pazo et al. 2001) 0.63
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 0.14 0.02 0.07
2 0.15 0.03 0.09
5 0.17 0.04 0.21
10 0.19 0.05 0.37
20 0.21 0.05 0.53
100 0.27 0.08 1.15
∞ 0.30 0.16 1.83
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
542_V 265_G 1.15 0.32 0.00
201_V 325_Q 1.14 0.31 0.00
263_L 67_I 0.99 0.22 0.00
277_S 67_I 0.99 0.22 0.00
342_A 21_V 0.97 0.21 0.00
170_L 210_V 0.96 0.20 0.00
18_I 233_A 0.94 0.19 0.00
513_V 185_F 0.91 0.18 0.00
252_G 232_V 0.87 0.16 0.00
246_F 66_V 0.85 0.16 0.00
542_V 133_I 0.84 0.15 0.00
244_D 229_L 0.84 0.15 0.00
104_T 189_L 0.84 0.15 0.00
9_R 230_R 0.84 0.15 0.00
373_N 248_A 0.84 0.15 0.00
541_K 279_E 0.83 0.15 0.00
487_G 21_V 0.82 0.14 0.00
509_T 114_A 0.82 0.14 0.00
6_V 73_M 0.81 0.14 0.00
473_Q 167_L 0.80 0.14 0.00
10_I 233_A 0.79 0.13 0.00
5_T 23_L 0.79 0.13 0.00
492_A 316_I 0.79 0.13 0.00
329_Q 257_M 0.79 0.13 0.00
428_I 326_A 0.78 0.13 0.00
203_V 259_L 0.78 0.13 0.00
141_R 300_V 0.77 0.12 0.00
390_S 123_L 0.77 0.12 0.00
205_G 265_G 0.77 0.12 0.00
276_T 86_R 0.77 0.12 0.00
222_I 233_A 0.77 0.12 0.00
158_R 21_V 0.76 0.12 0.00
341_L 97_I 0.76 0.12 0.00
263_L 206_L 0.76 0.12 0.00
43_Q 258_V 0.76 0.12 0.00
511_Q 100_S 0.76 0.12 0.00
446_M 301_S 0.76 0.12 0.00
7_R 23_L 0.75 0.12 0.00
297_A 257_M 0.75 0.12 0.00
495_A 119_Y 0.75 0.12 0.00
22_L 277_T 0.75 0.12 0.00
5_T 34_V 0.74 0.12 0.00
403_Y 165_L 0.74 0.12 0.00
492_A 208_I 0.74 0.12 0.00
24_M 119_Y 0.74 0.12 0.00
222_I 187_E 0.74 0.12 0.00
278_V 100_S 0.74 0.12 0.00
523_I 317_E 0.74 0.12 0.00
472_Q 25_D 0.74 0.11 0.00
53_I 185_F 0.74 0.11 0.00
6_V 122_K 0.74 0.11 0.00
17_I 120_L 0.74 0.11 0.00
131_D 133_I 0.73 0.11 0.00
263_L 205_L 0.73 0.11 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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