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OPENSEQ.org
wspAwspF
Genes: A B A+B
Length: 542 335 876
Sequences: 16042 3044 783
Seq/Len: 29.6 9.09 0.89
MirrorTree (Pazo et al. 2001) 0.58
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 0.01 0.08
2 0.15 0.01 0.30
5 0.17 0.02 0.66
10 0.19 0.02 0.76
20 0.21 0.03 0.89
100 0.27 0.05 1.51
∞ 0.30 0.13 2.27
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 301_S 1.40 0.66 0.00
271_S 20_L 1.14 0.43 0.00
247_G 28_I 1.11 0.41 0.00
308_E 77_V 1.11 0.41 0.00
516_L 62_V 1.07 0.37 0.00
126_Y 2_R 1.06 0.37 0.00
304_A 222_L 1.05 0.35 0.00
516_L 273_L 1.01 0.32 0.00
271_S 230_I 0.94 0.27 0.00
67_T 301_S 0.94 0.27 0.00
122_V 27_Q 0.93 0.27 0.00
535_N 115_A 0.93 0.26 0.00
20_I 156_I 0.91 0.25 0.00
415_R 249_Y 0.90 0.24 0.00
98_I 300_A 0.90 0.24 0.00
309_I 66_R 0.88 0.23 0.00
12_A 181_V 0.88 0.23 0.00
387_N 157_G 0.87 0.23 0.00
203_V 30_W 0.86 0.22 0.00
432_V 100_D 0.85 0.21 0.00
278_V 20_L 0.83 0.20 0.00
9_R 223_L 0.83 0.20 0.00
304_A 227_N 0.83 0.20 0.00
66_Q 81_V 0.83 0.20 0.00
497_Q 270_G 0.83 0.20 0.00
155_E 316_A 0.82 0.20 0.00
542_V 314_I 0.82 0.20 0.00
391_L 283_G 0.82 0.19 0.00
542_V 20_L 0.81 0.19 0.00
230_A 4_G 0.81 0.19 0.00
391_L 73_P 0.81 0.19 0.00
34_T 269_V 0.81 0.19 0.00
313_S 322_S 0.81 0.19 0.00
253_F 77_V 0.81 0.19 0.00
428_I 248_V 0.80 0.18 0.00
360_A 195_M 0.80 0.18 0.00
312_T 158_A 0.80 0.18 0.00
253_F 272_L 0.80 0.18 0.00
398_E 104_T 0.79 0.18 0.00
421_T 249_Y 0.79 0.18 0.00
223_V 24_P 0.79 0.18 0.00
301_E 228_N 0.78 0.17 0.00
143_E 301_S 0.78 0.17 0.00
444_M 198_W 0.78 0.17 0.00
258_E 20_L 0.78 0.17 0.00
308_E 187_V 0.78 0.17 0.00
498_I 96_Y 0.77 0.17 0.00
264_V 6_V 0.77 0.17 0.00
70_L 322_S 0.77 0.17 0.00
206_I 2_R 0.77 0.17 0.00
188_D 153_L 0.77 0.17 0.00
390_S 225_G 0.77 0.17 0.00
399_K 198_W 0.76 0.16 0.00
237_R 296_A 0.76 0.16 0.00
406_G 253_I 0.76 0.16 0.00
498_I 3_I 0.76 0.16 0.00
309_I 284_L 0.75 0.16 0.00
270_S 282_Q 0.75 0.16 0.00
419_D 184_V 0.75 0.16 0.00
387_N 253_I 0.75 0.16 0.00
421_T 100_D 0.75 0.16 0.00
503_V 50_V 0.75 0.16 0.00
127_L 77_V 0.75 0.16 0.00
505_L 90_V 0.75 0.16 0.00
246_F 88_H 0.75 0.16 0.00
414_V 198_W 0.74 0.15 0.00
238_L 18_R 0.74 0.15 0.00
414_V 234_R 0.74 0.15 0.00
50_M 197_E 0.74 0.15 0.00
352_M 58_V 0.74 0.15 0.00
276_T 312_A 0.74 0.15 0.00
19_A 62_V 0.73 0.15 0.00
506_G 284_L 0.73 0.15 0.00
379_I 155_A 0.73 0.15 0.00
244_D 240_Y 0.73 0.15 0.00
405_R 62_V 0.73 0.15 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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