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OPENSEQ.org
EttA-vs-TsaA
Genes: A B A+B
Length: 555 231 756
Sequences: 8126 3099 1628
Seq/Len: 14.64 13.42 2.15
MirrorTree (Pazo et al. 2001) 0.25
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 0.00 0.00
2 0.01 0.00 0.02
5 0.01 0.00 0.26
10 0.01 0.00 0.31
20 0.02 0.00 0.40
100 0.06 0.00 0.75
∞ 0.17 0.00 2.07
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
36_G 6_I 1.15 0.70 0.01
503_F 127_Y 1.02 0.56 0.01
380_I 195_L 0.96 0.50 0.01
346_I 90_I 0.93 0.46 0.01
161_A 172_D 0.91 0.44 0.01
363_S 91_G 0.90 0.43 0.01
248_L 127_Y 0.89 0.42 0.01
225_V 163_V 0.84 0.37 0.01
20_H 6_I 0.81 0.34 0.01
324_L 197_I 0.80 0.32 0.01
295_E 81_L 0.79 0.32 0.01
340_D 204_E 0.76 0.29 0.00
315_P 94_T 0.76 0.28 0.00
507_I 62_G 0.75 0.28 0.00
403_T 7_D 0.74 0.27 0.00
25_I 92_V 0.74 0.27 0.00
377_S 3_I 0.74 0.27 0.00
256_A 185_E 0.72 0.26 0.00
354_I 192_E 0.72 0.25 0.00
403_T 6_I 0.72 0.25 0.00
120_K 123_Y 0.71 0.25 0.00
32_G 218_L 0.71 0.24 0.00
295_E 40_P 0.70 0.24 0.00
379_T 20_D 0.70 0.23 0.00
253_Q 120_G 0.70 0.23 0.00
450_R 43_Q 0.70 0.23 0.00
203_R 50_G 0.70 0.23 0.00
514_Y 45_I 0.69 0.22 0.00
369_I 199_C 0.68 0.21 0.00
498_S 75_I 0.67 0.21 0.00
28_S 78_A 0.67 0.21 0.00
509_T 219_R 0.67 0.21 0.00
6_Y 89_M 0.66 0.20 0.00
295_E 132_N 0.66 0.20 0.00
330_R 169_A 0.66 0.20 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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