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OPENSEQ.org
EttA-vs-RsfS
Genes: A B A+B
Length: 555 105 632
Sequences: 8126 2682 1425
Seq/Len: 14.64 25.54 2.25
MirrorTree (Pazo et al. 2001) 0.18
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 0.01 0.00
2 0.01 0.01 0.00
5 0.01 0.01 0.02
10 0.01 0.01 0.03
20 0.02 0.01 0.09
100 0.06 0.01 0.56
∞ 0.17 0.01 2.16
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
498_S 44_S 0.99 0.54 0.00
497_I 75_A 0.94 0.49 0.00
48_L 89_V 0.93 0.48 0.00
35_I 9_F 0.86 0.40 0.00
212_V 16_D 0.86 0.40 0.00
328_N 84_D 0.86 0.39 0.00
63_A 42_G 0.82 0.36 0.00
59_I 50_S 0.81 0.34 0.00
249_E 87_V 0.80 0.33 0.00
227_G 45_S 0.80 0.33 0.00
457_K 19_G 0.79 0.33 0.00
107_V 36_C 0.78 0.31 0.00
507_I 99_E 0.77 0.31 0.00
83_E 38_I 0.76 0.30 0.00
47_T 93_E 0.74 0.28 0.00
226_A 48_V 0.74 0.28 0.00
438_Q 42_G 0.73 0.27 0.00
494_A 6_L 0.73 0.27 0.00
161_A 11_I 0.72 0.26 0.00
445_L 90_M 0.72 0.26 0.00
408_V 76_D 0.71 0.25 0.00
80_L 89_V 0.71 0.25 0.00
131_I 22_I 0.70 0.24 0.00
67_P 39_I 0.70 0.24 0.00
52_M 80_V 0.70 0.24 0.00
377_S 26_D 0.69 0.24 0.00
291_L 39_I 0.69 0.23 0.00
281_K 40_C 0.69 0.23 0.00
511_I 34_T 0.69 0.23 0.00
504_L 83_G 0.68 0.23 0.00
346_I 80_V 0.68 0.22 0.00
354_I 93_E 0.68 0.22 0.00
215_I 96_R 0.67 0.22 0.00
21_I 18_K 0.67 0.21 0.00
156_W 55_V 0.66 0.21 0.00
26_S 84_D 0.66 0.21 0.00
367_R 4_K 0.66 0.21 0.00
490_F 26_D 0.66 0.21 0.00
52_M 30_K 0.66 0.21 0.00
132_I 89_V 0.66 0.21 0.00
52_M 63_G 0.66 0.21 0.00
46_S 89_V 0.66 0.20 0.00
308_T 50_S 0.65 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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