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OPENSEQ.org
rrn5 uaf30 (B, 1-65)
Genes: A B A+B
Length: 101 65 153
Sequences: 2338 960 253
Seq/Len: 23.15 14.77 1.65
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 0.05 0.05 0.01
2 0.05 0.06 0.01
5 0.06 0.06 0.01
10 0.06 0.06 0.02
20 0.07 0.06 0.09
100 0.10 0.06 0.42
∞ 0.15 0.08 1.52
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
39_L 7_Y 1.19 0.66 0.01
29_S 15_L 1.14 0.62 0.01
43_K 44_G 1.10 0.58 0.00
32_R 3_E 1.04 0.51 0.00
17_E 39_D 1.03 0.50 0.00
29_S 28_V 1.02 0.49 0.00
36_W 11_I 1.02 0.49 0.00
65_R 24_T 1.02 0.48 0.00
36_W 32_L 1.00 0.47 0.00
70_D 19_D 0.99 0.46 0.00
12_D 41_E 0.92 0.38 0.00
28_Y 43_Q 0.90 0.37 0.00
76_Y 20_L 0.85 0.32 0.00
45_A 40_V 0.83 0.30 0.00
78_M 47_I 0.81 0.29 0.00
40_L 28_V 0.81 0.28 0.00
52_Y 22_T 0.79 0.27 0.00
63_R 28_V 0.79 0.27 0.00
16_E 6_D 0.79 0.27 0.00
36_W 37_A 0.79 0.26 0.00
59_S 22_T 0.78 0.26 0.00
81_E 41_E 0.78 0.26 0.00
24_C 29_R 0.77 0.25 0.00
78_M 28_V 0.76 0.24 0.00
6_I 44_G 0.76 0.24 0.00
83_V 24_T 0.75 0.23 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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