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OPENSEQ.org
rrn5 uaf30 (B, 110-200)
Genes: A B A+B
Length: 101 91 174
Sequences: 2338 1141 263
Seq/Len: 23.15 12.54 1.51
MirrorTree (Pazo et al. 2001) 0.04
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 0.03 0.01
2 0.05 0.03 0.01
5 0.06 0.03 0.01
10 0.06 0.03 0.02
20 0.07 0.04 0.07
100 0.10 0.04 0.35
∞ 0.15 0.07 1.37
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
14_D 21_L 1.10 0.54 0.00
68_G 39_L 1.06 0.51 0.00
16_E 63_L 1.00 0.44 0.00
53_R 17_L 0.96 0.40 0.00
68_G 25_L 0.94 0.39 0.00
22_F 66_I 0.91 0.35 0.00
65_R 23_S 0.89 0.33 0.00
72_A 52_N 0.85 0.30 0.00
91_E 63_L 0.83 0.28 0.00
40_L 45_A 0.79 0.25 0.00
25_L 26_G 0.78 0.24 0.00
21_F 61_E 0.78 0.24 0.00
66_K 19_K 0.77 0.23 0.00
26_S 27_E 0.77 0.23 0.00
79_S 59_C 0.76 0.23 0.00
40_L 13_R 0.76 0.23 0.00
72_A 25_L 0.75 0.22 0.00
81_E 8_S 0.75 0.22 0.00
23_W 47_N 0.75 0.22 0.00
44_S 53_N 0.74 0.22 0.00
35_E 54_K 0.74 0.21 0.00
38_S 71_T 0.74 0.21 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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