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OPENSEQ.org
L33-vs-S4
Genes: A B A+B
Length: 55 206 258
Sequences: 1895 1236 680
Seq/Len: 34.45 6 2.64
MirrorTree (Pazo et al. 2001) 0.52
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 0.08 0.09 0.01
2 0.08 0.09 0.03
5 0.08 0.09 0.06
10 0.08 0.09 0.11
20 0.08 0.09 0.42
100 0.10 0.09 1.15
∞ 0.13 0.09 2.61
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_S 110_T 1.02 0.63 0.01
44_R 200_I 0.97 0.57 0.01
39_F 82_L 0.94 0.53 0.00
12_V 143_V 0.85 0.43 0.00
29_T 182_F 0.83 0.41 0.00
17_T 49_S 0.80 0.37 0.00
50_K 77_K 0.80 0.37 0.00
24_T 10_K 0.77 0.34 0.00
30_K 10_K 0.74 0.31 0.00
33_K 46_P 0.74 0.31 0.00
13_S 91_L 0.74 0.30 0.00
41_P 158_A 0.74 0.30 0.00
9_I 162_A 0.73 0.30 0.00
39_F 110_T 0.73 0.29 0.00
37_K 62_R 0.72 0.29 0.00
28_R 78_E 0.72 0.28 0.00
45_Q 147_E 0.71 0.28 0.00
14_S 140_N 0.69 0.26 0.00
52_A 206_K 0.69 0.26 0.00
46_H 14_R 0.69 0.25 0.00
7_E 44_R 0.69 0.25 0.00
40_D 193_A 0.68 0.25 0.00
45_Q 45_K 0.67 0.24 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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