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OPENSEQ.org
3a0r
Genes: A B A+B
Length: 349 116 456
Sequences: 28109 89405 13208
Seq/Len: 80.54 770.73 28.96
MirrorTree (Pazo et al. 2001) 0.93
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 0.03 0.10 20.42
2 0.07 0.13 22.11
5 0.09 0.16 23.90
10 0.10 0.19 26.04
20 0.13 0.23 28.40
100 0.20 0.32 34.51
∞ 0.26 0.34 36.36
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
148_T 13_I 1.40 0.99 0.74
169_K 15_E 1.37 0.99 0.73
177_E 12_N 1.33 0.99 0.70
152_G 16_L 1.25 0.99 0.63
160_H 23_E 1.06 0.95 0.44
173_I 15_E 1.05 0.94 0.42
155_M 104_F 0.95 0.89 0.32
176_N 12_N 0.93 0.88 0.30
159_K 23_E 0.89 0.85 0.26
155_M 103_N 0.88 0.84 0.25
170_Y 19_E 0.71 0.63 0.13
166_T 22_Q 0.66 0.54 0.10
166_T 19_E 0.65 0.52 0.10
149_I 12_N 0.63 0.48 0.09
153_F 16_L 0.61 0.45 0.08
179_S 103_N 0.60 0.44 0.08
173_I 12_N 0.59 0.41 0.07
156_R 19_E 0.58 0.41 0.07
148_T 102_F 0.55 0.35 0.06
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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