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OPENSEQ.org
3a0r_A_B
Genes: A B A+B
Length: 334 116 443
Sequences: 11491 11885 1871
Seq/Len: 34.4 102.46 4.22
MirrorTree (Pazo et al. 2001) 0.54
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 0.01 2.45
2 0.05 0.02 2.76
5 0.06 0.06 3.09
10 0.07 0.10 3.53
20 0.09 0.13 4.16
100 0.13 0.21 7.19
∞ 0.21 0.29 10.02
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
161_K 15_E 1.62 0.99 0.91
140_T 13_I 1.46 0.97 0.85
144_G 16_L 1.19 0.89 0.65
148_R 20_E 1.13 0.86 0.59
162_Y 19_E 1.08 0.82 0.53
169_E 12_N 1.02 0.77 0.47
145_F 16_L 1.01 0.76 0.46
168_N 12_N 0.68 0.34 0.13
155_D 76_I 0.68 0.34 0.13
165_I 15_E 0.61 0.26 0.10
162_Y 20_E 0.58 0.23 0.08
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)
ID Seq/Len Name Options I_Prob Status
10439 29.39 3A0R_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.78 Done - Shared
1369 4.22 3a0r_A_B Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2013_03) 0.91 Done - Shared
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