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OPENSEQ.org
EttA-vs-L33
Genes: A B A+B
Length: 555 55 581
Sequences: 13557 1895 1918
Seq/Len: 24.43 34.45 3.3
MirrorTree (Pazo et al. 2001) 0.09
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 0.01 0.08 0.00
2 0.01 0.08 0.01
5 0.02 0.08 0.02
10 0.02 0.08 0.08
20 0.04 0.08 0.15
100 0.11 0.10 0.98
∞ 0.20 0.13 3.14
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
213_V 39_F 0.77 0.40 0.00
363_S 35_E 0.75 0.37 0.00
497_I 9_I 0.70 0.31 0.00
380_I 47_V 0.66 0.27 0.00
260_S 31_P 0.66 0.27 0.00
293_R 9_I 0.66 0.26 0.00
236_E 50_K 0.64 0.25 0.00
211_T 52_A 0.64 0.25 0.00
298_N 39_F 0.63 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)
ID Seq/Len Name Options I_Prob Status
5469 2.8 EttA-vs-L33 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5467 3.3 EttA-vs-L33 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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