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OPENSEQ.org
EttA-vs-L5
Genes: A B A+B
Length: 555 179 705
Sequences: 13557 2042 1558
Seq/Len: 24.43 11.41 2.21
MirrorTree (Pazo et al. 2001) 0.17
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 0.09 0.00
2 0.01 0.09 0.00
5 0.02 0.09 0.01
10 0.02 0.09 0.01
20 0.04 0.09 0.08
100 0.11 0.09 0.54
∞ 0.20 0.09 2.12
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
326_V 159_T 0.82 0.35 0.00
369_I 23_N 0.80 0.33 0.00
511_I 34_I 0.74 0.27 0.00
69_I 85_I 0.73 0.27 0.00
459_L 118_S 0.72 0.26 0.00
213_V 31_V 0.72 0.26 0.00
459_L 166_G 0.71 0.25 0.00
161_A 27_Q 0.70 0.24 0.00
60_E 146_V 0.69 0.23 0.00
436_V 19_E 0.69 0.23 0.00
510_H 152_L 0.69 0.23 0.00
449_E 143_Y 0.69 0.23 0.00
203_R 74_V 0.69 0.23 0.00
406_E 171_A 0.69 0.23 0.00
173_L 31_V 0.68 0.22 0.00
25_I 167_R 0.68 0.22 0.00
276_V 154_I 0.68 0.22 0.00
7_T 71_R 0.68 0.22 0.00
49_L 85_I 0.68 0.22 0.00
5_V 34_I 0.67 0.21 0.00
460_Q 56_D 0.67 0.21 0.00
330_R 154_I 0.66 0.21 0.00
22_L 147_D 0.66 0.21 0.00
324_L 24_S 0.66 0.21 0.00
404_V 87_C 0.66 0.20 0.00
215_I 120_K 0.65 0.20 0.00
23_K 173_F 0.65 0.20 0.00
374_Q 85_I 0.65 0.20 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
5491 1.87 EttA-vs-L5 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done
5466 2.21 EttA-vs-L5 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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