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OPENSEQ.org
EttA-vs-S7
Genes: A B A+B
Length: 555 179 682
Sequences: 12937 1765 1590
Seq/Len: 23.31 9.86 2.33
MirrorTree (Pazo et al. 2001) 0.12
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 0.10 0.00
2 0.01 0.10 0.01
5 0.01 0.10 0.02
10 0.02 0.10 0.05
20 0.03 0.10 0.09
100 0.11 0.10 0.53
∞ 0.19 0.10 2.17
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
12_G 146_E 1.00 0.57 0.00
271_K 119_R 0.90 0.46 0.00
369_I 118_L 0.88 0.43 0.00
25_I 18_F 0.85 0.40 0.00
251_K 134_A 0.85 0.39 0.00
427_Y 48_E 0.81 0.35 0.00
225_V 138_R 0.78 0.32 0.00
321_D 128_A 0.77 0.32 0.00
230_L 91_V 0.76 0.30 0.00
49_L 42_I 0.76 0.30 0.00
26_S 38_T 0.75 0.29 0.00
435_G 149_K 0.73 0.28 0.00
263_A 143_R 0.73 0.27 0.00
369_I 24_A 0.71 0.26 0.00
388_L 73_V 0.70 0.25 0.00
10_R 38_T 0.70 0.24 0.00
372_Q 76_K 0.69 0.24 0.00
161_A 138_R 0.69 0.24 0.00
324_L 21_E 0.69 0.24 0.00
338_L 107_A 0.68 0.23 0.00
151_L 104_I 0.68 0.23 0.00
197_S 104_I 0.68 0.23 0.00
54_G 39_A 0.67 0.23 0.00
363_S 104_I 0.67 0.22 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
5455 1.94 EttA-vs-S7 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5454 2.33 EttA-vs-S7 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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