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OPENSEQ.org
EttA-vs-L1
Genes: A B A+B
Length: 555 234 753
Sequences: 12617 2756 1845
Seq/Len: 22.73 11.78 2.45
MirrorTree (Pazo et al. 2001) 0.18
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 0.01
5 0.01 0.09 0.02
10 0.02 0.09 0.04
20 0.03 0.09 0.11
100 0.11 0.09 0.59
∞ 0.19 0.09 2.34
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
365_L 98_E 0.86 0.42 0.00
467_L 63_T 0.81 0.37 0.00
363_S 28_A 0.79 0.34 0.00
363_S 162_R 0.79 0.34 0.00
430_R 214_I 0.72 0.28 0.00
213_V 75_V 0.71 0.27 0.00
8_M 153_V 0.70 0.25 0.00
504_L 98_E 0.68 0.24 0.00
405_W 42_V 0.68 0.23 0.00
63_A 12_R 0.66 0.22 0.00
183_M 181_D 0.65 0.21 0.00
144_L 72_S 0.65 0.21 0.00
64_R 98_E 0.65 0.21 0.00
54_G 224_V 0.65 0.21 0.00
321_D 53_R 0.65 0.21 0.00
10_R 182_A 0.64 0.21 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
5453 2.56 EttA-vs-L1 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done
5452 2.45 EttA-vs-L1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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