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OPENSEQ.org
LCB1_LCB2_Pfam
Genes: A B A+B
Length: 401 360 704
Sequences: 18622 15827 866
Seq/Len: 46.44 43.96 1.23
MirrorTree (Pazo et al. 2001) 0.04
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.04 0.00
2 0.00 0.04 0.00
5 0.01 0.04 0.02
10 0.01 0.05 0.06
20 0.01 0.05 0.12
100 0.08 0.11 0.42
∞ 0.13 0.16 1.14
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
156_L 279_R 0.71 0.17 0.00
156_L 351_E 0.71 0.17 0.00
108_T 281_L 0.66 0.14 0.00
88_I 296_A 0.66 0.14 0.00
109_V 144_I 0.66 0.14 0.00
88_I 223_D 0.65 0.14 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)
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