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OPENSEQ.org
54
Genes: A B A+B
Length: 108 317 413
Sequences: 18157 31764 2092
Seq/Len: 168.12 100.2 5.07
MirrorTree (Pazo et al. 2001) 0.31
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 0.03 1.54
2 0.01 0.03 1.84
5 0.01 0.05 2.52
10 0.01 0.07 3.44
20 0.01 0.09 4.92
100 0.02 0.18 11.41
∞ 0.11 0.24 19.89
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
84_G 276_T 0.75 0.48 0.00
97_G 122_P 0.73 0.45 0.00
98_Q 178_D 0.62 0.30 0.00
24_L 208_E 0.59 0.27 0.00
20_D 252_F 0.59 0.27 0.00
61_D 63_L 0.57 0.25 0.00
83_N 283_A 0.56 0.23 0.00
8_T 132_V 0.55 0.23 0.00
85_E 233_S 0.55 0.22 0.00
47_D 257_E 0.54 0.22 0.00
72_I 205_R 0.54 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)
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