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OPENSEQ.org
6fsu_2gsk
Genes: A B A+B
Length: 420 590 964
Sequences: 3830 30360 2506
Seq/Len: 9.12 51.46 2.6
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 0.04 0.01
2 0.01 0.05 0.02
5 0.01 0.09 0.10
10 0.01 0.12 0.23
20 0.02 0.17 0.46
100 0.03 0.26 1.51
∞ 0.13 0.30 2.48
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
236_W 336_I 0.85 0.43 0.00
336_T 123_V 0.72 0.29 0.00
96_Q 566_D 0.72 0.28 0.00
43_A 164_L 0.71 0.27 0.00
234_T 202_L 0.70 0.27 0.00
198_G 105_Y 0.70 0.26 0.00
222_I 211_S 0.67 0.24 0.00
70_A 30_I 0.67 0.23 0.00
29_F 540_V 0.66 0.23 0.00
214_L 351_G 0.66 0.23 0.00
216_T 30_I 0.65 0.22 0.00
309_G 261_L 0.65 0.22 0.00
375_L 557_V 0.64 0.21 0.00
366_N 104_E 0.62 0.20 0.00
70_A 438_D 0.61 0.19 0.00
234_T 502_Q 0.60 0.18 0.00
373_I 353_A 0.59 0.18 0.00
179_Y 123_V 0.59 0.18 0.00
202_I 103_V 0.59 0.18 0.00
90_L 26_T 0.59 0.17 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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