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OPENSEQ.org
slf-mpk
Genes: A B A+B
Length: 389 384 720
Sequences: 2792 3973 304
Seq/Len: 7.18 10.35 0.42
MirrorTree (Pazo et al. 2001) 0.01
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 0.23 0.05 0.01
2 0.26 0.05 0.01
5 0.29 0.05 0.01
10 0.30 0.06 0.02
20 0.31 0.09 0.05
100 0.33 0.16 0.15
∞ 0.39 0.22 0.39
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
241_L 131_S 1.25 0.33 0.00
28_R 91_V 1.20 0.30 0.00
20_T 131_S 1.13 0.26 0.00
26_L 92_I 1.05 0.21 0.00
204_R 154_I 0.97 0.18 0.00
116_D 309_S 0.92 0.16 0.00
31_C 214_S 0.91 0.15 0.00
14_V 131_S 0.90 0.15 0.00
334_L 91_V 0.88 0.14 0.00
28_R 298_R 0.87 0.14 0.00
195_V 348_I 0.86 0.14 0.00
120_A 243_L 0.85 0.13 0.00
195_V 335_I 0.85 0.13 0.00
137_F 208_C 0.84 0.13 0.00
136_N 131_S 0.83 0.13 0.00
317_K 140_F 0.82 0.12 0.00
25_S 298_R 0.81 0.12 0.00
97_V 309_S 0.81 0.12 0.00
160_F 230_R 0.80 0.12 0.00
43_T 38_I 0.79 0.12 0.00
241_L 145_G 0.79 0.12 0.00
268_Y 217_V 0.79 0.12 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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