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OPENSEQ.org
3
Genes: A B A+B
Length: 261 251 481
Sequences: 4024 73242 2291
Seq/Len: 15.42 291.8 4.76
MirrorTree (Pazo et al. 2001) 0.58
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 0.17 0.10 3.27
2 0.17 0.11 3.40
5 0.17 0.15 3.55
10 0.17 0.19 3.90
20 0.17 0.24 4.47
100 0.18 0.35 6.23
∞ 0.24 0.37 6.95
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
194_S 169_E 0.82 0.57 0.00
41_A 44_S 0.79 0.52 0.00
34_F 44_S 0.77 0.49 0.00
222_M 142_L 0.72 0.42 0.00
231_F 33_L 0.70 0.39 0.00
133_G 24_S 0.70 0.39 0.00
259_Q 35_L 0.69 0.38 0.00
61_I 126_T 0.68 0.37 0.00
215_G 5_V 0.68 0.36 0.00
69_G 141_L 0.67 0.35 0.00
139_A 28_K 0.67 0.35 0.00
22_L 151_V 0.67 0.35 0.00
11_A 31_K 0.65 0.33 0.00
101_V 141_L 0.62 0.29 0.00
223_V 165_Q 0.62 0.29 0.00
136_I 106_K 0.62 0.29 0.00
142_F 106_K 0.62 0.29 0.00
225_V 180_D 0.61 0.29 0.00
154_S 76_L 0.61 0.28 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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