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OPENSEQ.org
C2-Tb
Genes: A B A+B
Length: 334 418 713
Sequences: 14390 1131 244
Seq/Len: 43.08 2.71 0.34
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 0.04 0.05 0.02
2 0.06 0.06 0.04
5 0.09 0.06 0.09
10 0.13 0.07 0.19
20 0.19 0.07 0.32
100 0.31 0.10 0.80
∞ 0.35 0.18 1.04
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
113_E 120_V 1.31 0.33 0.00
300_L 135_L 1.03 0.18 0.00
220_M 7_I 0.99 0.17 0.00
165_H 7_I 0.96 0.15 0.00
36_D 7_I 0.96 0.15 0.00
307_D 122_K 0.95 0.15 0.00
69_L 354_S 0.93 0.14 0.00
303_L 135_L 0.91 0.14 0.00
316_E 188_S 0.90 0.13 0.00
316_E 5_V 0.88 0.13 0.00
310_S 369_K 0.87 0.12 0.00
316_E 145_S 0.86 0.12 0.00
156_V 51_Y 0.85 0.12 0.00
94_I 17_G 0.85 0.12 0.00
217_L 151_L 0.85 0.12 0.00
128_T 275_T 0.84 0.12 0.00
127_L 40_S 0.84 0.12 0.00
42_R 7_I 0.84 0.12 0.00
87_L 169_V 0.83 0.11 0.00
298_D 361_S 0.83 0.11 0.00
50_S 32_P 0.83 0.11 0.00
127_L 151_L 0.81 0.11 0.00
175_W 120_V 0.81 0.11 0.00
95_T 7_I 0.79 0.10 0.00
322_Y 75_S 0.79 0.10 0.00
151_I 286_S 0.79 0.10 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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