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OPENSEQ.org
mtrce
Genes: A B A+B
Length: 412 467 800
Sequences: 9020 13086 3386
Seq/Len: 21.89 28.02 4.23
MirrorTree (Pazo et al. 2001) 0.75
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 0.02 0.00 1.32
2 0.03 0.00 3.15
5 0.03 0.02 3.59
10 0.05 0.04 3.70
20 0.06 0.06 3.85
100 0.11 0.14 4.53
∞ 0.20 0.21 5.58
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
142_A 411_L 2.24 1.00 0.99
138_P 415_H 2.16 1.00 0.99
143_D 204_V 1.61 0.99 0.94
143_D 207_R 1.50 0.98 0.92
142_A 202_I 1.40 0.96 0.88
136_Y 417_V 1.18 0.89 0.74
144_A 408_L 1.15 0.87 0.71
142_A 407_R 1.13 0.86 0.69
144_A 411_L 1.06 0.81 0.62
138_P 206_G 0.81 0.52 0.32
142_A 198_N 0.80 0.50 0.31
361_G 162_H 0.69 0.35 0.19
149_E 412_R 0.69 0.35 0.19
144_A 199_A 0.66 0.32 0.16
144_A 202_I 0.60 0.26 0.12
225_Q 284_I 0.60 0.26 0.12
327_T 443_T 0.60 0.25 0.12
341_E 232_A 0.58 0.23 0.11
102_Q 309_I 0.58 0.23 0.10
267_L 232_A 0.57 0.23 0.10
102_Q 421_L 0.57 0.22 0.10
111_G 429_S 0.57 0.22 0.10
315_V 265_F 0.56 0.21 0.10
363_K 145_E 0.56 0.21 0.09
329_M 316_G 0.56 0.21 0.09
149_E 417_V 0.55 0.20 0.09
40_R 340_T 0.55 0.20 0.09
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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