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OPENSEQ.org
trmd1
Genes: A B A+B
Length: 255 115 342
Sequences: 2542 1839 1704
Seq/Len: 9.97 15.99 4.98
MirrorTree (Pazo et al. 2001) 0.65
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 0.08 0.09 3.62
2 0.08 0.09 4.18
5 0.08 0.09 4.46
10 0.08 0.09 4.58
20 0.08 0.09 4.61
100 0.08 0.09 4.83
∞ 0.08 0.09 5.36
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
70_A 98_Y 0.98 0.77 0.02
114_R 63_K 0.81 0.56 0.01
162_H 63_K 0.74 0.46 0.01
73_A 43_F 0.70 0.41 0.01
58_P 27_E 0.68 0.38 0.01
145_A 32_V 0.68 0.37 0.01
226_N 43_F 0.67 0.37 0.01
191_E 17_V 0.67 0.36 0.01
150_D 88_R 0.67 0.36 0.01
142_E 63_K 0.66 0.35 0.01
26_V 58_A 0.63 0.31 0.01
114_R 9_E 0.62 0.30 0.01
203_E 99_Y 0.62 0.30 0.01
160_L 100_L 0.61 0.29 0.01
40_D 26_V 0.59 0.27 0.01
151_S 72_R 0.58 0.26 0.01
122_V 85_S 0.58 0.26 0.01
37_S 43_F 0.58 0.25 0.01
194_P 64_I 0.58 0.25 0.01
42_T 91_A 0.58 0.25 0.01
63_M 114_L 0.57 0.25 0.01
212_S 100_L 0.56 0.23 0.01
183_R 38_K 0.56 0.23 0.01
123_I 78_S 0.54 0.22 0.01
82_A 63_K 0.54 0.21 0.01
62_M 113_R 0.54 0.21 0.01
140_G 18_P 0.53 0.21 0.00
48_T 96_K 0.52 0.20 0.00
44_D 70_V 0.52 0.20 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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