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OPENSEQ.org
JcT-LamB
Genes: A B A+B
Length: 166 446 606
Sequences: 193 650 68
Seq/Len: 1.16 1.46 0.11
MirrorTree (Pazo et al. 2001) 0.07
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.00
10 0.01 0.00 0.00
20 0.01 0.00 0.01
100 0.01 0.04 0.03
∞ 0.05 0.09 0.11
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
31_I 118_E 1.11 0.11 0.00
153_V 11_A 1.06 0.10 0.00
22_L 226_N 1.02 0.09 0.00
27_I 25_A 1.02 0.09 0.00
27_I 8_L 0.98 0.09 0.00
70_V 116_L 0.98 0.09 0.00
8_S 305_M 0.94 0.08 0.00
20_G 31_Y 0.92 0.08 0.00
20_G 126_W 0.92 0.08 0.00
20_G 128_G 0.92 0.08 0.00
20_G 151_G 0.92 0.08 0.00
20_G 301_G 0.92 0.08 0.00
20_G 386_P 0.92 0.08 0.00
20_G 439_G 0.92 0.08 0.00
20_G 443_E 0.92 0.08 0.00
20_G 445_W 0.92 0.08 0.00
24_A 31_Y 0.92 0.08 0.00
24_A 126_W 0.92 0.08 0.00
24_A 128_G 0.92 0.08 0.00
24_A 151_G 0.92 0.08 0.00
24_A 301_G 0.92 0.08 0.00
24_A 386_P 0.92 0.08 0.00
24_A 439_G 0.92 0.08 0.00
24_A 443_E 0.92 0.08 0.00
24_A 445_W 0.92 0.08 0.00
29_G 31_Y 0.92 0.08 0.00
29_G 126_W 0.92 0.08 0.00
29_G 128_G 0.92 0.08 0.00
29_G 151_G 0.92 0.08 0.00
29_G 301_G 0.92 0.08 0.00
29_G 386_P 0.92 0.08 0.00
29_G 439_G 0.92 0.08 0.00
29_G 443_E 0.92 0.08 0.00
29_G 445_W 0.92 0.08 0.00
4_S 434_D 0.89 0.07 0.00
88_Y 203_Q 0.89 0.07 0.00
65_D 351_I 0.87 0.07 0.00
30_D 347_T 0.85 0.07 0.00
155_V 11_A 0.85 0.07 0.00
1_N 263_S 0.85 0.07 0.00
9_N 294_M 0.84 0.07 0.00
139_S 204_M 0.84 0.07 0.00
157_K 101_A 0.84 0.07 0.00
157_K 335_I 0.83 0.07 0.00
15_N 257_V 0.83 0.07 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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