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OPENSEQ.org
JcT-LamB(-signal peptide)
Genes: A B A+B
Length: 166 421 582
Sequences: 193 633 68
Seq/Len: 1.16 1.5 0.12
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 0.12
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
22_L 201_N 1.10 0.11 0.00
31_I 93_E 0.97 0.09 0.00
8_S 280_M 0.97 0.09 0.00
70_V 91_L 0.94 0.08 0.00
20_G 6_Y 0.90 0.08 0.00
20_G 101_W 0.90 0.08 0.00
20_G 103_G 0.90 0.08 0.00
20_G 126_G 0.90 0.08 0.00
20_G 276_G 0.90 0.08 0.00
20_G 414_G 0.90 0.08 0.00
20_G 418_E 0.90 0.08 0.00
20_G 420_W 0.90 0.08 0.00
24_A 6_Y 0.90 0.08 0.00
24_A 101_W 0.90 0.08 0.00
24_A 103_G 0.90 0.08 0.00
24_A 126_G 0.90 0.08 0.00
24_A 276_G 0.90 0.08 0.00
24_A 414_G 0.90 0.08 0.00
24_A 418_E 0.90 0.08 0.00
24_A 420_W 0.90 0.08 0.00
29_G 6_Y 0.90 0.08 0.00
29_G 101_W 0.90 0.08 0.00
29_G 103_G 0.90 0.08 0.00
29_G 126_G 0.90 0.08 0.00
29_G 276_G 0.90 0.08 0.00
29_G 414_G 0.90 0.08 0.00
29_G 418_E 0.90 0.08 0.00
29_G 420_W 0.90 0.08 0.00
30_D 322_T 0.90 0.08 0.00
15_N 232_V 0.87 0.07 0.00
88_Y 178_Q 0.86 0.07 0.00
1_N 31_K 0.85 0.07 0.00
20_G 361_P 0.85 0.07 0.00
24_A 361_P 0.85 0.07 0.00
29_G 361_P 0.85 0.07 0.00
157_K 310_I 0.84 0.07 0.00
5_G 37_E 0.84 0.07 0.00
106_A 93_E 0.84 0.07 0.00
66_R 141_L 0.83 0.07 0.00
27_I 215_F 0.82 0.07 0.00
65_D 326_I 0.81 0.07 0.00
125_G 238_S 0.81 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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