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OPENSEQ.org
cyayiscs
Genes: A B A+B
Length: 106 404 480
Sequences: 540 26545 403
Seq/Len: 5.09 65.71 0.84
MirrorTree (Pazo et al. 2001) 0.20
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 0.02 0.00
2 0.00 0.03 0.00
5 0.00 0.04 0.01
10 0.00 0.06 0.04
20 0.00 0.10 0.10
100 0.00 0.17 0.33
∞ 0.00 0.23 0.79
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
21_L 256_Y 1.23 0.49 0.00
62_L 272_G 1.12 0.40 0.00
39_L 282_K 1.04 0.34 0.00
50_I 127_Q 1.04 0.33 0.00
30_I 376_S 1.03 0.33 0.00
60_V 373_V 0.98 0.29 0.00
41_I 86_A 0.94 0.26 0.00
39_L 81_L 0.93 0.26 0.00
61_W 180_D 0.93 0.25 0.00
71_F 329_T 0.92 0.25 0.00
22_D 364_E 0.90 0.23 0.00
75_G 147_L 0.88 0.22 0.00
6_F 120_E 0.87 0.22 0.00
41_I 136_E 0.87 0.21 0.00
21_L 282_K 0.85 0.20 0.00
60_V 261_E 0.84 0.20 0.00
51_I 305_F 0.83 0.19 0.00
8_R 305_F 0.83 0.19 0.00
3_D 137_L 0.82 0.19 0.00
31_D 182_T 0.82 0.19 0.00
22_D 355_F 0.80 0.18 0.00
87_F 288_Y 0.80 0.17 0.00
32_C 119_F 0.80 0.17 0.00
30_I 353_I 0.80 0.17 0.00
32_C 160_V 0.79 0.17 0.00
59_Q 146_I 0.79 0.17 0.00
19_E 261_E 0.78 0.17 0.00
17_I 21_E 0.78 0.17 0.00
42_T 357_L 0.78 0.16 0.00
91_L 162_D 0.76 0.16 0.00
17_I 362_T 0.76 0.16 0.00
6_F 305_F 0.76 0.16 0.00
61_W 206_K 0.76 0.16 0.00
99_A 85_G 0.75 0.15 0.00
22_D 101_K 0.75 0.15 0.00
94_A 268_E 0.75 0.15 0.00
31_D 201_S 0.75 0.15 0.00
4_S 162_D 0.75 0.15 0.00
51_I 300_I 0.75 0.15 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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