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OPENSEQ.org
IscRIscS
Genes: A B A+B
Length: 162 404 528
Sequences: 5205 31466 1442
Seq/Len: 32.13 77.89 2.73
MirrorTree (Pazo et al. 2001) 0.56
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 0.01 0.07 1.42
2 0.01 0.09 1.60
5 0.01 0.11 2.22
10 0.02 0.12 2.55
20 0.02 0.15 2.99
100 0.03 0.25 4.63
∞ 0.10 0.29 7.02
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
121_L 41_H 0.99 0.60 0.00
125_T 132_I 0.74 0.32 0.00
3_L 253_G 0.73 0.30 0.00
60_G 206_K 0.73 0.30 0.00
60_G 180_D 0.73 0.30 0.00
92_C 351_S 0.72 0.29 0.00
47_S 160_V 0.71 0.28 0.00
125_T 263_M 0.70 0.27 0.00
24_G 163_I 0.70 0.27 0.00
32_S 162_D 0.70 0.27 0.00
17_V 159_V 0.69 0.26 0.00
32_S 294_E 0.68 0.25 0.00
87_V 174_G 0.66 0.23 0.00
102_D 73_S 0.66 0.23 0.00
79_V 197_V 0.65 0.23 0.00
3_L 234_G 0.65 0.22 0.00
126_L 147_L 0.64 0.22 0.00
77_G 71_F 0.64 0.22 0.00
73_S 97_I 0.64 0.22 0.00
106_T 150_I 0.62 0.21 0.00
78_E 135_K 0.62 0.20 0.00
31_I 136_E 0.62 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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