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OPENSEQ.org
IscSIscA
Genes: A B A+B
Length: 404 107 506
Sequences: 31466 2921 1046
Seq/Len: 77.89 27.3 2.07
MirrorTree (Pazo et al. 2001) 0.47
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 0.07 0.00 0.30
2 0.09 0.00 1.18
5 0.11 0.01 1.83
10 0.12 0.01 2.05
20 0.15 0.02 2.38
100 0.25 0.03 3.61
∞ 0.29 0.09 5.12
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
85_G 42_L 0.96 0.49 0.00
153_V 107_V 0.94 0.47 0.00
364_E 64_V 0.94 0.46 0.00
32_T 28_L 0.92 0.45 0.00
141_M 26_L 0.92 0.44 0.00
134_L 107_V 0.91 0.43 0.00
91_Q 107_V 0.89 0.41 0.00
98_I 69_L 0.88 0.40 0.00
162_D 79_F 0.86 0.38 0.00
12_T 59_G 0.86 0.38 0.00
230_M 13_V 0.85 0.37 0.00
264_A 3_I 0.84 0.35 0.00
142_R 59_G 0.81 0.33 0.00
272_G 45_V 0.80 0.32 0.00
34_G 5_L 0.80 0.32 0.00
13_T 12_R 0.79 0.31 0.00
96_H 62_V 0.79 0.30 0.00
126_P 95_V 0.77 0.29 0.00
287_V 10_A 0.77 0.29 0.00
294_E 30_V 0.77 0.29 0.00
97_I 95_V 0.76 0.28 0.00
144_D 6_S 0.76 0.28 0.00
342_L 30_V 0.76 0.28 0.00
71_F 97_D 0.75 0.27 0.00
160_V 49_T 0.75 0.27 0.00
379_R 60_V 0.75 0.27 0.00
297_A 107_V 0.75 0.27 0.00
159_V 60_V 0.74 0.27 0.00
99_T 79_F 0.74 0.26 0.00
370_I 45_V 0.73 0.26 0.00
59_A 64_V 0.73 0.26 0.00
383_L 72_L 0.73 0.25 0.00
141_M 15_T 0.73 0.25 0.00
40_S 5_L 0.73 0.25 0.00
344_L 18_A 0.73 0.25 0.00
197_V 107_V 0.73 0.25 0.00
123_Y 105_F 0.72 0.25 0.00
37_A 107_V 0.72 0.25 0.00
245_P 44_F 0.72 0.24 0.00
251_G 68_S 0.72 0.24 0.00
114_L 84_L 0.72 0.24 0.00
250_V 45_V 0.72 0.24 0.00
317_L 41_V 0.71 0.24 0.00
168_E 51_E 0.71 0.24 0.00
289_L 11_A 0.71 0.24 0.00
45_W 36_S 0.71 0.23 0.00
365_E 24_F 0.71 0.23 0.00
134_L 7_D 0.70 0.23 0.00
370_I 38_M 0.70 0.23 0.00
11_A 14_N 0.70 0.23 0.00
348_L 59_G 0.70 0.23 0.00
264_A 4_T 0.70 0.23 0.00
69_I 17_L 0.70 0.23 0.00
13_T 88_F 0.70 0.23 0.00
279_N 60_V 0.69 0.22 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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