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OPENSEQ.org
smeg
Genes: A B A+B
Length: 848 100 872
Sequences: 3644 1232 766
Seq/Len: 4.3 12.32 0.88
MirrorTree (Pazo et al. 2001) 0.14
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.06 0.02
2 0.01 0.06 0.02
5 0.01 0.06 0.03
10 0.01 0.06 0.03
20 0.01 0.06 0.04
100 0.03 0.06 0.13
∞ 0.13 0.09 0.81
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
622_V 64_V 1.45 0.70 0.01
489_G 96_M 1.09 0.38 0.00
663_I 64_V 1.08 0.38 0.00
108_I 96_M 1.03 0.34 0.00
487_V 22_S 1.01 0.32 0.00
176_R 40_S 0.94 0.27 0.00
529_S 76_S 0.93 0.26 0.00
729_Q 78_E 0.93 0.26 0.00
753_D 98_Q 0.90 0.24 0.00
773_L 31_V 0.90 0.24 0.00
544_R 40_S 0.90 0.24 0.00
349_E 50_F 0.89 0.24 0.00
725_D 35_P 0.89 0.24 0.00
732_D 71_V 0.89 0.23 0.00
717_I 48_K 0.89 0.23 0.00
280_G 75_G 0.87 0.22 0.00
139_I 90_A 0.87 0.22 0.00
336_A 38_L 0.85 0.21 0.00
243_K 79_S 0.84 0.20 0.00
754_K 53_S 0.84 0.20 0.00
203_V 88_H 0.83 0.20 0.00
752_S 32_W 0.83 0.20 0.00
789_I 20_V 0.83 0.20 0.00
755_A 31_V 0.83 0.20 0.00
177_N 69_K 0.83 0.20 0.00
344_P 43_T 0.82 0.20 0.00
498_K 78_E 0.82 0.19 0.00
346_Q 18_A 0.82 0.19 0.00
535_T 70_A 0.82 0.19 0.00
436_E 91_G 0.81 0.19 0.00
595_F 43_T 0.81 0.18 0.00
166_S 64_V 0.81 0.18 0.00
88_L 67_E 0.80 0.18 0.00
617_K 67_E 0.80 0.18 0.00
283_I 21_E 0.79 0.18 0.00
408_A 18_A 0.79 0.17 0.00
482_E 40_S 0.78 0.17 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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