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OPENSEQ.org
RsfS-vs-L33
Genes: A B A+B
Length: 105 55 157
Sequences: 2682 1895 1168
Seq/Len: 25.54 34.45 7.44
MirrorTree (Pazo et al. 2001) 0.44
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 0.08 0.01
2 0.01 0.08 0.02
5 0.01 0.08 0.03
10 0.01 0.08 0.09
20 0.01 0.08 0.30
100 0.01 0.10 1.21
∞ 0.01 0.13 7.30
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
90_M 39_F 0.91 0.80 0.01
90_M 33_K 0.85 0.73 0.01
14_I 53_K 0.83 0.71 0.01
54_H 50_K 0.81 0.68 0.01
83_G 33_K 0.76 0.60 0.01
93_E 29_T 0.72 0.56 0.01
14_I 10_K 0.71 0.53 0.01
2_Q 39_F 0.70 0.52 0.01
63_G 32_E 0.69 0.50 0.01
3_G 50_K 0.69 0.50 0.01
69_V 9_I 0.68 0.49 0.00
47_H 17_T 0.68 0.48 0.00
62_A 44_R 0.66 0.45 0.00
70_E 6_R 0.65 0.44 0.00
59_S 53_K 0.63 0.41 0.00
17_L 27_K 0.62 0.40 0.00
14_I 8_K 0.62 0.39 0.00
93_E 39_F 0.61 0.37 0.00
36_C 53_K 0.61 0.37 0.00
20_Q 24_T 0.60 0.36 0.00
94_S 9_I 0.59 0.35 0.00
39_I 28_R 0.59 0.35 0.00
97_L 50_K 0.59 0.35 0.00
40_C 23_T 0.59 0.35 0.00
25_L 32_E 0.58 0.34 0.00
74_S 37_K 0.58 0.33 0.00
41_T 46_H 0.57 0.33 0.00
102_K 33_K 0.57 0.33 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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