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OPENSEQ.org
L33-vs-S7
Genes: A B A+B
Length: 55 179 209
Sequences: 1895 1685 1003
Seq/Len: 34.45 9.41 4.8
MirrorTree (Pazo et al. 2001) 0.43
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 0.08 0.11 0.00
2 0.08 0.11 0.01
5 0.08 0.11 0.06
10 0.08 0.11 0.60
20 0.08 0.11 1.37
100 0.10 0.11 2.32
∞ 0.13 0.11 4.29
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
8_K 24_A 0.92 0.70 0.01
6_R 114_K 0.85 0.60 0.01
33_K 131_K 0.82 0.56 0.01
53_K 137_K 0.80 0.54 0.01
52_A 96_R 0.78 0.50 0.01
31_P 101_M 0.77 0.49 0.01
50_K 130_N 0.77 0.49 0.01
29_T 29_I 0.77 0.49 0.01
48_I 83_S 0.76 0.47 0.01
18_G 2_P 0.75 0.47 0.01
39_F 104_I 0.75 0.47 0.01
33_K 69_V 0.74 0.45 0.01
42_V 76_K 0.74 0.45 0.01
45_Q 134_A 0.71 0.42 0.00
44_R 107_A 0.71 0.41 0.00
35_E 129_E 0.71 0.41 0.00
33_K 155_R 0.71 0.41 0.00
17_T 96_R 0.70 0.40 0.00
30_K 143_R 0.70 0.40 0.00
35_E 87_V 0.70 0.40 0.00
7_E 67_E 0.69 0.39 0.00
33_K 4_R 0.69 0.38 0.00
27_K 24_A 0.69 0.38 0.00
13_S 20_S 0.68 0.37 0.00
15_A 135_V 0.67 0.36 0.00
39_F 56_K 0.67 0.35 0.00
28_R 142_H 0.66 0.35 0.00
35_E 50_L 0.65 0.33 0.00
53_K 36_K 0.65 0.33 0.00
24_T 24_A 0.65 0.33 0.00
46_H 100_A 0.65 0.32 0.00
3_K 73_V 0.64 0.32 0.00
41_P 122_N 0.64 0.31 0.00
44_R 26_F 0.64 0.31 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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