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OPENSEQ.org
ssa1 linker only with ydj1 jdomain
Genes: A B A+B
Length: 50 70 114
Sequences: 710 10285 256
Seq/Len: 14.2 146.93 2.25
MirrorTree (Pazo et al. 2001) 0.49
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 0.04 0.05 1.61
2 0.05 0.05 1.89
5 0.05 0.05 1.99
10 0.05 0.06 2.02
20 0.05 0.08 2.13
100 0.06 0.11 2.92
∞ 0.08 0.18 4.91
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
24_A 60_S 1.80 0.98 0.91
15_A 37_K 1.76 0.98 0.90
22_V 33_Y 1.49 0.92 0.77
39_L 43_A 1.44 0.91 0.73
9_S 28_K 1.34 0.86 0.65
9_S 51_S 1.33 0.85 0.64
24_A 55_E 1.32 0.85 0.63
39_L 37_K 1.31 0.84 0.62
22_V 70_G 1.30 0.83 0.61
1_F 37_K 1.28 0.82 0.59
30_D 10_I 1.24 0.80 0.55
7_N 51_S 1.19 0.75 0.50
7_N 28_K 1.07 0.64 0.37
21_A 59_D 1.07 0.63 0.37
50_I 15_V 1.05 0.62 0.35
10_I 50_A 1.04 0.60 0.34
27_L 30_A 1.00 0.56 0.30
39_L 30_A 0.99 0.55 0.29
1_F 15_V 0.98 0.53 0.28
22_V 44_A 0.97 0.53 0.27
36_Q 6_K 0.97 0.52 0.27
9_S 37_K 0.96 0.51 0.26
13_D 55_E 0.95 0.50 0.25
39_L 44_A 0.93 0.48 0.23
11_N 55_E 0.92 0.46 0.22
10_I 65_I 0.91 0.46 0.22
28_T 24_K 0.90 0.45 0.21
22_V 5_T 0.90 0.45 0.21
21_A 15_V 0.90 0.44 0.21
22_V 32_K 0.88 0.43 0.20
1_F 20_V 0.88 0.42 0.19
15_A 55_E 0.87 0.41 0.19
1_F 31_L 0.86 0.40 0.18
18_Y 68_Q 0.86 0.39 0.18
38_L 3_K 0.85 0.39 0.17
9_S 27_R 0.84 0.38 0.17
24_A 70_G 0.83 0.37 0.16
9_S 31_L 0.82 0.36 0.15
15_A 51_S 0.82 0.35 0.15
28_T 70_G 0.81 0.35 0.15
29_G 52_A 0.81 0.34 0.14
17_A 63_R 0.80 0.34 0.14
11_N 25_A 0.79 0.32 0.13
10_I 37_K 0.78 0.32 0.13
39_L 31_L 0.77 0.31 0.12
15_A 32_K 0.77 0.30 0.12
4_K 21_E 0.77 0.30 0.12
26_I 58_S 0.76 0.29 0.12
4_K 32_K 0.75 0.28 0.11
26_I 31_L 0.74 0.28 0.11
15_A 52_A 0.74 0.27 0.10
1_F 10_I 0.73 0.27 0.10
25_A 15_V 0.73 0.27 0.10
30_D 41_E 0.73 0.27 0.10
6_P 48_K 0.73 0.26 0.10
27_L 43_A 0.72 0.26 0.10
41_L 30_A 0.72 0.26 0.09
1_F 54_Y 0.72 0.26 0.09
38_L 38_N 0.71 0.25 0.09
35_T 30_A 0.71 0.25 0.09
15_A 42_E 0.71 0.25 0.09
15_A 58_S 0.70 0.24 0.09
37_D 30_A 0.70 0.24 0.09
49_G 50_A 0.70 0.24 0.08
18_Y 37_K 0.70 0.24 0.08
38_L 14_S 0.69 0.24 0.08
26_I 68_Q 0.69 0.23 0.08
28_T 58_S 0.69 0.23 0.08
24_A 61_E 0.68 0.23 0.08
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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