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OPENSEQ.org
TM3vsTssLTM
Genes: A B A+B
Length: 33 40 64
Sequences: 184 163 125
Seq/Len: 5.58 4.08 1.95
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 0.00 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.10
10 0.00 0.00 0.96
20 0.00 0.00 1.71
100 0.02 0.02 1.73
∞ 0.08 0.06 1.77
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
11_A 22_T 1.90 0.98 0.93
1_H 13_W 1.53 0.92 0.77
26_F 30_L 1.51 0.91 0.76
23_V 30_L 1.47 0.90 0.73
9_V 36_D 1.40 0.86 0.67
20_T 21_V 1.34 0.83 0.62
18_Q 27_W 1.33 0.82 0.61
25_S 22_T 1.24 0.76 0.52
8_A 15_S 1.21 0.73 0.48
17_A 29_V 1.10 0.62 0.36
8_A 17_G 1.09 0.61 0.35
26_F 27_W 1.07 0.59 0.34
24_V 21_V 1.05 0.57 0.32
25_S 30_L 1.02 0.54 0.29
25_S 39_A 1.02 0.53 0.28
31_S 25_G 1.01 0.53 0.28
1_H 12_Y 0.99 0.50 0.26
19_G 26_L 0.98 0.49 0.25
19_G 10_T 0.97 0.48 0.24
33_V 20_I 0.96 0.48 0.24
13_I 19_G 0.96 0.47 0.24
28_A 24_A 0.95 0.46 0.23
14_L 10_T 0.95 0.46 0.23
12_A 15_S 0.95 0.46 0.23
21_G 11_M 0.92 0.43 0.20
8_A 35_A 0.91 0.41 0.19
18_Q 26_L 0.90 0.41 0.18
17_A 32_S 0.90 0.40 0.18
7_L 26_L 0.88 0.38 0.17
13_I 24_A 0.88 0.38 0.17
18_Q 10_T 0.87 0.38 0.16
14_L 21_V 0.86 0.37 0.16
26_F 23_L 0.86 0.36 0.16
31_S 35_A 0.86 0.36 0.16
19_G 25_G 0.86 0.36 0.16
11_A 21_V 0.84 0.35 0.15
4_R 38_V 0.84 0.34 0.14
3_W 38_V 0.84 0.34 0.14
32_L 27_W 0.83 0.34 0.14
33_V 38_V 0.83 0.33 0.14
22_M 24_A 0.82 0.33 0.14
21_G 29_V 0.82 0.32 0.13
7_L 12_Y 0.81 0.32 0.13
10_M 18_A 0.81 0.32 0.13
27_L 40_R 0.81 0.31 0.12
33_V 37_Q 0.80 0.30 0.12
9_V 38_V 0.79 0.30 0.12
8_A 13_W 0.79 0.29 0.11
14_L 32_S 0.77 0.27 0.10
7_L 14_L 0.75 0.26 0.10
20_T 29_V 0.74 0.25 0.09
32_L 29_V 0.74 0.25 0.09
15_M 33_V 0.73 0.25 0.09
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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