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OPENSEQ.org
A-TssLtm_vs_B-TssM3
Genes: A B A+B
Length: 34 33 64
Sequences: 166 184 129
Seq/Len: 4.88 5.58 2.02
MirrorTree (Pazo et al. 2001) 0.70
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 1.09
20 0.00 0.00 1.93
100 0.02 0.02 1.91
∞ 0.06 0.08 1.97
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
7_W 1_H 1.54 0.93 0.54
24_L 26_F 1.54 0.93 0.53
16_T 11_A 1.48 0.91 0.49
30_D 9_V 1.41 0.87 0.42
24_L 23_V 1.39 0.86 0.41
15_V 20_T 1.37 0.85 0.39
26_S 17_A 1.25 0.77 0.29
16_T 25_S 1.23 0.76 0.28
23_V 17_A 1.21 0.74 0.26
21_W 18_Q 1.18 0.71 0.24
21_W 26_F 1.18 0.71 0.24
4_T 14_L 1.15 0.68 0.21
9_S 8_A 1.10 0.64 0.19
15_V 14_L 1.03 0.56 0.15
29_A 31_S 1.03 0.56 0.14
33_A 25_S 1.00 0.53 0.13
23_V 21_G 1.00 0.53 0.13
19_G 31_S 0.99 0.52 0.13
20_L 19_G 0.99 0.52 0.13
29_A 8_A 0.98 0.50 0.12
13_G 13_I 0.98 0.50 0.12
4_T 18_Q 0.97 0.49 0.12
6_Y 1_H 0.97 0.49 0.12
23_V 20_T 0.96 0.49 0.12
14_I 33_V 0.95 0.47 0.11
9_S 12_A 0.93 0.45 0.10
12_A 10_M 0.92 0.44 0.10
32_V 9_V 0.91 0.42 0.09
11_G 8_A 0.90 0.41 0.09
18_A 13_I 0.90 0.41 0.09
34_R 27_L 0.89 0.40 0.09
32_V 3_W 0.88 0.40 0.08
4_T 19_G 0.88 0.39 0.08
20_L 18_Q 0.88 0.39 0.08
25_S 30_R 0.84 0.35 0.07
15_V 24_V 0.84 0.35 0.07
5_M 21_G 0.84 0.35 0.07
10_W 15_M 0.82 0.33 0.06
8_L 7_L 0.81 0.32 0.06
21_W 32_L 0.81 0.32 0.06
6_Y 11_A 0.80 0.31 0.06
32_V 4_R 0.80 0.31 0.06
23_V 32_L 0.78 0.30 0.05
22_C 26_F 0.78 0.29 0.05
21_W 30_R 0.78 0.29 0.05
24_L 25_S 0.78 0.29 0.05
18_A 22_M 0.77 0.28 0.05
13_G 1_H 0.76 0.28 0.05
4_T 16_M 0.76 0.28 0.05
6_Y 26_F 0.76 0.28 0.05
18_A 6_S 0.75 0.26 0.05
7_W 8_A 0.75 0.26 0.05
32_V 7_L 0.74 0.26 0.04
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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