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OPENSEQ.org
SpcS - ExoS (B, 230-390)
Genes: A B A+B
Length: 88 161 229
Sequences: 1540 570 69
Seq/Len: 17.5 3.54 0.3
MirrorTree (Pazo et al. 2001) 0.16
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 0.05 0.00
2 0.01 0.05 0.00
5 0.01 0.06 0.00
10 0.01 0.06 0.00
20 0.01 0.06 0.00
100 0.01 0.06 0.03
∞ 0.07 0.08 0.28
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
34_L 149_N 1.74 0.58 0.00
46_E 154_L 1.57 0.46 0.00
47_Q 104_G 1.38 0.34 0.00
49_L 52_N 1.33 0.31 0.00
49_L 114_S 1.33 0.31 0.00
68_W 90_R 1.32 0.31 0.00
35_V 33_S 1.28 0.28 0.00
30_L 70_Q 1.23 0.26 0.00
48_T 90_R 1.18 0.23 0.00
21_S 108_H 1.18 0.23 0.00
49_L 43_Y 1.17 0.22 0.00
49_L 90_R 1.15 0.22 0.00
65_T 116_S 1.12 0.20 0.00
70_G 150_E 1.08 0.19 0.00
43_Q 90_R 1.07 0.18 0.00
30_L 86_V 1.05 0.17 0.00
26_L 120_G 1.04 0.17 0.00
22_L 89_F 1.04 0.17 0.00
67_G 44_T 1.03 0.17 0.00
20_L 132_T 0.99 0.15 0.00
35_V 129_T 0.97 0.15 0.00
27_V 140_D 0.96 0.14 0.00
58_V 157_K 0.96 0.14 0.00
44_I 115_T 0.93 0.13 0.00
28_A 130_I 0.93 0.13 0.00
34_L 145_S 0.91 0.13 0.00
52_V 30_G 0.91 0.13 0.00
53_A 32_H 0.91 0.13 0.00
48_T 89_F 0.90 0.12 0.00
45_Q 158_E 0.90 0.12 0.00
73_L 66_K 0.90 0.12 0.00
56_V 100_A 0.89 0.12 0.00
80_T 145_S 0.89 0.12 0.00
62_L 113_L 0.89 0.12 0.00
6_I 126_G 0.88 0.12 0.00
38_V 32_H 0.88 0.12 0.00
34_L 129_T 0.88 0.12 0.00
68_W 52_N 0.88 0.12 0.00
68_W 114_S 0.88 0.12 0.00
28_A 129_T 0.87 0.12 0.00
48_T 52_N 0.87 0.12 0.00
48_T 114_S 0.87 0.12 0.00
20_L 105_K 0.86 0.11 0.00
2_S 111_G 0.85 0.11 0.00
16_L 140_D 0.85 0.11 0.00
25_V 155_Y 0.85 0.11 0.00
44_I 54_A 0.84 0.11 0.00
84_V 40_L 0.84 0.11 0.00
43_Q 43_Y 0.84 0.11 0.00
61_V 157_K 0.83 0.10 0.00
13_T 46_I 0.83 0.10 0.00
3_S 88_T 0.82 0.10 0.00
46_E 90_R 0.82 0.10 0.00
69_L 85_V 0.82 0.10 0.00
64_A 53_R 0.81 0.10 0.00
1_M 138_G 0.81 0.10 0.00
76_F 70_Q 0.81 0.10 0.00
45_Q 117_L 0.81 0.10 0.00
25_V 106_V 0.80 0.10 0.00
56_V 109_D 0.79 0.10 0.00
72_E 59_Q 0.79 0.10 0.00
45_Q 155_Y 0.79 0.10 0.00
87_V 35_A 0.79 0.10 0.00
36_S 48_Y 0.78 0.09 0.00
13_T 80_G 0.78 0.09 0.00
35_V 158_E 0.78 0.09 0.00
37_L 59_Q 0.78 0.09 0.00
59_V 94_G 0.77 0.09 0.00
83_K 48_Y 0.77 0.09 0.00
51_F 52_N 0.77 0.09 0.00
51_F 114_S 0.77 0.09 0.00
84_V 56_R 0.77 0.09 0.00
15_W 39_A 0.77 0.09 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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