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OPENSEQ.org
BamA-Skp3
Genes: A B A+B
Length: 72 226 279
Sequences: 191 911 56
Seq/Len: 2.65 4.03 0.2
MirrorTree (Pazo et al. 2001) 0.49
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.00 0.01 0.03
∞ 0.00 0.04 0.19
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
64_A 191_V 1.62 0.39 0.00
54_L 145_L 1.50 0.32 0.00
58_P 145_L 1.48 0.31 0.00
54_L 119_R 1.46 0.30 0.00
23_N 180_W 1.35 0.24 0.00
49_Y 120_E 1.31 0.23 0.00
63_D 82_Q 1.28 0.22 0.00
3_I 75_K 1.26 0.21 0.00
21_E 182_G 1.24 0.20 0.00
62_T 118_E 1.21 0.19 0.00
61_I 151_G 1.21 0.19 0.00
17_Y 93_L 1.17 0.17 0.00
25_Y 160_N 1.16 0.17 0.00
57_R 149_V 1.15 0.17 0.00
19_I 186_D 1.15 0.17 0.00
17_Y 195_Y 1.15 0.17 0.00
61_I 66_Q 1.14 0.17 0.00
40_S 181_A 1.14 0.17 0.00
39_D 53_I 1.13 0.16 0.00
70_G 66_Q 1.10 0.15 0.00
45_D 191_V 1.09 0.15 0.00
58_P 134_F 1.08 0.15 0.00
4_K 219_A 1.08 0.15 0.00
45_D 99_T 1.06 0.14 0.00
66_F 24_L 1.03 0.13 0.00
46_I 155_T 1.03 0.13 0.00
22_V 201_V 1.03 0.13 0.00
65_I 193_Q 0.99 0.12 0.00
70_G 165_V 0.99 0.12 0.00
24_V 39_A 0.99 0.12 0.00
67_I 205_A 0.99 0.12 0.00
19_I 90_I 0.98 0.12 0.00
21_E 120_E 0.98 0.12 0.00
40_S 185_T 0.98 0.12 0.00
22_V 118_E 0.97 0.12 0.00
46_I 170_A 0.97 0.12 0.00
53_K 51_A 0.96 0.11 0.00
17_Y 205_A 0.96 0.11 0.00
58_P 181_A 0.96 0.11 0.00
66_F 186_D 0.95 0.11 0.00
53_K 50_I 0.95 0.11 0.00
11_K 77_E 0.95 0.11 0.00
41_V 96_Q 0.94 0.11 0.00
27_D 64_E 0.94 0.11 0.00
40_S 86_E 0.94 0.11 0.00
22_V 17_S 0.93 0.11 0.00
54_L 120_E 0.93 0.11 0.00
66_F 138_M 0.93 0.11 0.00
45_D 142_Y 0.92 0.10 0.00
17_Y 210_S 0.92 0.10 0.00
70_G 190_A 0.92 0.10 0.00
50_S 177_T 0.91 0.10 0.00
70_G 106_D 0.91 0.10 0.00
19_I 157_A 0.90 0.10 0.00
4_K 210_S 0.90 0.10 0.00
29_H 170_A 0.89 0.10 0.00
18_K 200_G 0.89 0.10 0.00
25_Y 120_E 0.89 0.10 0.00
24_V 84_K 0.89 0.10 0.00
49_Y 118_E 0.89 0.10 0.00
24_V 149_V 0.88 0.10 0.00
46_I 45_T 0.88 0.10 0.00
40_S 217_T 0.88 0.10 0.00
28_T 160_N 0.88 0.10 0.00
52_D 61_Q 0.88 0.10 0.00
69_K 138_M 0.88 0.10 0.00
61_I 116_I 0.87 0.09 0.00
25_Y 101_G 0.87 0.09 0.00
56_Y 156_Y 0.87 0.09 0.00
48_L 208_A 0.87 0.09 0.00
3_I 181_A 0.87 0.09 0.00
52_D 189_M 0.86 0.09 0.00
26_T 185_T 0.86 0.09 0.00
14_F 181_A 0.86 0.09 0.00
17_Y 140_S 0.86 0.09 0.00
49_Y 119_R 0.86 0.09 0.00
65_I 122_S 0.86 0.09 0.00
54_L 50_I 0.86 0.09 0.00
41_V 187_I 0.85 0.09 0.00
57_R 51_A 0.85 0.09 0.00
3_I 50_I 0.85 0.09 0.00
22_V 53_I 0.85 0.09 0.00
24_V 141_T 0.85 0.09 0.00
56_Y 82_Q 0.85 0.09 0.00
60_A 112_R 0.85 0.09 0.00
66_F 21_L 0.85 0.09 0.00
21_E 195_Y 0.84 0.09 0.00
64_A 186_D 0.84 0.09 0.00
25_Y 119_R 0.84 0.09 0.00
7_D 81_T 0.84 0.09 0.00
27_D 62_T 0.84 0.09 0.00
13_P 53_I 0.84 0.09 0.00
71_S 183_Q 0.83 0.09 0.00
8_S 167_D 0.83 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)
ID Seq/Len Name Options I_Prob Status
5332 0.37 BamA-Skp3 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2016_06b) 0.00 Done
5236 0.2 BamA-Skp3 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5234 0.1 BamA-Skp3 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06) Killed - Shared
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