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OPENSEQ.org
BamA-Skp3
Genes: A B A+B
Length: 72 226 281
Sequences: 358 911 105
Seq/Len: 4.97 4.03 0.37
MirrorTree (Pazo et al. 2001) 0.39
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 0.02
10 0.00 0.01 0.02
20 0.00 0.01 0.03
100 0.02 0.01 0.06
∞ 0.05 0.04 0.35
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
58_P 145_L 1.66 0.58 0.00
29_H 157_A 1.46 0.45 0.00
57_R 165_V 1.41 0.41 0.00
57_R 50_I 1.37 0.38 0.00
24_V 124_Q 1.34 0.36 0.00
17_Y 151_G 1.33 0.36 0.00
69_K 183_Q 1.32 0.35 0.00
66_F 186_D 1.29 0.33 0.00
22_V 56_Q 1.29 0.33 0.00
54_L 119_R 1.16 0.26 0.00
57_R 149_V 1.16 0.26 0.00
4_K 177_T 1.11 0.23 0.00
49_Y 161_G 1.10 0.23 0.00
71_S 165_V 1.10 0.23 0.00
25_Y 178_V 1.02 0.19 0.00
17_Y 195_Y 1.01 0.18 0.00
25_Y 73_R 1.00 0.18 0.00
18_K 66_Q 0.99 0.17 0.00
61_I 112_R 0.98 0.17 0.00
12_V 153_L 0.97 0.17 0.00
25_Y 160_N 0.97 0.17 0.00
26_T 77_E 0.96 0.16 0.00
51_S 38_N 0.96 0.16 0.00
61_I 114_K 0.95 0.16 0.00
70_G 106_D 0.94 0.15 0.00
24_V 84_K 0.94 0.15 0.00
70_G 161_G 0.94 0.15 0.00
70_G 53_I 0.94 0.15 0.00
40_S 181_A 0.93 0.15 0.00
17_Y 149_V 0.93 0.15 0.00
20_S 94_K 0.92 0.15 0.00
18_K 67_R 0.92 0.15 0.00
24_V 150_Y 0.92 0.14 0.00
21_E 195_Y 0.91 0.14 0.00
43_H 43_A 0.90 0.14 0.00
70_G 165_V 0.90 0.14 0.00
25_Y 101_G 0.89 0.14 0.00
25_Y 117_D 0.89 0.14 0.00
70_G 66_Q 0.89 0.14 0.00
3_I 61_Q 0.89 0.14 0.00
61_I 97_L 0.89 0.14 0.00
46_I 170_A 0.89 0.14 0.00
24_V 152_S 0.89 0.14 0.00
59_K 180_W 0.88 0.14 0.00
54_L 145_L 0.88 0.13 0.00
65_I 193_Q 0.88 0.13 0.00
48_L 87_A 0.88 0.13 0.00
56_Y 168_A 0.87 0.13 0.00
17_Y 210_S 0.87 0.13 0.00
27_D 72_L 0.87 0.13 0.00
61_I 51_A 0.87 0.13 0.00
43_H 90_I 0.87 0.13 0.00
58_P 181_A 0.87 0.13 0.00
57_R 207_G 0.84 0.12 0.00
30_V 109_R 0.84 0.12 0.00
67_I 110_Q 0.84 0.12 0.00
17_Y 93_L 0.84 0.12 0.00
70_G 195_Y 0.83 0.12 0.00
25_Y 46_G 0.82 0.12 0.00
67_I 149_V 0.82 0.12 0.00
43_H 162_F 0.82 0.12 0.00
45_D 183_Q 0.82 0.12 0.00
68_T 134_F 0.82 0.12 0.00
22_V 143_Q 0.82 0.12 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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