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OPENSEQ.org
O48503-4
Genes: A B A+B
Length: 72 95 146
Sequences: 36173 1619 96
Seq/Len: 502.4 17.04 0.66
MirrorTree (Pazo et al. 2001) 0.23
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 0.08 0.01 0.16
2 0.09 0.02 0.20
5 0.11 0.02 0.29
10 0.13 0.02 0.39
20 0.17 0.02 0.57
100 0.24 0.03 1.59
∞ 0.28 0.09 2.98
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
8_L 66_G 1.29 0.48 0.00
12_I 19_K 1.26 0.46 0.00
37_L 19_K 1.24 0.43 0.00
51_A 68_S 1.21 0.41 0.00
48_I 23_I 1.19 0.40 0.00
18_T 67_V 1.15 0.37 0.00
62_I 46_Y 1.13 0.35 0.00
29_S 38_L 1.13 0.35 0.00
24_I 20_Q 1.12 0.34 0.00
5_Y 72_L 1.11 0.34 0.00
39_D 14_A 1.06 0.30 0.00
57_L 16_R 1.06 0.30 0.00
6_S 53_P 1.05 0.29 0.00
39_D 61_L 1.04 0.29 0.00
23_A 57_R 1.02 0.27 0.00
42_T 61_L 1.02 0.27 0.00
56_E 67_V 1.02 0.27 0.00
18_T 70_A 1.01 0.27 0.00
29_S 43_L 1.00 0.26 0.00
22_F 49_S 0.99 0.26 0.00
61_D 14_A 0.98 0.25 0.00
8_L 46_Y 0.98 0.24 0.00
22_F 79_M 0.97 0.24 0.00
18_T 52_S 0.97 0.24 0.00
18_T 12_I 0.97 0.24 0.00
30_E 38_L 0.97 0.24 0.00
54_V 72_L 0.97 0.24 0.00
26_M 73_M 0.96 0.24 0.00
10_G 69_E 0.95 0.23 0.00
47_E 38_L 0.95 0.23 0.00
35_L 23_I 0.94 0.22 0.00
10_G 76_D 0.93 0.22 0.00
63_P 23_I 0.93 0.21 0.00
54_V 63_K 0.92 0.21 0.00
9_L 37_K 0.90 0.20 0.00
18_T 18_L 0.89 0.20 0.00
54_V 58_I 0.89 0.20 0.00
46_D 67_V 0.89 0.20 0.00
44_K 61_L 0.89 0.19 0.00
29_S 19_K 0.88 0.19 0.00
28_L 6_S 0.88 0.19 0.00
8_L 58_I 0.87 0.19 0.00
11_K 12_I 0.87 0.19 0.00
36_K 45_Q 0.87 0.18 0.00
30_E 53_P 0.87 0.18 0.00
37_L 13_M 0.87 0.18 0.00
60_Q 65_L 0.86 0.18 0.00
5_Y 70_A 0.86 0.18 0.00
59_P 61_L 0.83 0.17 0.00
43_W 12_I 0.83 0.17 0.00
18_T 2_Q 0.83 0.17 0.00
39_D 9_L 0.83 0.16 0.00
38_N 23_I 0.82 0.16 0.00
25_A 46_Y 0.81 0.16 0.00
14_E 13_M 0.81 0.16 0.00
10_G 49_S 0.81 0.16 0.00
50_K 11_Q 0.81 0.16 0.00
47_E 77_V 0.80 0.15 0.00
7_S 60_L 0.80 0.15 0.00
44_K 16_R 0.79 0.15 0.00
19_Q 78_P 0.79 0.15 0.00
26_M 40_K 0.79 0.15 0.00
56_E 6_S 0.79 0.15 0.00
11_K 40_K 0.78 0.14 0.00
6_S 43_L 0.78 0.14 0.00
29_S 37_K 0.78 0.14 0.00
54_V 70_A 0.78 0.14 0.00
48_I 14_A 0.78 0.14 0.00
23_A 55_Q 0.77 0.14 0.00
12_I 13_M 0.77 0.14 0.00
56_E 61_L 0.76 0.14 0.00
61_D 9_L 0.76 0.14 0.00
15_K 56_N 0.76 0.14 0.00
28_L 7_N 0.76 0.13 0.00
28_L 39_S 0.75 0.13 0.00
59_P 19_K 0.75 0.13 0.00
12_I 53_P 0.74 0.13 0.00
57_L 48_N 0.74 0.13 0.00
18_T 15_E 0.74 0.13 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
9045 0.41 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9044 0.18 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
8890 0.66 O48503-4 Δgene:(1, 20) A:(1E-10, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8882 0.06 O48503-4 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
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