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OPENSEQ.org
YhcB_LapA
Genes: A B A+B
Length: 132 102 231
Sequences: 262 1132 115
Seq/Len: 1.98 11.1 0.5
MirrorTree (Pazo et al. 2001) 0.85
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.08
∞ 0.00 0.00 0.49
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
15_I 58_L 1.75 0.74 0.01
12_V 11_L 1.68 0.69 0.01
35_Q 71_L 1.61 0.64 0.01
7_L 8_L 1.54 0.60 0.01
23_F 15_V 1.51 0.57 0.01
39_E 34_L 1.51 0.57 0.01
20_A 43_T 1.50 0.56 0.01
61_E 77_K 1.43 0.51 0.01
58_R 1_M 1.41 0.49 0.01
60_A 30_F 1.40 0.48 0.01
33_A 62_L 1.35 0.45 0.01
48_Y 68_R 1.29 0.41 0.00
46_D 96_H 1.27 0.39 0.00
15_I 11_L 1.26 0.38 0.00
39_E 70_S 1.23 0.36 0.00
81_S 30_F 1.23 0.36 0.00
73_L 42_S 1.23 0.35 0.00
22_R 36_Q 1.21 0.34 0.00
12_V 69_V 1.21 0.34 0.00
30_Q 92_A 1.21 0.34 0.00
77_M 14_F 1.20 0.34 0.00
127_T 89_T 1.19 0.33 0.00
39_E 28_V 1.18 0.32 0.00
115_R 36_Q 1.18 0.32 0.00
75_Q 12_A 1.17 0.32 0.00
27_K 74_A 1.15 0.30 0.00
29_R 15_V 1.15 0.30 0.00
49_R 87_P 1.13 0.29 0.00
24_G 8_L 1.13 0.29 0.00
125_L 38_E 1.13 0.29 0.00
42_K 43_T 1.12 0.28 0.00
94_P 14_F 1.11 0.28 0.00
80_S 2_K 1.10 0.28 0.00
115_R 41_I 1.08 0.26 0.00
124_L 21_G 1.08 0.26 0.00
72_Q 66_R 1.08 0.26 0.00
36_Y 7_F 1.08 0.26 0.00
81_S 32_Y 1.08 0.26 0.00
66_M 81_L 1.07 0.26 0.00
20_A 60_C 1.07 0.25 0.00
16_I 34_L 1.07 0.25 0.00
67_A 57_W 1.07 0.25 0.00
20_A 68_R 1.06 0.25 0.00
118_S 3_Y 1.06 0.25 0.00
40_K 36_Q 1.06 0.25 0.00
80_S 80_R 1.06 0.25 0.00
62_L 80_R 1.04 0.24 0.00
19_V 7_F 1.04 0.24 0.00
122_S 31_N 1.03 0.23 0.00
30_Q 10_V 1.03 0.23 0.00
54_S 13_I 1.03 0.23 0.00
118_S 89_T 1.02 0.23 0.00
50_E 12_A 1.01 0.22 0.00
62_L 78_I 1.01 0.22 0.00
91_E 64_W 1.01 0.22 0.00
54_S 73_R 1.00 0.22 0.00
5_Y 45_L 1.00 0.21 0.00
11_V 11_L 1.00 0.21 0.00
8_I 83_N 0.99 0.21 0.00
77_M 33_L 0.99 0.21 0.00
61_E 9_L 0.99 0.21 0.00
10_L 78_I 0.99 0.21 0.00
9_G 5_L 0.99 0.21 0.00
118_S 84_Q 0.99 0.21 0.00
37_E 8_L 0.99 0.21 0.00
24_G 66_R 0.98 0.21 0.00
44_E 45_L 0.98 0.20 0.00
34_L 59_I 0.98 0.20 0.00
67_A 56_G 0.97 0.20 0.00
125_L 88_A 0.97 0.20 0.00
20_A 5_L 0.97 0.20 0.00
38_L 76_R 0.97 0.20 0.00
8_I 26_Q 0.97 0.20 0.00
131_R 99_A 0.97 0.20 0.00
19_V 75_E 0.96 0.20 0.00
121_A 44_L 0.96 0.20 0.00
107_D 62_L 0.95 0.19 0.00
60_A 80_R 0.95 0.19 0.00
8_I 76_R 0.95 0.19 0.00
116_D 24_N 0.95 0.19 0.00
116_D 52_G 0.95 0.19 0.00
31_Q 49_F 0.95 0.19 0.00
52_L 30_F 0.95 0.19 0.00
7_L 36_Q 0.95 0.19 0.00
110_P 11_L 0.94 0.19 0.00
52_L 32_Y 0.94 0.19 0.00
124_L 44_L 0.94 0.18 0.00
115_R 62_L 0.93 0.18 0.00
74_Y 30_F 0.93 0.18 0.00
83_S 10_V 0.93 0.18 0.00
5_Y 16_I 0.93 0.18 0.00
131_R 4_L 0.93 0.18 0.00
10_L 54_A 0.92 0.18 0.00
7_L 62_L 0.91 0.17 0.00
121_A 49_F 0.91 0.17 0.00
19_V 23_Q 0.91 0.17 0.00
122_S 46_A 0.90 0.17 0.00
41_N 12_A 0.90 0.17 0.00
13_G 24_N 0.90 0.17 0.00
13_G 52_G 0.90 0.17 0.00
27_K 81_L 0.90 0.17 0.00
39_E 75_E 0.90 0.17 0.00
74_Y 42_S 0.90 0.17 0.00
122_S 2_K 0.89 0.16 0.00
52_L 42_S 0.89 0.16 0.00
75_Q 31_N 0.89 0.16 0.00
56_F 49_F 0.89 0.16 0.00
55_H 4_L 0.89 0.16 0.00
77_M 45_L 0.88 0.16 0.00
24_G 74_A 0.88 0.16 0.00
62_L 56_G 0.87 0.16 0.00
74_Y 57_W 0.87 0.15 0.00
120_G 81_L 0.86 0.15 0.00
74_Y 19_T 0.86 0.15 0.00
81_S 59_I 0.86 0.15 0.00
74_Y 32_Y 0.86 0.15 0.00
66_M 74_A 0.86 0.15 0.00
79_K 5_L 0.86 0.15 0.00
66_M 9_L 0.86 0.15 0.00
44_E 65_L 0.85 0.15 0.00
17_G 13_I 0.85 0.15 0.00
12_V 29_T 0.85 0.15 0.00
10_L 11_L 0.85 0.15 0.00
63_L 30_F 0.85 0.15 0.00
11_V 54_A 0.85 0.15 0.00
23_F 11_L 0.85 0.15 0.00
126_R 27_Q 0.85 0.15 0.00
1_M 34_L 0.84 0.15 0.00
1_M 23_Q 0.84 0.14 0.00
6_A 15_V 0.84 0.14 0.00
118_S 46_A 0.84 0.14 0.00
36_Y 4_L 0.84 0.14 0.00
80_S 4_L 0.84 0.14 0.00
101_E 55_I 0.84 0.14 0.00
69_D 35_A 0.83 0.14 0.00
20_A 67_V 0.83 0.14 0.00
63_L 5_L 0.83 0.14 0.00
27_K 1_M 0.83 0.14 0.00
4_E 15_V 0.83 0.14 0.00
34_L 18_V 0.83 0.14 0.00
6_A 50_A 0.83 0.14 0.00
62_L 3_Y 0.83 0.14 0.00
45_L 22_A 0.83 0.14 0.00
67_A 36_Q 0.83 0.14 0.00
52_L 61_G 0.82 0.14 0.00
71_R 82_E 0.82 0.14 0.00
77_M 39_Y 0.82 0.14 0.00
128_G 55_I 0.82 0.14 0.00
7_L 81_L 0.82 0.14 0.00
69_D 22_A 0.82 0.14 0.00
126_R 4_L 0.82 0.14 0.00
119_E 56_G 0.81 0.14 0.00
54_S 71_L 0.81 0.13 0.00
31_Q 66_R 0.81 0.13 0.00
4_E 38_E 0.81 0.13 0.00
111_V 27_Q 0.81 0.13 0.00
52_L 43_T 0.81 0.13 0.00
12_V 80_R 0.81 0.13 0.00
38_L 44_L 0.81 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
5752 0.01 j1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
2676 0.01 yhc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed
2602 0.5 YhcB_LapA Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.01 Done
2110 0.54 hdr25-lapa Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.18 Done
2107 0 hdr25-lapa Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_03) Killed
2105 0.35 hdr25-lapa Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed
2103 0.07 hdr25-lapa Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed
2084 0.01 hdr25-lapa Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed
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