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OPENSEQ.org
hdr25-lapa
Genes: A B A+B
Length: 132 102 225
Sequences: 287 1144 122
Seq/Len: 2.17 11.22 0.54
MirrorTree (Pazo et al. 2001) 0.82
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 0.00 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 0.52
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
35_Q 71_L 1.96 0.86 0.18
39_E 28_V 1.62 0.67 0.07
12_V 11_L 1.58 0.64 0.07
33_A 62_L 1.54 0.61 0.06
42_K 43_T 1.42 0.53 0.04
45_L 9_L 1.36 0.47 0.03
60_A 30_F 1.34 0.46 0.03
44_E 45_L 1.32 0.45 0.03
15_I 58_L 1.31 0.44 0.03
73_L 42_S 1.30 0.43 0.03
122_S 31_N 1.28 0.42 0.03
24_G 66_R 1.25 0.39 0.02
74_Y 42_S 1.24 0.38 0.02
39_E 70_S 1.24 0.38 0.02
20_A 43_T 1.22 0.37 0.02
29_R 15_V 1.20 0.35 0.02
61_E 77_K 1.17 0.34 0.02
52_L 42_S 1.17 0.33 0.02
7_L 8_L 1.16 0.32 0.02
75_Q 12_A 1.12 0.30 0.01
4_E 38_E 1.10 0.28 0.01
81_S 30_F 1.10 0.28 0.01
77_M 53_F 1.08 0.28 0.01
30_Q 10_V 1.08 0.28 0.01
10_L 11_L 1.08 0.27 0.01
72_Q 32_Y 1.08 0.27 0.01
52_L 30_F 1.07 0.27 0.01
99_L 56_G 1.07 0.27 0.01
64_D 77_K 1.07 0.27 0.01
8_I 14_F 1.07 0.27 0.01
122_S 5_L 1.06 0.26 0.01
103_E 54_A 1.05 0.25 0.01
62_L 5_L 1.04 0.25 0.01
48_Y 68_R 1.04 0.25 0.01
45_L 76_R 1.03 0.25 0.01
128_G 55_I 1.02 0.24 0.01
115_R 36_Q 1.02 0.24 0.01
40_K 36_Q 1.02 0.24 0.01
80_S 80_R 1.01 0.23 0.01
55_H 54_A 1.01 0.23 0.01
77_M 14_F 1.01 0.23 0.01
47_E 41_I 1.01 0.23 0.01
95_F 44_L 1.01 0.23 0.01
73_L 79_K 1.00 0.23 0.01
24_G 8_L 1.00 0.23 0.01
111_V 4_L 1.00 0.23 0.01
125_L 38_E 1.00 0.23 0.01
125_L 11_L 0.99 0.22 0.01
90_A 36_Q 0.99 0.22 0.01
129_A 55_I 0.99 0.22 0.01
124_L 21_G 0.99 0.22 0.01
71_R 70_S 0.99 0.22 0.01
125_L 10_V 0.99 0.22 0.01
13_G 2_K 0.98 0.22 0.01
19_V 7_F 0.98 0.22 0.01
71_R 39_Y 0.98 0.21 0.01
15_I 11_L 0.97 0.21 0.01
5_Y 45_L 0.96 0.21 0.01
113_M 11_L 0.95 0.20 0.01
67_A 56_G 0.95 0.20 0.01
23_F 8_L 0.95 0.20 0.01
112_Q 72_A 0.95 0.20 0.01
102_S 74_A 0.94 0.20 0.01
124_L 44_L 0.94 0.19 0.01
101_E 71_L 0.94 0.19 0.01
124_L 20_L 0.93 0.19 0.01
77_M 45_L 0.93 0.19 0.01
121_A 44_L 0.93 0.19 0.01
72_Q 74_A 0.93 0.19 0.01
118_S 50_A 0.93 0.19 0.01
10_L 42_S 0.93 0.19 0.01
16_I 12_A 0.93 0.19 0.01
81_S 38_E 0.92 0.19 0.01
48_Y 28_V 0.92 0.18 0.01
12_V 80_R 0.92 0.18 0.01
73_L 76_R 0.91 0.18 0.01
19_V 23_Q 0.91 0.18 0.01
7_L 36_Q 0.91 0.18 0.01
52_L 64_W 0.91 0.18 0.01
81_S 32_Y 0.91 0.18 0.01
27_K 75_E 0.91 0.18 0.01
118_S 44_L 0.91 0.18 0.01
58_R 1_M 0.90 0.18 0.01
10_L 54_A 0.90 0.18 0.01
103_E 9_L 0.90 0.17 0.01
20_A 68_R 0.90 0.17 0.01
72_Q 41_I 0.90 0.17 0.01
106_N 11_L 0.90 0.17 0.01
68_H 1_M 0.89 0.17 0.01
10_L 69_V 0.89 0.17 0.01
120_G 81_L 0.89 0.17 0.01
71_R 77_K 0.88 0.17 0.01
115_R 41_I 0.88 0.17 0.01
118_S 3_Y 0.88 0.17 0.01
16_I 8_L 0.88 0.17 0.01
5_Y 16_I 0.88 0.17 0.01
63_L 86_S 0.87 0.16 0.01
66_M 49_F 0.87 0.16 0.01
65_T 9_L 0.87 0.16 0.01
82_S 58_L 0.86 0.16 0.01
34_L 27_Q 0.86 0.16 0.01
25_N 76_R 0.86 0.16 0.01
8_I 18_V 0.86 0.16 0.01
86_P 32_Y 0.86 0.16 0.01
33_A 54_A 0.86 0.16 0.01
51_E 93_V 0.86 0.16 0.01
81_S 44_L 0.86 0.16 0.01
88_L 34_L 0.86 0.16 0.01
54_S 73_R 0.86 0.16 0.01
76_H 56_G 0.86 0.16 0.01
59_S 80_R 0.85 0.16 0.01
12_V 20_L 0.85 0.15 0.01
118_S 89_T 0.85 0.15 0.01
59_S 49_F 0.84 0.15 0.01
81_S 42_S 0.84 0.15 0.01
17_G 45_L 0.84 0.15 0.01
77_M 39_Y 0.84 0.15 0.01
130_K 7_F 0.83 0.15 0.01
120_G 35_A 0.83 0.15 0.01
67_A 36_Q 0.83 0.15 0.01
52_L 61_G 0.83 0.15 0.01
62_L 63_F 0.83 0.14 0.01
109_A 4_L 0.83 0.14 0.01
69_D 63_F 0.82 0.14 0.01
10_L 78_I 0.82 0.14 0.01
126_R 4_L 0.82 0.14 0.01
14_I 94_V 0.82 0.14 0.01
4_E 73_R 0.82 0.14 0.01
126_R 68_R 0.82 0.14 0.01
6_A 50_A 0.82 0.14 0.01
111_V 69_V 0.82 0.14 0.01
62_L 80_R 0.82 0.14 0.01
59_S 54_A 0.82 0.14 0.01
52_L 43_T 0.81 0.14 0.01
54_S 13_I 0.81 0.14 0.01
52_L 3_Y 0.81 0.14 0.01
50_E 36_Q 0.81 0.14 0.01
45_L 22_A 0.81 0.14 0.01
62_L 56_G 0.80 0.14 0.00
63_L 40_R 0.80 0.14 0.00
95_F 7_F 0.80 0.14 0.00
51_E 20_L 0.80 0.14 0.00
38_L 76_R 0.80 0.14 0.00
66_M 15_V 0.80 0.14 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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