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OPENSEQ.org
1UB4
Genes: A B A+B
Length: 82 111 189
Sequences: 437 1963 305
Seq/Len: 5.33 17.68 1.61
MirrorTree (Pazo et al. 2001) 0.69
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 1.58
2 0.00 0.00 1.60
5 0.00 0.01 1.62
10 0.00 0.01 1.63
20 0.00 0.02 1.65
100 0.01 0.04 1.69
∞ 0.05 0.12 1.88
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
53_F 104_A 1.78 0.96 0.79
9_W 25_Q 1.54 0.89 0.61
58_L 105_K 1.31 0.76 0.40
21_L 65_S 1.30 0.75 0.39
58_L 40_N 1.29 0.75 0.39
68_H 61_E 1.27 0.73 0.37
4_S 99_L 1.25 0.71 0.34
73_W 79_K 1.25 0.70 0.34
56_A 38_M 1.20 0.67 0.30
63_T 58_Y 1.14 0.60 0.25
68_H 39_Y 1.06 0.52 0.19
21_L 35_S 1.05 0.52 0.19
43_I 99_L 1.05 0.51 0.18
62_I 60_F 0.95 0.41 0.13
19_A 73_A 0.95 0.41 0.13
44_I 95_A 0.95 0.41 0.13
11_N 13_I 0.94 0.40 0.12
20_T 106_I 0.94 0.40 0.12
66_N 58_Y 0.94 0.39 0.12
68_H 57_G 0.94 0.39 0.12
7_K 81_I 0.93 0.39 0.12
78_D 86_R 0.92 0.38 0.11
42_L 100_Q 0.91 0.37 0.11
70_N 34_L 0.91 0.36 0.11
16_R 76_D 0.91 0.36 0.11
78_D 82_A 0.90 0.36 0.10
29_I 32_V 0.90 0.36 0.10
59_V 9_M 0.90 0.36 0.10
16_R 25_Q 0.89 0.35 0.10
40_G 42_K 0.89 0.35 0.10
46_P 28_H 0.88 0.34 0.10
17_I 84_R 0.88 0.34 0.10
2_I 49_V 0.88 0.34 0.10
58_L 10_G 0.86 0.32 0.09
17_I 69_R 0.86 0.32 0.09
21_L 16_D 0.86 0.32 0.09
57_E 37_F 0.85 0.31 0.08
58_L 26_A 0.84 0.30 0.08
59_V 61_E 0.84 0.30 0.08
50_E 70_D 0.84 0.30 0.08
78_D 24_E 0.83 0.29 0.07
48_R 32_V 0.82 0.29 0.07
12_S 25_Q 0.82 0.29 0.07
3_H 32_V 0.82 0.28 0.07
61_D 102_I 0.82 0.28 0.07
80_E 82_A 0.82 0.28 0.07
9_W 74_L 0.81 0.28 0.07
39_D 110_I 0.81 0.28 0.07
32_E 73_A 0.81 0.28 0.07
77_K 98_E 0.81 0.27 0.07
14_A 46_C 0.81 0.27 0.07
71_I 56_K 0.80 0.27 0.07
12_S 27_G 0.80 0.27 0.07
66_N 61_E 0.80 0.27 0.07
62_I 59_P 0.80 0.27 0.07
73_W 48_C 0.79 0.26 0.06
81_V 100_Q 0.79 0.26 0.06
78_D 27_G 0.79 0.26 0.06
23_Q 98_E 0.79 0.26 0.06
19_A 94_V 0.79 0.26 0.06
50_E 18_D 0.79 0.26 0.06
76_P 45_M 0.79 0.26 0.06
42_L 71_G 0.78 0.25 0.06
27_L 93_T 0.78 0.25 0.06
75_E 11_D 0.77 0.25 0.06
63_T 61_E 0.77 0.25 0.06
42_L 21_K 0.77 0.24 0.06
55_L 60_F 0.77 0.24 0.06
25_L 79_K 0.77 0.24 0.06
6_V 33_V 0.77 0.24 0.06
52_V 15_V 0.76 0.24 0.06
62_I 61_E 0.76 0.24 0.06
66_N 59_P 0.76 0.24 0.06
33_V 70_D 0.76 0.23 0.06
66_N 56_K 0.76 0.23 0.05
8_R 51_C 0.75 0.23 0.05
7_K 80_S 0.75 0.23 0.05
25_L 69_R 0.75 0.23 0.05
2_I 93_T 0.75 0.23 0.05
9_W 61_E 0.75 0.23 0.05
12_S 29_R 0.74 0.23 0.05
80_E 22_G 0.74 0.22 0.05
66_N 83_W 0.74 0.22 0.05
63_T 54_Q 0.74 0.22 0.05
34_K 104_A 0.74 0.22 0.05
22_M 83_W 0.74 0.22 0.05
59_V 60_F 0.73 0.22 0.05
14_A 34_L 0.73 0.22 0.05
55_L 82_A 0.73 0.22 0.05
13_P 36_P 0.73 0.21 0.05
30_D 9_M 0.73 0.21 0.05
20_T 26_A 0.73 0.21 0.05
15_V 81_I 0.73 0.21 0.05
45_E 18_D 0.72 0.21 0.05
56_A 73_A 0.72 0.21 0.05
6_V 94_V 0.72 0.21 0.04
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
4753 3.27 TA_five Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.77 Done - Shared
0721 2.49 1UB4_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.69 Done - Shared
0719 1.61 1UB4 Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.79 Done - Shared
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