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OPENSEQ.org
BA4bis
Genes: A B A+B
Length: 120 113 207
Sequences: 309 406 264
Seq/Len: 2.58 3.59 1.28
MirrorTree (Pazo et al. 2001) 0.77
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 1.12
2 0.00 0.00 1.13
5 0.00 0.01 1.13
10 0.00 0.01 1.13
20 0.01 0.02 1.13
100 0.01 0.02 1.13
∞ 0.03 0.05 1.14
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
38_L 49_Q 1.45 0.80 0.04
82_E 93_I 1.44 0.79 0.04
83_A 72_V 1.36 0.73 0.03
45_I 57_L 1.36 0.73 0.03
104_I 87_K 1.34 0.72 0.03
102_K 65_K 1.28 0.67 0.03
52_P 70_A 1.25 0.65 0.02
36_Y 53_E 1.21 0.60 0.02
19_S 107_V 1.18 0.57 0.02
109_Y 109_V 1.17 0.57 0.02
47_P 79_R 1.15 0.54 0.02
19_S 35_A 1.12 0.52 0.02
82_E 60_T 1.10 0.49 0.01
40_K 56_T 1.08 0.47 0.01
99_Q 34_Y 1.06 0.46 0.01
77_V 77_R 1.04 0.44 0.01
26_F 94_D 1.04 0.44 0.01
101_D 87_K 1.03 0.43 0.01
53_F 86_K 1.03 0.43 0.01
13_I 111_V 1.03 0.42 0.01
26_F 19_V 1.02 0.42 0.01
24_L 87_K 1.02 0.42 0.01
47_P 48_K 1.01 0.41 0.01
13_I 63_Q 1.00 0.40 0.01
21_E 100_L 1.00 0.40 0.01
56_I 48_K 0.99 0.39 0.01
46_E 111_V 0.99 0.39 0.01
32_K 33_F 0.99 0.39 0.01
50_W 64_M 0.98 0.38 0.01
103_N 55_I 0.98 0.38 0.01
112_V 32_K 0.97 0.38 0.01
38_L 81_S 0.97 0.37 0.01
68_N 80_V 0.97 0.37 0.01
33_A 33_F 0.97 0.37 0.01
45_I 53_E 0.96 0.36 0.01
72_Y 15_S 0.96 0.36 0.01
26_F 107_V 0.94 0.35 0.01
72_Y 27_K 0.93 0.34 0.01
95_Q 94_D 0.93 0.34 0.01
28_I 26_H 0.93 0.34 0.01
20_L 84_V 0.93 0.33 0.01
20_L 27_K 0.93 0.33 0.01
117_R 27_K 0.93 0.33 0.01
38_L 13_T 0.93 0.33 0.01
77_V 103_I 0.92 0.33 0.01
109_Y 59_I 0.92 0.33 0.01
105_A 22_D 0.92 0.32 0.01
98_S 75_I 0.91 0.32 0.01
100_H 68_E 0.91 0.32 0.01
19_S 54_E 0.91 0.32 0.01
28_I 23_L 0.91 0.32 0.01
36_Y 49_Q 0.91 0.32 0.01
15_W 16_G 0.91 0.31 0.01
95_Q 82_D 0.90 0.31 0.01
41_I 48_K 0.90 0.31 0.01
106_R 55_I 0.90 0.31 0.01
19_S 17_G 0.90 0.31 0.01
77_V 48_K 0.90 0.31 0.01
93_Q 74_H 0.90 0.31 0.01
98_S 111_V 0.89 0.30 0.01
31_R 83_V 0.89 0.30 0.01
26_F 99_M 0.89 0.30 0.01
45_I 104_G 0.88 0.29 0.01
55_E 22_D 0.88 0.29 0.01
31_R 107_V 0.88 0.29 0.01
53_F 65_K 0.88 0.29 0.01
71_I 63_Q 0.88 0.29 0.01
14_R 13_T 0.88 0.29 0.01
65_I 18_N 0.87 0.28 0.01
39_H 34_Y 0.87 0.28 0.01
11_K 59_I 0.87 0.28 0.01
16_V 55_I 0.86 0.28 0.01
86_V 75_I 0.86 0.28 0.01
93_Q 111_V 0.86 0.27 0.01
80_F 81_S 0.85 0.27 0.01
28_I 102_R 0.85 0.27 0.01
15_W 103_I 0.85 0.27 0.01
63_I 52_M 0.85 0.27 0.01
45_I 64_M 0.85 0.27 0.01
47_P 52_M 0.85 0.27 0.01
39_H 50_Q 0.84 0.26 0.01
33_A 87_K 0.84 0.26 0.01
94_T 97_V 0.84 0.26 0.01
27_P 81_S 0.83 0.26 0.01
31_R 105_K 0.83 0.26 0.01
59_G 91_F 0.83 0.25 0.01
20_L 19_V 0.83 0.25 0.01
84_L 50_Q 0.83 0.25 0.01
116_R 93_I 0.83 0.25 0.01
76_Y 96_L 0.83 0.25 0.01
36_Y 63_Q 0.82 0.25 0.01
65_I 61_Q 0.82 0.25 0.01
81_E 101_S 0.82 0.25 0.01
26_F 91_F 0.82 0.25 0.01
102_K 28_Q 0.81 0.24 0.01
13_I 80_V 0.81 0.24 0.01
85_Y 77_R 0.81 0.24 0.01
33_A 89_S 0.81 0.24 0.01
109_Y 80_V 0.81 0.24 0.01
75_M 100_L 0.80 0.23 0.01
33_A 55_I 0.80 0.23 0.01
42_Q 23_L 0.80 0.23 0.01
80_F 101_S 0.80 0.23 0.01
114_Q 17_G 0.80 0.23 0.01
60_V 7_S 0.79 0.22 0.01
102_K 49_Q 0.79 0.22 0.01
115_Q 57_L 0.78 0.22 0.01
29_T 89_S 0.78 0.22 0.01
28_I 29_D 0.78 0.22 0.01
19_S 63_Q 0.78 0.22 0.01
112_V 72_V 0.78 0.22 0.01
99_Q 55_I 0.78 0.21 0.01
80_F 100_L 0.78 0.21 0.01
45_I 73_L 0.77 0.21 0.01
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
14476 1.28 BA4bis Δgene:(0, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.04 Done - Shared
14474 BA4 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Running
14215 1.26 higBA4Long Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.04 Done
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