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OPENSEQ.org
3bwu_F_D
Genes: A B A+B
Length: 142 125 267
Sequences: 2900 294 182
Seq/Len: 20.42 2.35 0.68
MirrorTree (Pazo et al. 2001) 0.43
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 0.30 0.01 0.22
2 0.31 0.01 0.62
5 0.51 0.01 0.66
10 0.52 0.01 0.66
20 0.52 0.01 0.68
100 0.54 0.01 0.72
∞ 0.56 0.05 0.83
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
119_L 97_V 1.52 0.68 0.00
78_G 69_L 1.50 0.66 0.00
131_I 97_V 1.38 0.56 0.00
115_F 19_L 1.36 0.54 0.00
136_T 109_Q 1.21 0.42 0.00
9_E 93_L 1.20 0.41 0.00
51_V 30_P 1.20 0.41 0.00
99_A 9_L 1.19 0.40 0.00
125_P 104_L 1.19 0.40 0.00
43_P 98_Q 1.18 0.40 0.00
21_A 75_N 1.18 0.39 0.00
6_V 42_G 1.17 0.39 0.00
126_V 109_Q 1.16 0.38 0.00
139_L 93_L 1.15 0.37 0.00
37_F 51_F 1.13 0.35 0.00
49_S 39_L 1.11 0.34 0.00
128_A 5_N 1.09 0.33 0.00
111_N 72_M 1.07 0.31 0.00
103_T 37_I 1.07 0.31 0.00
3_G 107_G 1.06 0.31 0.00
133_A 40_N 1.05 0.30 0.00
82_Q 8_F 1.04 0.29 0.00
117_A 104_L 1.02 0.28 0.00
25_F 62_P 1.02 0.27 0.00
136_T 75_N 1.01 0.27 0.00
126_V 30_P 1.00 0.27 0.00
4_C 31_G 1.00 0.26 0.00
133_A 39_L 0.99 0.26 0.00
46_N 107_G 0.98 0.25 0.00
42_S 62_P 0.97 0.25 0.00
125_P 105_D 0.97 0.25 0.00
56_T 19_L 0.97 0.25 0.00
66_L 105_D 0.97 0.24 0.00
6_V 57_E 0.96 0.24 0.00
83_L 110_R 0.96 0.24 0.00
9_E 36_D 0.95 0.23 0.00
17_L 104_L 0.94 0.23 0.00
15_V 58_Q 0.94 0.23 0.00
57_G 6_P 0.94 0.23 0.00
137_F 29_P 0.94 0.22 0.00
136_T 8_F 0.93 0.22 0.00
129_G 31_G 0.93 0.22 0.00
89_N 87_D 0.93 0.22 0.00
79_L 104_L 0.93 0.22 0.00
9_E 68_Q 0.92 0.22 0.00
20_N 3_Y 0.92 0.21 0.00
129_G 116_P 0.92 0.21 0.00
119_L 51_F 0.91 0.21 0.00
92_P 37_I 0.91 0.21 0.00
67_L 119_F 0.91 0.21 0.00
112_T 115_I 0.91 0.21 0.00
54_G 5_N 0.91 0.21 0.00
112_T 113_L 0.91 0.21 0.00
8_A 95_T 0.91 0.21 0.00
29_G 6_P 0.90 0.21 0.00
4_C 116_P 0.90 0.21 0.00
131_I 62_P 0.90 0.20 0.00
115_F 95_T 0.89 0.20 0.00
133_A 78_S 0.89 0.20 0.00
25_F 119_F 0.89 0.20 0.00
45_G 98_Q 0.89 0.20 0.00
108_G 42_G 0.89 0.20 0.00
118_R 49_V 0.88 0.20 0.00
94_N 23_E 0.88 0.20 0.00
71_N 113_L 0.88 0.20 0.00
51_V 118_A 0.87 0.19 0.00
14_T 15_A 0.87 0.19 0.00
121_A 113_L 0.86 0.18 0.00
95_A 114_T 0.85 0.18 0.00
123_Q 96_M 0.85 0.18 0.00
81_I 60_I 0.85 0.18 0.00
26_N 48_D 0.85 0.18 0.00
45_G 41_N 0.85 0.18 0.00
140_E 45_A 0.84 0.17 0.00
20_N 39_L 0.84 0.17 0.00
59_A 65_T 0.84 0.17 0.00
21_A 36_D 0.84 0.17 0.00
23_K 65_T 0.84 0.17 0.00
36_P 9_L 0.83 0.17 0.00
90_Q 73_G 0.83 0.17 0.00
89_N 24_N 0.83 0.17 0.00
131_I 104_L 0.83 0.17 0.00
88_Q 35_V 0.82 0.17 0.00
33_P 120_M 0.82 0.16 0.00
129_G 90_C 0.82 0.16 0.00
2_N 20_S 0.82 0.16 0.00
128_A 67_A 0.82 0.16 0.00
77_S 82_M 0.81 0.16 0.00
18_M 46_T 0.81 0.16 0.00
120_M 38_Y 0.81 0.16 0.00
32_T 73_G 0.81 0.16 0.00
3_G 78_S 0.81 0.16 0.00
132_N 62_P 0.80 0.16 0.00
94_N 8_F 0.80 0.16 0.00
35_V 55_D 0.80 0.16 0.00
82_Q 36_D 0.80 0.15 0.00
132_N 97_V 0.80 0.15 0.00
15_V 73_G 0.79 0.15 0.00
139_L 5_N 0.79 0.15 0.00
28_I 49_V 0.79 0.15 0.00
43_P 1_D 0.79 0.15 0.00
29_G 79_V 0.78 0.15 0.00
70_E 8_F 0.78 0.15 0.00
84_L 49_V 0.78 0.14 0.00
44_C 64_L 0.78 0.14 0.00
23_K 120_M 0.77 0.14 0.00
88_Q 107_G 0.77 0.14 0.00
7_A 22_F 0.77 0.14 0.00
108_G 53_T 0.77 0.14 0.00
37_F 70_A 0.77 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.52 > 0.4) of paralogs.
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