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OPENSEQ.org
test
Genes: A B A+B
Length: 139 287 424
Sequences: 1498 1911 1024
Seq/Len: 10.78 6.66 2.42
MirrorTree (Pazo et al. 2001) 0.76
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 0.03
2 0.00 0.00 2.30
5 0.00 0.00 2.36
10 0.00 0.00 2.37
20 0.00 0.00 2.40
100 0.00 0.00 2.44
∞ 0.01 0.02 2.61
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
43_L 56_L 1.69 0.97 0.86
9_V 215_L 1.39 0.89 0.67
40_A 207_L 1.21 0.79 0.49
95_A 189_L 1.20 0.78 0.48
69_I 221_R 1.12 0.71 0.41
75_G 197_D 1.08 0.67 0.37
71_E 244_M 1.08 0.67 0.36
71_E 26_M 1.03 0.61 0.31
49_G 5_K 1.03 0.61 0.31
51_I 237_A 1.02 0.60 0.30
12_A 6_E 1.01 0.59 0.29
89_D 242_A 0.98 0.56 0.27
28_G 209_E 0.98 0.56 0.27
72_V 170_I 0.97 0.54 0.26
23_K 16_N 0.96 0.54 0.25
5_Y 46_A 0.96 0.53 0.25
67_G 222_R 0.95 0.53 0.24
71_E 48_T 0.94 0.51 0.23
32_E 224_V 0.92 0.49 0.22
41_P 206_Y 0.90 0.47 0.20
72_V 242_A 0.90 0.46 0.20
48_P 30_S 0.90 0.46 0.20
86_R 26_M 0.89 0.45 0.19
34_G 223_Y 0.88 0.44 0.19
73_Q 55_H 0.88 0.44 0.18
64_Y 14_V 0.88 0.43 0.18
8_D 48_T 0.87 0.43 0.18
43_L 52_V 0.87 0.43 0.18
10_V 28_A 0.86 0.41 0.17
131_V 172_S 0.86 0.41 0.17
16_M 82_S 0.85 0.41 0.17
10_V 231_G 0.85 0.41 0.17
71_E 206_Y 0.85 0.41 0.16
36_Y 277_L 0.85 0.41 0.16
64_Y 235_N 0.84 0.40 0.16
10_V 233_V 0.84 0.40 0.16
45_A 215_L 0.84 0.39 0.15
23_K 242_A 0.84 0.39 0.15
30_E 215_L 0.84 0.39 0.15
59_H 160_Y 0.82 0.38 0.15
49_G 92_N 0.82 0.38 0.14
88_Q 224_V 0.82 0.37 0.14
80_L 35_S 0.82 0.37 0.14
32_E 234_E 0.82 0.37 0.14
34_G 5_K 0.82 0.37 0.14
66_S 160_Y 0.81 0.36 0.14
67_G 45_Y 0.81 0.36 0.14
77_V 35_S 0.81 0.36 0.14
82_D 222_R 0.81 0.36 0.14
99_K 16_N 0.80 0.35 0.13
12_A 146_L 0.80 0.35 0.13
79_V 160_Y 0.80 0.35 0.13
66_S 49_M 0.79 0.34 0.13
45_A 228_V 0.79 0.34 0.13
30_E 209_E 0.79 0.34 0.12
25_Q 242_A 0.79 0.34 0.12
44_T 278_T 0.79 0.34 0.12
25_Q 191_L 0.79 0.34 0.12
17_F 177_N 0.78 0.33 0.12
67_G 25_E 0.78 0.33 0.12
26_V 212_P 0.78 0.33 0.12
50_M 170_I 0.78 0.33 0.12
109_S 249_A 0.78 0.33 0.12
88_Q 10_K 0.77 0.32 0.12
77_V 219_L 0.77 0.32 0.12
115_Y 215_L 0.77 0.32 0.12
11_S 30_S 0.77 0.32 0.11
82_D 178_T 0.76 0.31 0.11
53_I 279_E 0.76 0.31 0.11
84_A 244_M 0.76 0.31 0.11
25_Q 127_N 0.76 0.31 0.11
43_L 160_Y 0.76 0.30 0.11
59_H 231_G 0.76 0.30 0.11
7_L 165_L 0.75 0.30 0.11
69_I 238_S 0.75 0.30 0.11
9_V 139_G 0.75 0.30 0.11
12_A 91_L 0.75 0.30 0.11
58_G 81_V 0.75 0.30 0.11
84_A 52_V 0.75 0.30 0.11
127_A 19_K 0.75 0.30 0.10
101_K 136_Q 0.74 0.29 0.10
84_A 144_P 0.74 0.29 0.10
64_Y 52_V 0.74 0.29 0.10
114_D 178_T 0.74 0.29 0.10
17_F 60_N 0.74 0.29 0.10
27_T 14_V 0.74 0.29 0.10
28_G 82_S 0.74 0.29 0.10
57_H 231_G 0.74 0.29 0.10
44_T 158_Q 0.74 0.29 0.10
5_Y 97_K 0.74 0.29 0.10
100_R 145_S 0.74 0.29 0.10
1_M 60_N 0.74 0.29 0.10
132_I 177_N 0.74 0.29 0.10
18_S 212_P 0.73 0.28 0.10
53_I 12_A 0.73 0.28 0.10
69_I 140_M 0.73 0.28 0.10
19_G 124_S 0.73 0.28 0.09
12_A 30_S 0.72 0.27 0.09
108_S 97_K 0.72 0.27 0.09
104_E 172_S 0.72 0.27 0.09
62_F 188_L 0.72 0.27 0.09
66_S 52_V 0.72 0.27 0.09
60_E 249_A 0.72 0.27 0.09
39_H 237_A 0.72 0.27 0.09
34_G 267_K 0.72 0.27 0.09
30_E 133_V 0.72 0.27 0.09
67_G 216_L 0.71 0.27 0.09
11_S 258_I 0.71 0.27 0.09
81_A 222_R 0.71 0.27 0.09
75_G 56_L 0.71 0.26 0.09
78_T 146_L 0.71 0.26 0.09
29_S 182_V 0.71 0.26 0.09
54_V 55_H 0.71 0.26 0.09
53_I 174_K 0.70 0.26 0.08
136_K 215_L 0.70 0.25 0.08
18_S 183_P 0.70 0.25 0.08
82_D 168_L 0.70 0.25 0.08
106_I 120_S 0.69 0.25 0.08
129_L 232_V 0.69 0.25 0.08
81_A 165_L 0.69 0.25 0.08
123_A 240_Q 0.69 0.24 0.08
107_S 134_V 0.69 0.24 0.08
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
1209 3.2 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.51 Done - Shared
1208 2.42 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.86 Done - Shared
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