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OPENSEQ.org
2H1C
Genes: A B A+B
Length: 78 139 213
Sequences: 787 8919 427
Seq/Len: 10.09 64.17 2
MirrorTree (Pazo et al. 2001) 0.79
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 0.04 1.97
2 0.00 0.05 2.00
5 0.01 0.08 2.05
10 0.01 0.09 2.09
20 0.02 0.11 2.12
100 0.03 0.15 2.31
∞ 0.09 0.20 2.80
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
50_S 26_D 1.91 0.98 0.94
55_I 70_L 1.62 0.95 0.84
63_E 15_P 1.57 0.93 0.81
18_K 75_I 1.52 0.92 0.78
56_G 13_L 1.35 0.84 0.64
49_G 26_D 1.31 0.81 0.60
23_A 57_N 1.25 0.77 0.54
38_N 102_A 1.24 0.76 0.54
47_R 26_D 1.14 0.67 0.43
59_I 62_R 1.13 0.66 0.41
55_I 62_R 1.10 0.64 0.39
56_G 12_P 1.07 0.60 0.36
18_K 34_Y 1.06 0.59 0.34
16_A 33_V 1.05 0.58 0.34
56_G 70_L 1.05 0.58 0.33
3_S 134_F 1.05 0.57 0.33
5_V 51_L 1.03 0.56 0.31
45_T 31_E 1.00 0.52 0.28
65_E 15_P 1.00 0.52 0.28
14_H 93_A 0.98 0.50 0.27
55_I 116_L 0.97 0.49 0.26
73_D 111_A 0.96 0.48 0.25
43_Q 43_L 0.96 0.48 0.25
69_G 125_S 0.96 0.47 0.24
17_I 50_L 0.95 0.47 0.24
49_G 32_D 0.95 0.47 0.24
34_L 98_K 0.95 0.47 0.24
10_S 118_V 0.93 0.45 0.22
6_I 67_I 0.93 0.44 0.22
70_R 94_K 0.92 0.43 0.21
69_G 122_D 0.92 0.43 0.21
25_G 124_G 0.91 0.42 0.20
9_L 22_V 0.90 0.41 0.19
73_D 90_R 0.89 0.41 0.19
13_T 4_L 0.89 0.40 0.19
70_R 95_T 0.89 0.40 0.19
18_K 111_A 0.89 0.40 0.19
32_I 127_F 0.88 0.39 0.18
43_Q 77_P 0.88 0.39 0.18
7_R 11_E 0.88 0.39 0.18
15_N 35_L 0.87 0.38 0.18
57_Q 12_P 0.87 0.38 0.18
58_E 132_A 0.87 0.38 0.17
32_I 67_I 0.86 0.37 0.17
4_V 38_I 0.86 0.37 0.17
19_F 75_I 0.86 0.37 0.17
9_L 85_I 0.86 0.37 0.17
26_R 45_L 0.85 0.36 0.16
21_A 42_E 0.85 0.36 0.16
71_N 58_V 0.85 0.36 0.16
73_D 130_D 0.84 0.35 0.15
31_E 8_V 0.82 0.33 0.14
72_T 95_T 0.82 0.33 0.14
33_R 24_W 0.82 0.33 0.14
9_L 132_A 0.82 0.33 0.14
3_S 3_L 0.82 0.33 0.14
5_V 6_T 0.81 0.32 0.14
67_V 122_D 0.81 0.32 0.14
6_I 131_V 0.81 0.32 0.13
73_D 103_A 0.81 0.32 0.13
27_S 5_D 0.80 0.31 0.13
9_L 30_L 0.80 0.31 0.13
30_A 76_L 0.80 0.31 0.13
67_V 37_A 0.80 0.31 0.13
35_I 46_G 0.80 0.30 0.13
40_A 118_V 0.80 0.30 0.13
14_H 49_L 0.79 0.30 0.12
56_G 66_S 0.79 0.30 0.12
29_E 121_R 0.79 0.30 0.12
16_A 116_L 0.79 0.30 0.12
38_N 88_Q 0.79 0.30 0.12
72_T 47_V 0.79 0.30 0.12
59_I 113_Q 0.78 0.29 0.12
55_I 9_I 0.78 0.29 0.12
75_E 36_S 0.78 0.29 0.12
55_I 66_S 0.78 0.29 0.12
51_M 70_L 0.78 0.29 0.12
24_A 46_G 0.78 0.29 0.12
66_D 54_K 0.77 0.28 0.11
71_N 60_H 0.77 0.28 0.11
34_L 96_H 0.76 0.28 0.11
55_I 67_I 0.76 0.27 0.11
16_A 124_G 0.75 0.27 0.10
66_D 13_L 0.74 0.26 0.10
73_D 132_A 0.74 0.26 0.10
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
4879 2 2H1C Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
0737 1.16 2H1O_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.64 Done
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