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OPENSEQ.org
4P78
Genes: A B A+B
Length: 66 135 193
Sequences: 1821 1147 672
Seq/Len: 27.59 8.5 3.48
MirrorTree (Pazo et al. 2001) 0.54
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 0.01 0.00 3.34
2 0.01 0.01 3.38
5 0.02 0.02 3.38
10 0.03 0.03 3.38
20 0.04 0.03 3.39
100 0.05 0.05 3.41
∞ 0.10 0.09 3.55
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 27_A 2.12 1.00 0.99
30_T 44_V 1.81 0.99 0.97
53_L 15_D 1.59 0.98 0.93
50_S 15_D 1.53 0.97 0.91
30_T 48_A 1.52 0.97 0.91
41_T 45_H 1.51 0.97 0.90
30_T 45_H 1.36 0.94 0.84
50_S 9_K 1.26 0.89 0.77
50_S 13_G 1.20 0.86 0.72
43_P 26_F 1.09 0.78 0.61
43_P 37_N 1.04 0.74 0.56
39_I 52_E 1.01 0.71 0.52
39_I 54_F 0.91 0.58 0.39
8_K 133_I 0.86 0.52 0.34
32_C 52_E 0.86 0.52 0.33
25_S 43_A 0.84 0.49 0.31
55_R 65_R 0.78 0.42 0.25
60_I 57_P 0.77 0.41 0.24
50_S 12_E 0.75 0.38 0.22
47_K 108_I 0.74 0.37 0.21
53_L 25_F 0.74 0.37 0.21
50_S 29_N 0.73 0.36 0.20
52_G 8_F 0.72 0.35 0.19
60_I 25_F 0.72 0.34 0.19
56_Q 25_F 0.70 0.32 0.17
30_T 86_P 0.70 0.32 0.17
1_M 85_D 0.69 0.31 0.17
38_K 45_H 0.69 0.31 0.16
29_V 5_I 0.69 0.31 0.16
42_L 2_I 0.68 0.30 0.16
34_P 21_I 0.67 0.29 0.15
33_K 22_D 0.67 0.28 0.15
4_G 131_E 0.63 0.25 0.12
47_K 7_I 0.63 0.25 0.12
8_K 72_L 0.62 0.24 0.12
50_S 10_T 0.62 0.24 0.12
31_L 23_G 0.62 0.23 0.11
18_R 48_A 0.61 0.23 0.11
49_I 25_F 0.61 0.23 0.11
4_G 114_T 0.61 0.23 0.11
41_T 41_A 0.60 0.22 0.11
3_S 27_A 0.60 0.22 0.10
36_V 52_E 0.60 0.22 0.10
61_A 37_N 0.60 0.22 0.10
58_Q 78_I 0.59 0.21 0.10
32_C 48_A 0.59 0.21 0.10
54_L 30_T 0.59 0.21 0.10
15_W 53_G 0.58 0.21 0.10
24_N 44_V 0.58 0.20 0.09
60_I 28_G 0.58 0.20 0.09
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
4871 3.48 4P78 Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.99 Done - Shared
0732 2.84 4P78_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.97 Done
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