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OPENSEQ.org
4P78_Jackhmmer
Genes: A B A+B
Length: 66 135 193
Sequences: 1439 927 549
Seq/Len: 21.8 6.87 2.84
MirrorTree (Pazo et al. 2001) 0.52
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 0.00 2.73
2 0.00 0.00 2.74
5 0.01 0.01 2.75
10 0.01 0.01 2.75
20 0.02 0.02 2.76
100 0.03 0.03 2.78
∞ 0.07 0.06 2.89
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 1.96 0.99 0.97
41_T 45_H 1.76 0.99 0.94
30_T 48_A 1.73 0.98 0.94
30_T 44_V 1.65 0.98 0.92
53_L 15_D 1.46 0.94 0.85
50_S 13_G 1.43 0.93 0.83
43_P 37_N 1.37 0.91 0.80
30_T 45_H 1.36 0.91 0.79
50_S 15_D 1.31 0.89 0.75
50_S 9_K 1.25 0.85 0.70
43_P 26_F 1.06 0.70 0.50
39_I 52_E 1.02 0.65 0.45
39_I 54_F 1.01 0.64 0.44
50_S 10_T 0.99 0.62 0.41
49_I 25_F 0.94 0.56 0.36
60_I 25_F 0.91 0.52 0.33
32_C 52_E 0.87 0.47 0.28
50_S 12_E 0.85 0.45 0.26
52_G 8_F 0.85 0.44 0.26
42_L 2_I 0.83 0.42 0.24
31_L 23_G 0.78 0.37 0.20
29_V 5_I 0.77 0.35 0.19
35_G 54_F 0.72 0.30 0.15
15_W 45_H 0.71 0.29 0.14
56_Q 25_F 0.70 0.28 0.14
60_I 22_D 0.70 0.28 0.14
3_S 27_A 0.68 0.26 0.12
47_K 108_I 0.68 0.26 0.12
27_S 40_E 0.67 0.26 0.12
52_G 10_T 0.67 0.25 0.12
1_M 85_D 0.67 0.25 0.11
42_L 100_M 0.66 0.25 0.11
12_D 68_D 0.66 0.24 0.11
15_W 53_G 0.66 0.24 0.11
33_K 23_G 0.66 0.24 0.11
29_V 40_E 0.64 0.23 0.10
45_P 41_A 0.63 0.22 0.10
36_V 52_E 0.63 0.22 0.10
1_M 41_A 0.62 0.21 0.09
56_Q 41_A 0.62 0.21 0.09
25_S 43_A 0.62 0.21 0.09
45_P 108_I 0.61 0.20 0.09
41_T 42_F 0.61 0.20 0.09
1_M 107_A 0.61 0.20 0.09
42_L 44_V 0.60 0.20 0.08
42_L 72_L 0.60 0.20 0.08
18_R 48_A 0.60 0.20 0.08
7_I 67_I 0.59 0.19 0.08
38_K 45_H 0.59 0.19 0.08
6_L 62_D 0.59 0.19 0.08
32_C 48_A 0.59 0.18 0.07
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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