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OPENSEQ.org
DI2210001_3TCJ
Genes: A B A+B
Length: 36 105 139
Sequences: 636 763 557
Seq/Len: 17.67 7.27 4.01
MirrorTree (Pazo et al. 2001) 0.58
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 3.91
2 0.00 0.01 3.91
5 0.00 0.02 3.91
10 0.00 0.02 3.89
20 0.00 0.02 3.89
100 0.01 0.02 3.89
∞ 0.01 0.02 3.95
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
28_S 74_S 1.80 0.99 0.96
19_V 71_Q 1.70 0.99 0.94
19_V 70_Q 1.56 0.98 0.91
9_K 30_D 1.50 0.97 0.89
31_D 79_I 1.40 0.96 0.85
32_E 11_D 1.38 0.95 0.83
15_G 51_P 1.34 0.95 0.81
1_R 27_D 1.25 0.91 0.74
20_A 32_L 1.17 0.87 0.67
16_M 51_P 1.16 0.86 0.66
20_A 33_N 1.13 0.84 0.63
19_V 33_N 1.12 0.84 0.62
33_N 76_P 1.07 0.80 0.58
30_A 37_V 1.06 0.79 0.56
22_F 65_F 1.03 0.76 0.52
9_K 31_N 1.00 0.73 0.48
22_F 68_L 0.98 0.72 0.47
9_K 28_L 0.96 0.69 0.44
29_F 74_S 0.95 0.67 0.42
29_F 3_Q 0.94 0.67 0.42
11_E 52_S 0.92 0.65 0.40
23_I 34_T 0.92 0.64 0.40
19_V 51_P 0.89 0.60 0.36
30_A 19_P 0.89 0.60 0.36
22_F 71_Q 0.89 0.60 0.35
28_S 101_L 0.84 0.54 0.31
5_A 100_F 0.83 0.53 0.29
9_K 100_F 0.83 0.52 0.29
16_M 31_N 0.82 0.51 0.28
30_A 21_F 0.79 0.46 0.25
17_A 30_D 0.77 0.44 0.23
19_V 38_I 0.76 0.42 0.22
20_A 21_F 0.74 0.40 0.20
32_E 74_S 0.72 0.38 0.19
23_I 38_I 0.72 0.38 0.19
24_E 72_M 0.71 0.37 0.18
29_F 71_Q 0.71 0.37 0.18
19_V 55_C 0.71 0.36 0.18
33_N 74_S 0.71 0.36 0.17
31_D 9_N 0.69 0.34 0.16
17_A 31_N 0.69 0.34 0.16
26_N 87_L 0.69 0.34 0.16
11_E 82_E 0.68 0.32 0.15
7_R 89_T 0.68 0.32 0.15
20_A 22_V 0.67 0.32 0.15
14_E 89_T 0.66 0.30 0.14
18_E 47_D 0.65 0.30 0.14
29_F 14_S 0.65 0.29 0.13
21_R 10_K 0.64 0.28 0.13
16_M 67_M 0.64 0.28 0.12
29_F 105_I 0.64 0.28 0.12
21_R 22_V 0.63 0.27 0.12
25_M 90_F 0.63 0.27 0.12
29_F 18_Y 0.63 0.27 0.12
26_N 90_F 0.63 0.27 0.12
6_E 81_S 0.63 0.27 0.12
18_E 50_A 0.62 0.27 0.12
23_I 79_I 0.62 0.27 0.12
28_S 25_Q 0.62 0.27 0.12
6_E 96_A 0.62 0.26 0.11
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
7796 4.01 DI2210001_3TCJ Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 4) msa: Jackhmmer (r132) 0.96 Done - Shared
7784 0.44 DI2210001_3TCJ Δgene:(1, ∞) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (r132) 0.03 Done - Shared
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