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OPENSEQ.org
DI2210001_3TCJ
Genes: A B A+B
Length: 36 105 137
Sequences: 61 763 60
Seq/Len: 1.69 7.27 0.44
MirrorTree (Pazo et al. 2001) 0.80
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 0.44
2 0.00 0.01 0.44
5 0.00 0.02 0.41
10 0.00 0.02 0.43
20 0.00 0.02 0.43
100 0.00 0.02 0.43
∞ 0.01 0.02 0.43
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
3_L 73_T 1.86 0.76 0.03
26_N 71_Q 1.56 0.57 0.01
6_E 25_Q 1.50 0.52 0.01
14_E 68_L 1.23 0.33 0.01
35_D 74_S 1.22 0.33 0.01
13_Q 74_S 1.22 0.32 0.01
21_R 68_L 1.14 0.27 0.00
22_F 4_F 1.13 0.27 0.00
23_I 72_M 1.13 0.27 0.00
10_A 4_F 1.11 0.26 0.00
1_R 77_V 1.10 0.25 0.00
9_K 73_T 1.09 0.24 0.00
11_E 13_S 1.08 0.24 0.00
15_G 11_D 1.07 0.23 0.00
7_R 84_V 1.07 0.23 0.00
14_E 61_D 1.06 0.23 0.00
20_A 99_D 1.05 0.23 0.00
3_L 79_I 1.05 0.23 0.00
25_M 6_L 1.05 0.22 0.00
28_S 4_F 1.02 0.21 0.00
26_N 83_P 1.01 0.20 0.00
6_E 54_L 0.99 0.20 0.00
15_G 80_L 0.99 0.20 0.00
29_F 82_E 0.99 0.19 0.00
24_E 43_I 0.99 0.19 0.00
1_R 48_K 0.98 0.19 0.00
29_F 47_D 0.98 0.19 0.00
1_R 98_I 0.97 0.19 0.00
14_E 51_P 0.97 0.18 0.00
15_G 52_S 0.96 0.18 0.00
22_F 18_Y 0.96 0.18 0.00
19_V 70_Q 0.96 0.18 0.00
10_A 92_N 0.96 0.18 0.00
29_F 4_F 0.95 0.18 0.00
1_R 19_P 0.94 0.17 0.00
9_K 67_M 0.93 0.17 0.00
18_E 4_F 0.93 0.17 0.00
29_F 38_I 0.93 0.17 0.00
14_E 17_T 0.92 0.16 0.00
3_L 78_K 0.91 0.16 0.00
5_A 46_L 0.91 0.16 0.00
20_A 100_F 0.90 0.16 0.00
4_R 96_A 0.89 0.15 0.00
35_D 72_M 0.88 0.15 0.00
9_K 72_M 0.87 0.14 0.00
28_S 31_N 0.87 0.14 0.00
9_K 96_A 0.87 0.14 0.00
11_E 77_V 0.87 0.14 0.00
3_L 90_F 0.86 0.14 0.00
18_E 23_D 0.85 0.14 0.00
16_M 103_T 0.84 0.13 0.00
5_A 37_V 0.84 0.13 0.00
20_A 9_N 0.84 0.13 0.00
30_A 103_T 0.83 0.13 0.00
1_R 59_H 0.83 0.13 0.00
19_V 42_P 0.83 0.13 0.00
19_V 103_T 0.82 0.13 0.00
6_E 66_I 0.82 0.13 0.00
13_Q 36_L 0.82 0.13 0.00
6_E 84_V 0.82 0.13 0.00
21_R 86_E 0.82 0.13 0.00
26_N 74_S 0.81 0.12 0.00
21_R 77_V 0.81 0.12 0.00
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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