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OPENSEQ.org
ab2Re
Genes: A B A+B
Length: 30 44 70
Sequences: 880 1920 307
Seq/Len: 29.33 43.64 4.39
MirrorTree (Pazo et al. 2001) 0.39
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 0.93 0.93 4.15
2 0.94 0.94 4.15
5 0.94 0.95 4.15
10 0.94 0.95 4.15
20 0.94 0.95 4.15
100 0.94 0.95 4.15
∞ 0.95 0.95 4.15
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
16_V 27_V 2.05 1.00 0.99
23_S 23_L 2.03 1.00 0.99
21_S 32_S 1.85 1.00 0.97
27_V 38_I 1.81 1.00 0.97
20_A 20_G 1.78 1.00 0.97
5_V 5_I 1.72 0.99 0.96
21_S 43_D 1.70 0.99 0.96
14_A 25_A 1.64 0.99 0.95
12_N 12_N 1.64 0.99 0.95
13_G 13_S 1.63 0.99 0.95
28_T 39_D 1.62 0.99 0.94
10_G 21_S 1.57 0.99 0.93
8_F 8_A 1.52 0.98 0.92
10_G 10_T 1.47 0.98 0.90
19_T 30_E 1.47 0.98 0.90
11_G 22_K 1.47 0.98 0.90
15_A 26_V 1.45 0.97 0.89
25_V 36_A 1.43 0.97 0.89
16_V 16_L 1.41 0.97 0.88
6_K 6_G 1.39 0.96 0.87
11_G 11_N 1.34 0.95 0.85
26_N 37_K 1.34 0.95 0.84
22_N 22_K 1.32 0.95 0.84
20_A 31_G 1.29 0.94 0.81
28_T 28_A 1.26 0.93 0.80
17_D 17_R 1.25 0.92 0.78
8_F 19_G 1.24 0.92 0.78
27_V 27_V 1.19 0.90 0.74
10_G 32_S 1.17 0.89 0.72
11_G 33_S 1.16 0.88 0.72
18_Q 29_Q 1.12 0.86 0.68
24_S 24_L 1.11 0.85 0.67
21_S 21_S 1.10 0.84 0.65
22_N 33_S 1.08 0.83 0.64
24_S 35_R 1.04 0.80 0.59
14_A 14_A 1.00 0.76 0.55
25_V 25_A 0.96 0.71 0.49
26_N 26_V 0.93 0.68 0.45
15_A 15_Q 0.92 0.67 0.44
16_V 38_I 0.86 0.59 0.38
14_A 3_A 0.82 0.54 0.33
19_T 19_G 0.82 0.53 0.32
13_G 35_R 0.80 0.51 0.30
5_V 16_L 0.79 0.49 0.28
6_K 17_R 0.72 0.40 0.21
29_Q 18_Q 0.69 0.37 0.19
2_E 29_Q 0.68 0.34 0.18
13_G 24_L 0.67 0.33 0.17
4_T 4_I 0.66 0.33 0.16
14_A 38_I 0.64 0.30 0.15
19_T 41_T 0.64 0.29 0.14
29_Q 29_Q 0.63 0.29 0.14
27_V 26_V 0.62 0.27 0.13
3_M 3_A 0.60 0.26 0.12
17_D 28_A 0.60 0.26 0.12
18_Q 9_G 0.57 0.22 0.10
4_T 15_Q 0.56 0.22 0.10
10_G 5_I 0.56 0.22 0.10
27_V 11_N 0.56 0.22 0.10
12_N 2_A 0.55 0.21 0.09
12_N 9_G 0.54 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.94 > 0.4) of paralogs.
  • For sequence B, there is a high ratio (0.95 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
0565 4.39 ab2Re Δgene:(0, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.99 Done
0564 0.01 ab2Re Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed
0563 0.01 ab2Re Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
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