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OPENSEQ.org
LoaP_CTD-S10
Genes: A B A+B
Length: 62 103 154
Sequences: 3899 1151 299
Seq/Len: 62.89 11.17 1.94
MirrorTree (Pazo et al. 2001) 0.62
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.09 0.01
2 0.01 0.09 0.02
5 0.01 0.09 0.05
10 0.01 0.09 0.42
20 0.02 0.09 1.81
100 0.03 0.09 2.92
∞ 0.09 0.09 5.52
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
14_T 47_K 1.57 0.93 0.56
56_K 22_S 1.46 0.89 0.47
45_D 61_D 1.40 0.86 0.41
15_E 61_D 1.34 0.82 0.36
41_M 55_A 1.27 0.78 0.31
19_K 83_K 1.21 0.73 0.26
9_G 28_E 1.20 0.72 0.25
35_A 32_R 1.11 0.64 0.19
12_I 10_R 1.11 0.63 0.19
13_I 103_A 1.10 0.63 0.19
9_G 14_Y 1.09 0.61 0.18
25_I 41_V 1.09 0.61 0.18
29_D 81_S 1.08 0.60 0.17
50_V 84_T 1.07 0.59 0.17
26_I 53_L 1.06 0.58 0.16
25_I 24_E 1.06 0.58 0.16
12_I 49_I 1.04 0.56 0.15
31_H 22_S 1.02 0.54 0.14
13_I 92_E 1.02 0.53 0.14
25_I 85_V 1.00 0.51 0.13
30_R 83_K 0.96 0.47 0.11
45_D 47_K 0.96 0.47 0.11
45_D 90_S 0.96 0.47 0.11
19_K 41_V 0.95 0.46 0.11
32_K 65_Q 0.95 0.46 0.11
36_I 29_T 0.95 0.46 0.11
50_V 101_I 0.90 0.40 0.09
8_D 50_I 0.90 0.40 0.09
4_G 99_I 0.89 0.40 0.09
37_L 15_D 0.89 0.39 0.09
50_V 33_T 0.89 0.39 0.09
32_K 31_K 0.88 0.38 0.08
23_S 96_G 0.88 0.38 0.08
7_L 16_H 0.86 0.36 0.07
11_V 4_K 0.86 0.36 0.07
36_I 58_K 0.86 0.36 0.07
15_E 52_I 0.85 0.35 0.07
18_L 41_V 0.85 0.35 0.07
11_V 10_R 0.85 0.35 0.07
27_R 29_T 0.84 0.35 0.07
19_K 99_I 0.84 0.35 0.07
11_V 45_T 0.84 0.34 0.07
30_R 52_I 0.84 0.34 0.07
10_E 79_R 0.84 0.34 0.07
24_N 53_L 0.83 0.33 0.07
13_I 89_M 0.82 0.33 0.06
45_D 46_E 0.82 0.33 0.06
5_E 15_D 0.82 0.32 0.06
34_R 56_V 0.81 0.32 0.06
33_R 59_Y 0.81 0.31 0.06
41_M 15_D 0.81 0.31 0.06
5_E 52_I 0.81 0.31 0.06
23_S 38_S 0.80 0.31 0.06
20_G 13_G 0.80 0.30 0.06
21_Y 93_L 0.79 0.29 0.06
51_S 98_E 0.79 0.29 0.06
30_R 64_E 0.79 0.29 0.05
24_N 48_Q 0.77 0.27 0.05
45_D 99_I 0.77 0.27 0.05
20_G 56_V 0.77 0.27 0.05
45_D 58_K 0.76 0.27 0.05
22_E 99_I 0.76 0.26 0.05
14_T 36_R 0.75 0.26 0.05
34_R 47_K 0.74 0.25 0.04
5_E 17_K 0.74 0.25 0.04
37_L 27_V 0.74 0.25 0.04
48_V 69_R 0.73 0.24 0.04
55_V 46_E 0.73 0.24 0.04
4_G 80_P 0.73 0.24 0.04
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
13968 3.18 LoaP_CTD-S10_dgene_100 Δgene:(1, 100) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.66 Done - Shared
13967 5.92 LoaP_CTD-S10_dgene_inf Δgene:(1, ∞) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.08 Done - Shared
13965 1.94 LoaP_CTD-S10 Δgene:(1, 20) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.56 Done - Shared
13964 0.01 LoaP_CTD-S10 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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