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OPENSEQ.org
LoaP_CTD-S10_dgene_100
Genes: A B A+B
Length: 62 103 154
Sequences: 3899 1151 490
Seq/Len: 62.89 11.17 3.18
MirrorTree (Pazo et al. 2001) 0.70
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 1.83
100 0.03 0.09 2.97
∞ 0.09 0.09 5.53
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
12_I 10_R 1.45 0.95 0.66
45_D 61_D 1.23 0.86 0.46
35_A 32_R 1.22 0.86 0.45
13_I 103_A 1.20 0.84 0.43
56_K 22_S 1.20 0.84 0.43
51_S 30_A 1.19 0.84 0.43
15_E 61_D 1.17 0.82 0.40
26_I 55_A 1.15 0.81 0.38
6_I 80_P 1.08 0.75 0.32
13_I 6_K 1.08 0.75 0.32
37_L 32_R 1.08 0.74 0.32
23_S 96_G 1.06 0.73 0.30
19_K 83_K 1.05 0.72 0.30
55_V 46_E 1.02 0.69 0.27
24_N 48_Q 0.99 0.65 0.24
51_S 13_G 0.93 0.58 0.20
41_M 55_A 0.93 0.57 0.19
13_I 20_D 0.92 0.57 0.19
23_S 47_K 0.92 0.56 0.19
25_I 91_L 0.86 0.49 0.15
29_D 95_A 0.85 0.48 0.14
22_E 50_I 0.84 0.46 0.14
31_H 22_S 0.83 0.46 0.14
35_A 68_M 0.83 0.46 0.14
28_I 103_A 0.83 0.45 0.13
9_G 72_K 0.82 0.45 0.13
50_V 9_I 0.82 0.45 0.13
17_P 14_Y 0.82 0.45 0.13
6_I 78_L 0.82 0.44 0.13
29_D 83_K 0.81 0.43 0.12
33_R 58_K 0.80 0.41 0.12
27_R 38_S 0.80 0.41 0.12
40_R 98_E 0.78 0.40 0.11
31_H 27_V 0.78 0.40 0.11
8_D 50_I 0.78 0.40 0.11
25_I 96_G 0.78 0.40 0.11
25_I 85_V 0.78 0.40 0.11
14_T 34_G 0.76 0.38 0.10
14_T 79_R 0.74 0.35 0.09
32_K 31_K 0.74 0.35 0.09
36_I 41_V 0.74 0.35 0.09
50_V 101_I 0.74 0.34 0.09
22_E 41_V 0.74 0.34 0.09
15_E 49_I 0.73 0.34 0.09
41_M 23_A 0.72 0.33 0.09
30_R 52_I 0.72 0.33 0.08
19_K 19_V 0.72 0.33 0.08
26_I 31_K 0.71 0.32 0.08
7_L 18_L 0.71 0.32 0.08
35_A 94_P 0.71 0.32 0.08
28_I 52_I 0.71 0.31 0.08
57_K 22_S 0.70 0.31 0.08
48_V 95_A 0.70 0.30 0.08
55_V 92_E 0.70 0.30 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
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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