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OPENSEQ.org
LoaP_CTD-S10_dgene_inf
Genes: A B A+B
Length: 62 103 154
Sequences: 3899 1151 912
Seq/Len: 62.89 11.17 5.92
MirrorTree (Pazo et al. 2001) 0.63
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 1.87
100 0.03 0.09 2.92
∞ 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
40_R 64_E 1.08 0.89 0.08
21_Y 89_M 1.02 0.84 0.07
41_M 55_A 0.99 0.82 0.06
11_V 43_L 0.96 0.80 0.06
45_D 61_D 0.93 0.77 0.05
37_L 32_R 0.91 0.75 0.05
23_S 50_I 0.88 0.71 0.04
51_S 72_K 0.85 0.67 0.04
54_I 99_I 0.84 0.66 0.04
25_I 9_I 0.82 0.63 0.04
25_I 89_M 0.82 0.62 0.04
13_I 6_K 0.81 0.61 0.03
5_E 10_R 0.80 0.60 0.03
49_D 102_K 0.79 0.58 0.03
35_A 36_R 0.78 0.56 0.03
26_I 31_K 0.78 0.56 0.03
25_I 90_S 0.77 0.55 0.03
45_D 74_L 0.77 0.55 0.03
26_I 55_A 0.76 0.55 0.03
53_E 82_N 0.76 0.54 0.03
57_K 48_Q 0.75 0.53 0.03
51_S 30_A 0.75 0.53 0.03
35_A 21_A 0.75 0.52 0.03
35_A 32_R 0.73 0.49 0.03
39_V 17_K 0.73 0.49 0.03
9_G 82_N 0.72 0.48 0.03
30_R 19_V 0.72 0.48 0.03
23_S 30_A 0.72 0.48 0.02
18_L 95_A 0.71 0.47 0.02
13_I 51_T 0.71 0.47 0.02
38_N 14_Y 0.70 0.45 0.02
48_V 15_D 0.70 0.45 0.02
6_I 78_L 0.70 0.45 0.02
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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