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OPENSEQ.org
TA_fifteen
Genes: A B A+B
Length: 79 95 164
Sequences: 1344 4405 672
Seq/Len: 17.01 46.37 4.1
MirrorTree (Pazo et al. 2001) 0.62
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 0.01 0.01 3.86
2 0.01 0.03 3.89
5 0.02 0.04 3.95
10 0.03 0.05 4.00
20 0.03 0.06 4.11
100 0.05 0.08 4.39
∞ 0.09 0.13 5.07
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
59_V 50_C 1.67 0.99 0.93
55_D 77_S 1.66 0.99 0.92
63_K 50_C 1.51 0.98 0.88
63_K 65_Q 1.39 0.96 0.81
54_E 10_R 1.26 0.92 0.72
65_R 8_D 1.20 0.89 0.67
62_V 76_I 1.14 0.86 0.61
63_K 49_D 1.00 0.74 0.45
56_A 47_M 0.91 0.63 0.35
52_S 77_S 0.87 0.58 0.30
56_A 63_V 0.85 0.56 0.29
22_K 30_L 0.85 0.56 0.29
62_V 74_F 0.81 0.51 0.25
28_S 5_L 0.80 0.49 0.24
65_R 14_E 0.78 0.46 0.22
60_E 3_Y 0.76 0.43 0.20
52_S 14_E 0.75 0.42 0.19
8_I 9_E 0.73 0.40 0.18
3_S 82_E 0.73 0.40 0.18
72_V 6_D 0.72 0.38 0.17
45_P 64_Y 0.71 0.37 0.16
72_V 15_W 0.71 0.37 0.16
35_L 30_L 0.70 0.35 0.15
43_R 68_D 0.69 0.34 0.14
17_Y 24_E 0.69 0.34 0.14
62_V 8_D 0.69 0.34 0.14
26_T 22_V 0.68 0.33 0.14
14_A 5_L 0.68 0.33 0.14
26_T 19_G 0.67 0.32 0.13
26_T 72_V 0.66 0.31 0.13
57_E 3_Y 0.65 0.30 0.12
42_E 66_V 0.65 0.30 0.12
78_E 24_E 0.65 0.29 0.12
71_P 1_M 0.64 0.29 0.12
55_D 54_K 0.64 0.29 0.11
37_Y 47_M 0.63 0.27 0.11
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
4762 4.1 TA_fifteen Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.93 Done - Shared
0725 3.75 4FXE_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.83 Done
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