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OPENSEQ.org
new_ampa_tarp
Genes: A B A+B
Length: 193 154 334
Sequences: 1543 1669 160
Seq/Len: 7.99 10.84 0.48
MirrorTree (Pazo et al. 2001) 0.22
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 0.11 0.15 0.03
2 0.13 0.17 0.06
5 0.13 0.18 0.10
10 0.13 0.19 0.14
20 0.14 0.19 0.17
100 0.15 0.20 0.29
∞ 0.17 0.22 0.46
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
34_Y 8_L 1.17 0.31 0.00
130_G 8_L 1.00 0.21 0.00
32_W 16_W 0.98 0.20 0.00
94_L 11_L 0.97 0.20 0.00
10_L 11_L 0.96 0.19 0.00
130_G 93_G 0.93 0.18 0.00
15_G 24_I 0.92 0.17 0.00
20_F 23_Y 0.91 0.17 0.00
131_L 112_A 0.89 0.16 0.00
173_I 128_N 0.88 0.16 0.00
166_F 144_M 0.86 0.15 0.00
46_G 108_A 0.84 0.14 0.00
128_S 19_I 0.83 0.14 0.00
15_G 19_I 0.82 0.13 0.00
154_K 30_L 0.82 0.13 0.00
104_L 84_R 0.82 0.13 0.00
25_I 80_D 0.82 0.13 0.00
130_G 102_I 0.82 0.13 0.00
115_R 66_S 0.81 0.13 0.00
144_N 11_L 0.81 0.13 0.00
163_S 36_F 0.80 0.13 0.00
32_W 89_R 0.79 0.12 0.00
26_A 123_A 0.78 0.12 0.00
136_G 86_L 0.78 0.12 0.00
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
5946 0.48 new_ampa_tarp Δgene:(1, ∞) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5913 0.2 new_ampa_tarp Δgene:(1, 100) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5912 0.17 new_ampa_tarp Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5910 0.11 new_ampa_tarp Δgene:(1, 20) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2016_06b) Killed - Shared
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