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OPENSEQ.org
new_ampa_tarp
Genes: A B A+B
Length: 193 154 333
Sequences: 1543 1669 58
Seq/Len: 7.99 10.84 0.17
MirrorTree (Pazo et al. 2001) 0.56
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
51_C 10_P 1.34 0.22 0.00
10_L 27_S 1.21 0.17 0.00
48_W 144_M 1.20 0.17 0.00
27_V 144_M 1.17 0.16 0.00
48_W 138_G 1.17 0.16 0.00
161_G 16_W 1.17 0.16 0.00
10_L 11_L 1.12 0.14 0.00
138_I 27_S 1.11 0.14 0.00
131_L 112_A 1.04 0.12 0.00
131_L 107_T 1.02 0.12 0.00
168_A 7_F 0.98 0.11 0.00
51_C 106_Y 0.98 0.11 0.00
21_S 140_L 0.97 0.11 0.00
27_V 138_G 0.97 0.10 0.00
167_G 104_S 0.96 0.10 0.00
102_G 26_V 0.96 0.10 0.00
32_W 10_P 0.94 0.10 0.00
32_W 16_W 0.93 0.10 0.00
140_Y 101_I 0.93 0.10 0.00
129_A 41_W 0.91 0.09 0.00
97_I 142_L 0.91 0.09 0.00
170_S 97_F 0.91 0.09 0.00
178_G 101_I 0.91 0.09 0.00
47_L 136_L 0.90 0.09 0.00
107_A 108_A 0.90 0.09 0.00
168_A 117_E 0.89 0.09 0.00
51_C 110_L 0.89 0.09 0.00
22_L 84_R 0.88 0.09 0.00
22_L 85_S 0.88 0.09 0.00
114_T 122_S 0.88 0.09 0.00
129_A 91_V 0.88 0.09 0.00
13_T 122_S 0.85 0.08 0.00
91_F 74_F 0.85 0.08 0.00
140_Y 143_A 0.85 0.08 0.00
32_W 106_Y 0.85 0.08 0.00
180_L 78_G 0.84 0.08 0.00
132_S 84_R 0.83 0.08 0.00
118_I 66_S 0.83 0.08 0.00
163_S 69_F 0.82 0.08 0.00
105_C 11_L 0.82 0.08 0.00
168_A 109_N 0.82 0.08 0.00
168_A 144_M 0.82 0.08 0.00
87_A 141_G 0.82 0.08 0.00
167_G 106_Y 0.81 0.08 0.00
97_I 15_I 0.81 0.08 0.00
61_C 87_S 0.81 0.08 0.00
39_G 72_G 0.81 0.07 0.00
25_I 67_L 0.80 0.07 0.00
98_L 63_I 0.80 0.07 0.00
10_L 93_G 0.80 0.07 0.00
25_I 88_G 0.80 0.07 0.00
168_A 105_S 0.80 0.07 0.00
88_S 67_L 0.79 0.07 0.00
106_I 11_L 0.79 0.07 0.00
20_F 66_S 0.78 0.07 0.00
48_W 106_Y 0.78 0.07 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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