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OPENSEQ.org
new_ampa_tarp
Genes: A B A+B
Length: 193 154 339
Sequences: 844 1394 69
Seq/Len: 4.37 9.05 0.2
MirrorTree (Pazo et al. 2001) 0.43
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 0.12 0.16 0.03
2 0.14 0.18 0.04
5 0.15 0.19 0.07
10 0.15 0.20 0.10
20 0.15 0.20 0.11
100 0.17 0.22 0.20
∞ 0.18 0.24 0.30
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
46_G 108_A 1.24 0.20 0.00
32_W 16_W 1.21 0.19 0.00
25_I 132_V 1.20 0.19 0.00
129_A 63_I 1.16 0.17 0.00
130_G 8_L 1.16 0.17 0.00
147_D 91_V 1.11 0.16 0.00
147_D 130_A 1.08 0.14 0.00
51_C 16_W 1.06 0.14 0.00
178_G 134_Y 1.04 0.13 0.00
163_S 14_E 1.01 0.12 0.00
32_W 108_A 0.99 0.12 0.00
48_W 62_G 0.98 0.12 0.00
161_G 2_P 0.98 0.12 0.00
51_C 125_S 0.93 0.11 0.00
185_F 101_I 0.93 0.11 0.00
14_V 142_L 0.92 0.10 0.00
170_S 89_R 0.89 0.10 0.00
163_S 126_L 0.89 0.10 0.00
161_G 98_F 0.89 0.10 0.00
22_L 150_E 0.89 0.10 0.00
32_W 107_T 0.88 0.10 0.00
113_K 55_S 0.88 0.10 0.00
161_G 106_Y 0.88 0.10 0.00
95_S 126_L 0.88 0.10 0.00
93_I 151_F 0.88 0.10 0.00
78_A 8_L 0.88 0.09 0.00
163_S 44_E 0.85 0.09 0.00
72_D 28_V 0.85 0.09 0.00
21_S 24_I 0.84 0.09 0.00
32_W 112_A 0.84 0.09 0.00
32_W 106_Y 0.83 0.09 0.00
18_A 27_S 0.83 0.09 0.00
178_G 74_F 0.83 0.09 0.00
51_C 108_A 0.83 0.09 0.00
127_V 52_T 0.83 0.09 0.00
149_S 19_I 0.82 0.08 0.00
27_V 140_L 0.82 0.08 0.00
105_C 4_V 0.81 0.08 0.00
10_L 60_E 0.81 0.08 0.00
161_G 101_I 0.81 0.08 0.00
32_W 109_N 0.81 0.08 0.00
147_D 144_M 0.81 0.08 0.00
46_G 16_W 0.81 0.08 0.00
63_Q 19_I 0.81 0.08 0.00
84_A 144_M 0.81 0.08 0.00
19_A 95_W 0.80 0.08 0.00
130_G 106_Y 0.80 0.08 0.00
128_S 36_F 0.80 0.08 0.00
164_F 117_E 0.80 0.08 0.00
28_G 140_L 0.80 0.08 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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