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OPENSEQ.org
beta2_gas_1
Genes: A B A+B
Length: 413 394 744
Sequences: 2859 1191 136
Seq/Len: 6.92 3.02 0.18
MirrorTree (Pazo et al. 2001) 0.06
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 0.08 0.02 0.00
2 0.10 0.02 0.00
5 0.11 0.03 0.01
10 0.12 0.03 0.01
20 0.14 0.03 0.03
100 0.17 0.03 0.12
∞ 0.18 0.04 0.17
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
217_F 183_D 1.13 0.15 0.00
150_A 194_D 1.05 0.13 0.00
148_N 314_E 0.96 0.11 0.00
106_C 242_T 0.94 0.10 0.00
184_C 206_G 0.93 0.10 0.00
350_Y 72_G 0.92 0.10 0.00
66_T 66_N 0.92 0.10 0.00
152_V 255_M 0.91 0.10 0.00
278_I 335_T 0.90 0.10 0.00
187_N 72_G 0.90 0.09 0.00
222_V 151_K 0.89 0.09 0.00
261_S 372_I 0.88 0.09 0.00
164_T 30_L 0.88 0.09 0.00
338_E 183_D 0.88 0.09 0.00
277_I 123_E 0.88 0.09 0.00
72_I 263_T 0.88 0.09 0.00
321_F 189_D 0.86 0.09 0.00
304_R 159_V 0.86 0.09 0.00
150_A 182_I 0.86 0.09 0.00
166_F 144_P 0.85 0.09 0.00
62_E 79_A 0.84 0.08 0.00
216_V 71_E 0.84 0.08 0.00
104_F 296_L 0.83 0.08 0.00
214_I 160_R 0.82 0.08 0.00
91_A 171_L 0.82 0.08 0.00
167_L 175_A 0.81 0.08 0.00
229_Q 319_T 0.81 0.08 0.00
72_I 123_E 0.81 0.08 0.00
185_Y 61_R 0.81 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
2484 0.2 beta2_gas_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.00 Done
2465 0.18 beta2_gas_1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.00 Done
1318 0.01 P63092-p07550 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
1317 0 P63092-p07550 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
1316 0.03 P63092-p07550 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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