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OPENSEQ.org
beta2_gas_2
Genes: A B A+B
Length: 413 394 738
Sequences: 2589 1191 145
Seq/Len: 6.27 3.02 0.2
MirrorTree (Pazo et al. 2001) 0.17
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 0.07 0.02 0.00
2 0.07 0.02 0.00
5 0.09 0.03 0.00
10 0.10 0.03 0.01
20 0.11 0.03 0.02
100 0.14 0.03 0.10
∞ 0.16 0.04 0.18
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
333_R 197_L 1.19 0.18 0.00
112_I 244_I 1.11 0.15 0.00
106_C 376_F 1.09 0.15 0.00
216_V 27_E 1.03 0.13 0.00
318_N 179_L 1.00 0.12 0.00
148_N 144_P 0.99 0.12 0.00
111_S 61_R 0.97 0.12 0.00
273_K 185_I 0.95 0.11 0.00
162_G 72_G 0.94 0.11 0.00
166_F 144_P 0.94 0.11 0.00
270_K 159_V 0.94 0.11 0.00
331_D 68_F 0.93 0.11 0.00
129_V 315_F 0.90 0.10 0.00
325_I 299_E 0.90 0.10 0.00
115_L 180_D 0.90 0.10 0.00
38_I 197_L 0.89 0.10 0.00
323_P 219_F 0.89 0.10 0.00
133_F 80_A 0.89 0.10 0.00
47_I 314_E 0.87 0.09 0.00
231_Q 167_N 0.86 0.09 0.00
33_V 68_F 0.86 0.09 0.00
81_V 185_I 0.85 0.09 0.00
135_I 80_A 0.85 0.09 0.00
131_R 215_D 0.85 0.09 0.00
42_L 276_I 0.85 0.09 0.00
294_I 137_V 0.84 0.09 0.00
135_I 157_E 0.83 0.09 0.00
275_L 306_S 0.83 0.09 0.00
132_Y 71_E 0.83 0.09 0.00
202_A 299_E 0.82 0.08 0.00
294_I 185_I 0.82 0.08 0.00
171_M 256_V 0.81 0.08 0.00
210_V 160_R 0.81 0.08 0.00
282_F 368_D 0.81 0.08 0.00
267_K 197_L 0.81 0.08 0.00
160_V 72_G 0.79 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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