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OPENSEQ.org
D1_GS2
Genes: A B A+B
Length: 446 394 767
Sequences: 629 2903 91
Seq/Len: 1.41 7.37 0.12
MirrorTree (Pazo et al. 2001) 0.08
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 0.06 0.01 0.00
2 0.07 0.01 0.00
5 0.08 0.01 0.00
10 0.08 0.01 0.00
20 0.09 0.01 0.01
100 0.11 0.02 0.04
∞ 0.14 0.02 0.11
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
125_I 61_R 1.35 0.18 0.00
217_I 313_P 1.13 0.12 0.00
32_L 28_K 1.12 0.12 0.00
296_P 373_R 1.03 0.10 0.00
33_L 68_F 1.01 0.10 0.00
278_M 301_V 0.99 0.09 0.00
290_I 138_P 0.98 0.09 0.00
157_I 24_K 0.97 0.09 0.00
75_V 31_Q 0.97 0.09 0.00
62_F 169_Y 0.96 0.09 0.00
336_D 33_D 0.94 0.08 0.00
98_I 150_A 0.93 0.08 0.00
152_V 178_F 0.91 0.08 0.00
101_A 270_L 0.91 0.08 0.00
341_F 132_L 0.91 0.08 0.00
72_L 279_N 0.90 0.08 0.00
271_L 185_I 0.90 0.08 0.00
331_Y 179_L 0.90 0.08 0.00
264_F 185_I 0.90 0.08 0.00
39_L 178_F 0.89 0.08 0.00
138_K 121_N 0.89 0.08 0.00
125_I 92_V 0.89 0.07 0.00
72_L 56_I 0.88 0.07 0.00
200_V 63_L 0.86 0.07 0.00
125_I 43_L 0.86 0.07 0.00
193_T 186_K 0.85 0.07 0.00
169_T 308_I 0.85 0.07 0.00
33_L 61_R 0.84 0.07 0.00
215_T 287_V 0.84 0.07 0.00
294_I 180_D 0.84 0.07 0.00
290_I 28_K 0.84 0.07 0.00
121_R 28_K 0.84 0.07 0.00
63_V 239_N 0.83 0.07 0.00
278_M 105_T 0.83 0.07 0.00
118_S 108_A 0.82 0.07 0.00
320_G 182_I 0.82 0.07 0.00
333_F 142_F 0.82 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
6145 0.12 D1_GS2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
2526 0.1 D1_GaS1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) Killed - Shared
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