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OPENSEQ.org
retry
Genes: A B A+B
Length: 174 248 377
Sequences: 3738 3302 307
Seq/Len: 21.48 13.31 0.81
MirrorTree (Pazo et al. 2001) 0.47
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 0.03 0.08 0.00
2 0.04 0.10 0.00
5 0.05 0.13 0.01
10 0.06 0.15 0.01
20 0.07 0.15 0.03
100 0.10 0.18 0.11
∞ 0.16 0.24 0.73
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
50_I 57_Y 1.11 0.39 0.00
169_G 40_L 1.05 0.33 0.00
161_G 182_R 0.98 0.28 0.00
105_N 95_T 0.96 0.27 0.00
97_L 218_P 0.94 0.26 0.00
140_Q 45_N 0.94 0.25 0.00
95_E 79_I 0.94 0.25 0.00
169_G 133_T 0.93 0.25 0.00
148_L 43_A 0.88 0.21 0.00
28_Q 164_A 0.86 0.21 0.00
109_V 63_A 0.86 0.20 0.00
43_Q 140_R 0.86 0.20 0.00
129_L 65_A 0.86 0.20 0.00
12_D 236_D 0.85 0.20 0.00
71_R 87_Y 0.84 0.20 0.00
168_H 133_T 0.84 0.19 0.00
40_L 151_P 0.83 0.19 0.00
11_D 133_T 0.83 0.19 0.00
60_E 64_A 0.83 0.19 0.00
114_E 111_F 0.83 0.19 0.00
144_A 102_V 0.82 0.18 0.00
139_A 224_R 0.82 0.18 0.00
138_F 153_F 0.81 0.18 0.00
102_L 179_D 0.81 0.18 0.00
123_V 107_L 0.80 0.17 0.00
91_P 140_R 0.80 0.17 0.00
57_L 82_A 0.79 0.17 0.00
140_Q 69_N 0.79 0.17 0.00
127_E 87_Y 0.79 0.17 0.00
170_T 232_A 0.78 0.16 0.00
100_L 32_A 0.78 0.16 0.00
13_D 165_N 0.78 0.16 0.00
67_D 103_Y 0.77 0.16 0.00
14_V 148_A 0.77 0.16 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
4358 0.24 retry Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done
4357 0.81 retry Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done
4354 0 activmatch Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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