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OPENSEQ.org
NtoN5
Genes: A B A+B
Length: 244 212 426
Sequences: 200 11389 85
Seq/Len: 0.82 53.72 0.2
MirrorTree (Pazo et al. 2001) 0.12
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 0.13 0.04 0.01
2 0.14 0.04 0.01
5 0.15 0.05 0.01
10 0.15 0.05 0.02
20 0.15 0.05 0.03
100 0.15 0.07 0.09
∞ 0.16 0.10 0.19
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
159_C 151_Y 1.30 0.23 0.00
188_C 134_W 1.29 0.22 0.00
121_L 58_N 1.20 0.19 0.00
136_C 134_W 1.19 0.18 0.00
159_C 134_W 1.18 0.18 0.00
113_C 113_P 1.17 0.18 0.00
113_C 186_Y 1.16 0.17 0.00
80_C 117_P 1.16 0.17 0.00
41_S 190_V 1.10 0.15 0.00
110_C 113_P 1.09 0.15 0.00
173_C 134_W 1.08 0.15 0.00
68_C 18_W 1.08 0.14 0.00
131_C 134_W 1.07 0.14 0.00
131_C 113_P 1.04 0.13 0.00
200_D 199_S 1.04 0.13 0.00
133_P 159_I 1.03 0.13 0.00
21_A 150_Y 1.01 0.13 0.00
101_C 134_W 0.98 0.12 0.00
28_V 202_S 0.97 0.12 0.00
154_P 117_P 0.96 0.11 0.00
161_C 186_Y 0.93 0.11 0.00
32_C 209_T 0.92 0.10 0.00
32_C 59_L 0.90 0.10 0.00
177_Y 199_S 0.90 0.10 0.00
56_E 159_I 0.89 0.10 0.00
133_P 199_S 0.89 0.10 0.00
173_C 113_P 0.89 0.10 0.00
131_C 151_Y 0.88 0.10 0.00
10_C 202_S 0.87 0.09 0.00
107_G 134_W 0.86 0.09 0.00
68_C 120_V 0.86 0.09 0.00
142_A 177_V 0.85 0.09 0.00
173_C 151_Y 0.85 0.09 0.00
117_F 127_H 0.85 0.09 0.00
173_C 130_I 0.84 0.09 0.00
71_C 190_V 0.84 0.09 0.00
80_C 18_W 0.84 0.09 0.00
101_C 197_R 0.83 0.09 0.00
117_F 176_L 0.83 0.09 0.00
173_C 186_Y 0.82 0.08 0.00
173_C 117_P 0.82 0.08 0.00
115_P 126_S 0.81 0.08 0.00
46_C 148_S 0.81 0.08 0.00
97_V 120_V 0.81 0.08 0.00
41_S 120_V 0.81 0.08 0.00
149_V 79_I 0.80 0.08 0.00
178_W 52_R 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
6293 0.1 NtoN7 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
6292 0.12 NtoN6 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
6291 0.2 NtoN5 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
6290 0.11 NtoN4 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
6289 0.11 NtoN3 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
6287 0.12 NtoN2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
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