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OPENSEQ.org
comp1
Genes: A B A+B
Length: 137 72 199
Sequences: 362 94 71
Seq/Len: 2.64 1.31 0.36
MirrorTree (Pazo et al. 2001) 0.24
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.04
2 0.01 0.01 0.04
5 0.01 0.01 0.05
10 0.01 0.01 0.05
20 0.01 0.01 0.07
100 0.01 0.01 0.14
∞ 0.09 0.11 0.34
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
37_V 11_Y 1.47 0.44 0.00
53_E 35_L 1.16 0.25 0.00
123_M 7_T 1.13 0.23 0.00
118_V 63_I 1.11 0.23 0.00
66_I 63_I 1.10 0.22 0.00
42_E 22_D 1.09 0.22 0.00
131_D 20_T 1.08 0.21 0.00
99_Y 40_L 1.07 0.21 0.00
85_G 17_R 1.06 0.20 0.00
71_D 22_D 1.05 0.20 0.00
33_L 45_S 1.04 0.19 0.00
6_K 11_Y 1.01 0.18 0.00
73_N 22_D 0.99 0.17 0.00
64_M 20_T 0.95 0.16 0.00
49_A 17_R 0.95 0.16 0.00
131_D 19_Q 0.94 0.15 0.00
53_E 10_D 0.94 0.15 0.00
35_V 22_D 0.92 0.14 0.00
126_Q 39_E 0.91 0.14 0.00
123_M 6_L 0.91 0.14 0.00
87_K 69_K 0.90 0.14 0.00
46_A 13_M 0.90 0.14 0.00
99_Y 26_R 0.88 0.13 0.00
16_A 13_M 0.88 0.13 0.00
24_E 63_I 0.88 0.13 0.00
98_S 7_T 0.87 0.13 0.00
123_M 9_T 0.87 0.13 0.00
89_K 10_D 0.86 0.13 0.00
128_K 11_Y 0.86 0.12 0.00
99_Y 15_L 0.85 0.12 0.00
89_K 17_R 0.85 0.12 0.00
7_I 13_M 0.84 0.12 0.00
31_E 60_Y 0.84 0.12 0.00
120_K 19_Q 0.81 0.11 0.00
35_V 63_I 0.81 0.11 0.00
120_K 18_C 0.80 0.11 0.00
63_E 19_Q 0.80 0.11 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
8605 0.4 comp Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8604 0.36 comp1 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8603 0.08 comp Δgene:(1, 20) A:(1E-06, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
8602 0.07 comp Δgene:(1, 20) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
8601 0 comp Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed - Shared
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