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OPENSEQ.org
ETF-Mcd (A, 160-548)
Genes: A B A+B
Length: 389 253 630
Sequences: 17875 2636 1199
Seq/Len: 45.95 10.42 1.9
MirrorTree (Pazo et al. 2001) 0.14
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 0.10 0.01 0.48
2 0.11 0.01 0.76
5 0.15 0.01 1.01
10 0.18 0.01 1.19
20 0.20 0.02 1.38
100 0.25 0.03 1.87
∞ 0.31 0.08 2.91
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
107_K 86_V 0.82 0.32 0.00
275_A 203_L 0.80 0.30 0.00
142_V 140_G 0.80 0.30 0.00
150_V 43_V 0.79 0.29 0.00
120_L 210_D 0.76 0.27 0.00
180_R 178_V 0.74 0.25 0.00
263_V 83_A 0.73 0.24 0.00
138_R 117_V 0.73 0.24 0.00
105_A 178_V 0.69 0.21 0.00
351_N 72_L 0.66 0.19 0.00
148_W 52_A 0.65 0.18 0.00
378_I 56_T 0.65 0.18 0.00
168_L 212_G 0.64 0.18 0.00
266_N 249_E 0.63 0.17 0.00
7_E 73_R 0.63 0.17 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
6020 2.97 ETF-Mcd (A, 160-548) infinit Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6019 1.9 ETF-Mcd (A, 160-548) Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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