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OPENSEQ.org
beta flap (A, 50-660) (A, 100-200) (B, 1-45)
Genes: A B A+B
Length: 101 45 142
Sequences: 7718 707 1406
Seq/Len: 76.42 15.71 9.9
MirrorTree (Pazo et al. 2001) 0.07
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 0.04 0.09 0.01
2 0.04 0.09 0.01
5 0.05 0.09 0.07
10 0.06 0.09 0.19
20 0.06 0.09 0.34
100 0.13 0.09 2.04
∞ 0.24 0.09 9.63
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
87_L 13_A 0.84 0.80 0.00
41_S 1_V 0.81 0.77 0.00
81_N 36_I 0.78 0.73 0.00
41_S 31_H 0.74 0.67 0.00
47_L 36_I 0.71 0.62 0.00
40_Q 44_N 0.70 0.61 0.00
81_N 22_V 0.70 0.60 0.00
5_N 5_T 0.69 0.59 0.00
55_F 27_L 0.65 0.52 0.00
53_K 39_D 0.64 0.49 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
9989 9.79 beta flap (A, 50-660) (A, 100-200) (B, 1-45) Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9988 9.9 beta flap (A, 50-660) (A, 100-200) (B, 1-45) Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9987 0.35 beta flap (A, 50-660) (A, 100-200) (B, 1-45) Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
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