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OPENSEQ.org
1F6M
Genes: A B A+B
Length: 320 108 415
Sequences: 30584 25481 2376
Seq/Len: 95.58 235.94 5.73
MirrorTree (Pazo et al. 2001) 0.33
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 0.02 0.04 1.55
2 0.02 0.04 1.89
5 0.04 0.05 2.70
10 0.06 0.06 3.75
20 0.09 0.07 5.55
100 0.17 0.13 13.71
∞ 0.23 0.21 22.79
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
214_Q 67_A 0.62 0.33 0.00
122_P 97_G 0.60 0.31 0.00
205_R 72_I 0.59 0.29 0.00
276_T 84_G 0.59 0.29 0.00
111_A 87_A 0.57 0.27 0.00
205_R 71_G 0.57 0.27 0.00
256_L 14_T 0.56 0.26 0.00
277_S 81_F 0.56 0.26 0.00
79_I 101_E 0.56 0.26 0.00
150_V 65_G 0.56 0.26 0.00
239_L 80_L 0.56 0.25 0.00
157_A 83_N 0.55 0.24 0.00
232_E 53_L 0.54 0.24 0.00
313_L 58_L 0.54 0.23 0.00
16_A 42_L 0.53 0.23 0.00
247_P 66_T 0.53 0.23 0.00
173_L 96_K 0.53 0.23 0.00
11_L 17_L 0.52 0.22 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
13399 5.73 1F6M Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9132 4.93 1F6M Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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