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OPENSEQ.org
Sig-Pcra
Genes: A B A+B
Length: 371 739 964
Sequences: 602 3698 569
Seq/Len: 1.62 5 0.59
MirrorTree (Pazo et al. 2001) 0.27
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 0.09 0.00
2 0.02 0.09 0.00
5 0.02 0.09 0.01
10 0.02 0.09 0.02
20 0.02 0.09 0.04
100 0.02 0.10 0.08
∞ 0.04 0.16 0.51
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
319_R 259_W 1.01 0.24 0.00
184_Y 236_V 0.97 0.23 0.00
137_R 125_I 0.97 0.22 0.00
184_Y 172_V 0.89 0.18 0.00
292_D 76_V 0.86 0.17 0.00
182_K 608_G 0.84 0.16 0.00
334_E 190_L 0.84 0.16 0.00
236_E 62_I 0.84 0.16 0.00
243_A 356_I 0.83 0.16 0.00
119_E 170_D 0.83 0.15 0.00
242_I 41_L 0.82 0.15 0.00
180_Y 321_I 0.81 0.15 0.00
251_E 583_E 0.80 0.14 0.00
295_A 241_E 0.80 0.14 0.00
184_Y 560_I 0.80 0.14 0.00
102_V 582_E 0.80 0.14 0.00
367_K 131_E 0.80 0.14 0.00
57_G 124_V 0.79 0.14 0.00
238_T 400_R 0.78 0.14 0.00
63_L 395_I 0.78 0.13 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
9472 0.59 Sig-Pcra Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9471 0.49 Sig-Pcra Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9470 0.52 Sig-Pcra Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9469 0.59 Sig-Pcra Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9466 0.59 Sig-Pcra Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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