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OPENSEQ.org
CA-VC
Genes: A B A+B
Length: 81 112 191
Sequences: 15179 13114 5712
Seq/Len: 187.4 117.09 29.91
MirrorTree (Pazo et al. 2001) 0.41
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 0.01 0.00 29.60
2 0.01 0.00 30.46
5 0.02 0.01 31.28
10 0.04 0.02 32.57
20 0.06 0.03 33.66
100 0.14 0.09 37.67
∞ 0.22 0.18 42.47
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
47_D 8_Q 0.69 0.60 0.00
71_R 12_N 0.60 0.43 0.00
68_L 74_G 0.56 0.37 0.00
51_R 60_R 0.54 0.33 0.00
9_R 102_G 0.53 0.32 0.00
71_R 60_R 0.52 0.32 0.00
52_R 12_N 0.50 0.28 0.00
69_T 12_N 0.48 0.26 0.00
27_R 44_D 0.47 0.24 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
5317 29.97 CA-VC Δgene:(1, 1) A:(1E-10, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done
5310 63.68 CA-VC Δgene:(1, 1) A:(1E-10, 8) B:(1E-20, 1) msa: HHblits (2015_06) 0.00 Done
5256 29.91 CA-VC Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done
5255 0.01 CA-VC Δgene:(1, 1) A:(1E-20, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed
5254 0.01 CA-VC Δgene:(1, 1) A:(1E-40, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed
5253 73.84 CA-VC Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
5252 0.01 CA-VC Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed
5251 80.51 CA-VC Δgene:(1, 1) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done
5250 75.52 CA-VC Δgene:(1, 1) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
5248 87.39 CA-VC Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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