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OPENSEQ.org
yhcb-murg
Genes: A B A+B
Length: 176 363 535
Sequences: 2216 16158 1333
Seq/Len: 12.59 44.51 2.49
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 0.01 0.04 0.00
2 0.01 0.10 0.01
5 0.01 0.13 0.04
10 0.02 0.15 0.07
20 0.02 0.17 0.15
100 0.04 0.26 0.97
∞ 0.12 0.34 2.47
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
163_R 233_N 0.75 0.31 0.00
48_D 117_P 0.74 0.29 0.00
19_E 207_D 0.73 0.28 0.00
163_R 119_I 0.70 0.26 0.00
95_A 92_K 0.70 0.25 0.00
46_L 272_I 0.67 0.23 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
0496 2.49 yhcb-murg Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0495 1.81 yhcb-murg Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0491 0.06 yhcb-murg Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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