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OPENSEQ.org
yhcb-murg
Genes: A B A+B
Length: 176 363 536
Sequences: 2216 7415 969
Seq/Len: 12.59 20.43 1.81
MirrorTree (Pazo et al. 2001) 0.11
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 0.02 0.00
2 0.01 0.03 0.00
5 0.01 0.05 0.01
10 0.02 0.05 0.03
20 0.02 0.05 0.06
100 0.04 0.12 0.47
∞ 0.12 0.26 1.80
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
153_E 189_V 0.83 0.32 0.00
168_V 264_V 0.82 0.31 0.00
65_S 135_S 0.81 0.30 0.00
67_L 328_I 0.81 0.30 0.00
71_I 279_G 0.81 0.30 0.00
88_G 244_M 0.80 0.29 0.00
162_G 95_A 0.71 0.22 0.00
127_P 26_R 0.70 0.21 0.00
3_I 258_K 0.70 0.21 0.00
67_L 189_V 0.69 0.20 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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