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OPENSEQ.org
PhoB-PHoR
Genes: A B A+B
Length: 229 431 588
Sequences: 36248 12732 3882
Seq/Len: 158.29 29.54 6.6
MirrorTree (Pazo et al. 2001) 0.57
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 0.01 3.40
2 0.02 0.02 3.96
5 0.04 0.02 4.45
10 0.06 0.03 5.12
20 0.10 0.05 5.88
100 0.20 0.11 8.83
∞ 0.25 0.21 11.02
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
16_E 241_K 1.36 0.98 0.68
14_I 220_T 1.26 0.97 0.59
17_M 224_G 1.01 0.87 0.34
21_V 228_M 0.98 0.84 0.31
13_P 249_Q 0.89 0.75 0.23
20_F 242_A 0.84 0.69 0.20
16_E 225_Y 0.84 0.69 0.19
17_M 225_Y 0.73 0.53 0.12
16_E 245_T 0.65 0.41 0.09
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
10827 6.6 PhoB-PHoR Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.68 Done - Shared
0714 6.76 BR Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 1.00 Done
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