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OPENSEQ.org
EcfG_PhyR_Coev
Genes: A B A+B
Length: 218 266 435
Sequences: 5626 18101 392
Seq/Len: 25.81 68.05 0.9
MirrorTree (Pazo et al. 2001) 0.23
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 0.05
2 0.01 0.04 0.10
5 0.01 0.06 0.27
10 0.01 0.07 0.42
20 0.02 0.10 0.81
100 0.05 0.16 2.54
∞ 0.17 0.23 5.25
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
67_K 208_I 1.09 0.39 0.00
182_T 36_L 1.06 0.37 0.00
176_G 38_A 0.88 0.23 0.00
145_L 172_A 0.86 0.22 0.00
60_L 90_M 0.81 0.19 0.00
25_V 247_V 0.79 0.18 0.00
14_D 239_T 0.76 0.16 0.00
165_A 58_R 0.75 0.16 0.00
184_L 87_Q 0.75 0.16 0.00
134_L 147_E 0.73 0.15 0.00
162_C 160_V 0.73 0.15 0.00
35_Q 52_P 0.73 0.15 0.00
62_Q 208_I 0.72 0.15 0.00
169_I 238_I 0.71 0.14 0.00
34_K 143_V 0.71 0.14 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
4409 0.9 EcfG_PhyR_Coev Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4406 5.51 EcfG_PhyR_Coev Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4401 0.46 EcfG_PhyR_Coev Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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