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OPENSEQ.org
RelA vs ComGA
Genes: A B A+B
Length: 734 356 1076
Sequences: 2617 7255 1454
Seq/Len: 3.57 20.38 1.35
MirrorTree (Pazo et al. 2001) 0.06
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.09 0.00
2 0.00 0.10 0.00
5 0.00 0.10 0.02
10 0.00 0.12 0.03
20 0.01 0.12 0.08
100 0.02 0.15 0.45
∞ 0.05 0.18 1.33
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
621_V 115_S 1.01 0.42 0.00
432_V 9_K 0.94 0.35 0.00
419_I 64_S 0.92 0.34 0.00
641_I 169_I 0.92 0.33 0.00
164_S 203_I 0.89 0.31 0.00
550_L 237_T 0.87 0.29 0.00
546_V 287_S 0.85 0.28 0.00
519_K 199_G 0.84 0.27 0.00
218_V 195_T 0.81 0.25 0.00
284_I 34_I 0.80 0.23 0.00
535_A 117_D 0.79 0.23 0.00
724_R 140_L 0.79 0.23 0.00
24_H 268_I 0.79 0.23 0.00
89_D 268_I 0.79 0.23 0.00
233_N 213_L 0.78 0.22 0.00
86_T 34_I 0.78 0.22 0.00
158_E 269_A 0.77 0.22 0.00
154_H 213_L 0.76 0.21 0.00
191_A 131_S 0.76 0.21 0.00
191_A 231_T 0.76 0.21 0.00
623_V 82_K 0.76 0.21 0.00
58_A 57_I 0.76 0.21 0.00
235_K 229_A 0.76 0.21 0.00
34_Y 237_T 0.75 0.21 0.00
300_I 210_M 0.75 0.20 0.00
238_F 227_R 0.75 0.20 0.00
470_T 197_S 0.75 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
2260 1.35 RelA vs ComGA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done
2259 0.08 RelA vs ComGA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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