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OPENSEQ.org
AraC-RNAP D
Genes: A B A+B
Length: 118 511 583
Sequences: 42068 788 99
Seq/Len: 356.51 1.54 0.17
MirrorTree (Pazo et al. 2001) 0.03
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 0.03 0.01 0.01
2 0.05 0.01 0.02
5 0.10 0.01 0.04
10 0.13 0.01 0.08
20 0.18 0.01 0.16
100 0.28 0.01 0.55
∞ 0.32 0.02 1.26
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
104_A 280_V 1.31 0.21 0.00
92_K 46_Q 1.11 0.14 0.00
24_A 69_E 1.06 0.13 0.00
26_V 156_A 1.01 0.11 0.00
18_D 267_D 0.99 0.11 0.00
95_T 267_D 0.99 0.11 0.00
93_K 287_I 0.99 0.11 0.00
21_F 361_I 0.99 0.11 0.00
64_L 289_K 0.95 0.10 0.00
23_I 171_E 0.94 0.10 0.00
65_L 362_N 0.94 0.10 0.00
70_M 355_I 0.92 0.10 0.00
69_R 134_V 0.92 0.10 0.00
26_V 303_I 0.92 0.10 0.00
26_V 380_V 0.90 0.09 0.00
18_D 337_V 0.90 0.09 0.00
75_V 511_I 0.89 0.09 0.00
85_L 339_R 0.89 0.09 0.00
8_A 331_H 0.88 0.09 0.00
28_Q 41_I 0.88 0.09 0.00
65_L 59_A 0.88 0.09 0.00
72_I 308_G 0.86 0.08 0.00
91_F 12_L 0.85 0.08 0.00
95_T 297_M 0.85 0.08 0.00
76_G 12_L 0.85 0.08 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
6558 0.33 AraC-RNAP D whole genome 1 iteration Δgene:(1, ∞) A:(1E-20, 1) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6557 1.37 AraC-RNAP D whole genome Δgene:(1, ∞) A:(1E-20, 4) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
6554 0 AraC-RNAP D whole genome Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6537 1.38 AraC-RNAP D whole genome Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6536 0.17 AraC-RNAP D Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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