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AraC-RNAP D whole genome 1 iteration
Genes: A B A+B
Length: 118 511 573
Sequences: 8821 788 190
Seq/Len: 74.75 1.54 0.33
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 0.01 0.00
2 0.02 0.01 0.00
5 0.04 0.01 0.00
10 0.06 0.01 0.00
20 0.08 0.01 0.00
100 0.14 0.01 0.03
∞ 0.21 0.02 0.30
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
45_L 14_T 1.15 0.23 0.00
76_G 296_K 1.13 0.22 0.00
23_I 153_A 1.05 0.19 0.00
73_A 337_V 1.00 0.17 0.00
98_S 53_I 0.95 0.15 0.00
62_K 24_Y 0.95 0.15 0.00
93_K 316_F 0.91 0.14 0.00
15_H 354_T 0.91 0.13 0.00
43_Q 282_T 0.90 0.13 0.00
22_D 300_K 0.89 0.13 0.00
12_I 328_E 0.89 0.13 0.00
81_F 254_E 0.87 0.12 0.00
68_T 149_D 0.87 0.12 0.00
35_S 308_G 0.87 0.12 0.00
3_N 197_D 0.85 0.12 0.00
97_A 21_Y 0.85 0.12 0.00
89_R 35_I 0.85 0.12 0.00
58_I 289_K 0.84 0.12 0.00
15_H 39_D 0.84 0.11 0.00
4_R 484_A 0.82 0.11 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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