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OPENSEQ.org
corrected factor-RNAP
Genes: A B A+B
Length: 210 613 781
Sequences: 10962 719 628
Seq/Len: 52.2 1.17 0.8
MirrorTree (Pazo et al. 2001) 0.18
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 0.02 0.01 0.00
2 0.03 0.01 0.00
5 0.04 0.01 0.01
10 0.05 0.01 0.02
20 0.07 0.01 0.04
100 0.12 0.01 0.21
∞ 0.21 0.02 0.76
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
208_G 161_L 1.11 0.38 0.00
58_K 316_F 1.11 0.38 0.00
55_E 160_D 1.07 0.35 0.00
30_L 515_E 0.99 0.28 0.00
197_I 151_V 0.98 0.28 0.00
140_V 533_D 0.94 0.25 0.00
204_I 317_N 0.94 0.25 0.00
28_S 144_L 0.93 0.24 0.00
169_T 193_D 0.91 0.23 0.00
173_I 336_E 0.88 0.22 0.00
146_Q 498_L 0.88 0.21 0.00
56_E 515_E 0.85 0.20 0.00
76_L 347_I 0.85 0.20 0.00
193_D 357_Q 0.83 0.19 0.00
92_A 182_G 0.82 0.18 0.00
89_A 17_K 0.82 0.18 0.00
57_G 19_Q 0.81 0.18 0.00
28_S 39_D 0.81 0.18 0.00
9_D 39_D 0.81 0.18 0.00
205_V 14_T 0.81 0.17 0.00
190_M 149_D 0.80 0.17 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)
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