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OPENSEQ.org
PcrA_tudor_only vs RPOB_C
Genes: A B A+B
Length: 52 593 580
Sequences: 488 1404 67
Seq/Len: 9.38 2.37 0.12
MirrorTree (Pazo et al. 2001) 0.25
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 0.00 0.09 0.00
2 0.00 0.09 0.00
5 0.00 0.09 0.00
10 0.00 0.09 0.00
20 0.00 0.09 0.00
100 0.00 0.09 0.02
∞ 0.00 0.09 0.10
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
31_I 355_I 1.66 0.29 0.00
42_L 8_V 1.46 0.21 0.00
47_A 368_I 1.25 0.15 0.00
3_V 212_D 1.22 0.14 0.00
17_V 346_Y 1.21 0.14 0.00
42_L 319_I 1.20 0.14 0.00
42_L 238_D 1.15 0.12 0.00
44_A 177_M 1.14 0.12 0.00
6_R 74_V 1.13 0.12 0.00
18_V 74_V 1.08 0.11 0.00
49_I 310_R 1.07 0.11 0.00
51_K 183_K 1.02 0.10 0.00
17_V 132_V 1.00 0.09 0.00
52_V 335_I 1.00 0.09 0.00
6_R 495_I 0.96 0.09 0.00
4_G 82_V 0.93 0.08 0.00
35_S 427_D 0.93 0.08 0.00
25_D 229_I 0.89 0.08 0.00
28_E 259_R 0.89 0.07 0.00
49_I 536_Q 0.89 0.07 0.00
42_L 348_P 0.88 0.07 0.00
1_W 313_I 0.86 0.07 0.00
47_A 414_K 0.85 0.07 0.00
43_L 229_I 0.85 0.07 0.00
3_V 313_I 0.85 0.07 0.00
11_K 87_A 0.85 0.07 0.00
6_R 73_A 0.85 0.07 0.00
50_E 229_I 0.84 0.07 0.00
34_P 524_V 0.83 0.07 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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