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OPENSEQ.org
cPCRA_RNAPbeta
Genes: A B A+B
Length: 281 150 429
Sequences: 9438 2267 1993
Seq/Len: 33.59 15.11 4.65
MirrorTree (Pazo et al. 2001) 0.20
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 0.05 0.00 0.01
2 0.05 0.00 0.01
5 0.05 0.00 0.03
10 0.06 0.00 0.10
20 0.06 0.00 0.19
100 0.20 0.00 1.03
∞ 0.24 0.00 4.62
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
61_K 145_I 0.91 0.68 0.01
48_A 85_C 0.89 0.65 0.01
98_Y 70_Y 0.88 0.63 0.01
194_L 16_G 0.82 0.55 0.01
267_G 137_V 0.81 0.55 0.01
197_E 81_D 0.81 0.54 0.01
169_A 137_V 0.79 0.51 0.01
99_D 118_K 0.79 0.51 0.01
230_T 100_L 0.78 0.50 0.00
13_N 101_R 0.77 0.48 0.00
50_K 137_V 0.76 0.47 0.00
171_A 145_I 0.74 0.45 0.00
31_K 137_V 0.74 0.45 0.00
233_F 52_A 0.74 0.44 0.00
17_R 126_E 0.73 0.43 0.00
275_T 52_A 0.72 0.42 0.00
106_I 53_F 0.70 0.39 0.00
81_T 78_P 0.69 0.38 0.00
181_N 35_F 0.69 0.38 0.00
47_V 92_Y 0.69 0.37 0.00
52_H 39_I 0.68 0.36 0.00
149_G 77_E 0.68 0.36 0.00
167_K 62_Y 0.68 0.36 0.00
164_V 93_S 0.67 0.35 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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