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OPENSEQ.org
1B39_A CDK2 kinase ATP,ACE 1FPZ_F CDK inhibitor 3
Genes: A B A+B
Length: 299 212 476
Sequences: 68640 1525 465
Seq/Len: 229.57 7.19 0.98
MirrorTree (Pazo et al. 2001) 0.10
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 0.19 0.06 0.07
2 0.21 0.06 0.13
5 0.24 0.07 0.31
10 0.27 0.07 0.57
20 0.29 0.08 0.91
100 0.33 0.09 1.68
∞ 0.34 0.11 1.79
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
189_S 48_L 1.08 0.41 0.00
189_S 62_K 1.02 0.36 0.00
80_V 102_I 0.93 0.28 0.00
211_D 67_L 0.86 0.23 0.00
81_F 150_V 0.81 0.20 0.00
20_Y 150_V 0.77 0.17 0.00
190_L 159_S 0.76 0.17 0.00
263_L 59_N 0.75 0.17 0.00
80_V 186_Y 0.72 0.15 0.00
56_L 136_T 0.72 0.15 0.00
47_S 71_G 0.72 0.15 0.00
79_L 59_N 0.72 0.15 0.00
16_Y 117_A 0.71 0.15 0.00
79_L 67_L 0.70 0.14 0.00
82_E 164_P 0.70 0.14 0.00
65_V 91_N 0.70 0.14 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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