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OPENSEQ.org
4hr7_ab
Genes: A B A+B
Length: 443 80 516
Sequences: 12806 5921 1904
Seq/Len: 28.91 74.01 3.69
MirrorTree (Pazo et al. 2001) 0.57
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 2.98
2 0.03 0.01 3.51
5 0.04 0.01 3.57
10 0.09 0.01 3.57
20 0.12 0.01 3.64
100 0.16 0.04 3.82
∞ 0.25 0.14 4.48
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
34_S 73_D 1.68 0.99 0.92
72_I 69_P 0.93 0.63 0.35
34_S 72_F 0.79 0.45 0.21
69_A 69_P 0.75 0.39 0.18
67_I 73_D 0.74 0.39 0.17
40_K 50_Q 0.72 0.35 0.15
185_E 49_N 0.67 0.30 0.12
73_T 36_G 0.66 0.29 0.12
167_R 50_Q 0.66 0.29 0.12
195_V 67_G 0.64 0.27 0.11
88_N 59_V 0.63 0.26 0.10
421_I 11_M 0.63 0.26 0.10
223_A 48_M 0.61 0.24 0.09
284_I 47_M 0.61 0.24 0.09
164_R 49_N 0.59 0.22 0.08
331_A 19_P 0.59 0.22 0.08
418_Q 48_M 0.58 0.21 0.08
341_P 33_V 0.58 0.21 0.07
220_I 61_A 0.57 0.20 0.07
217_G 47_M 0.57 0.20 0.07
367_H 15_F 0.56 0.20 0.07
382_I 11_M 0.56 0.19 0.07
245_I 41_I 0.56 0.19 0.07
216_Q 7_V 0.55 0.18 0.06
169_V 73_D 0.55 0.18 0.06
185_E 50_Q 0.55 0.18 0.06
397_A 29_V 0.55 0.18 0.06
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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