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OPENSEQ.org
dnak linker and dnaj hpd_mayer 2018 cell paper check
Genes: A B A+B
Length: 60 60 119
Sequences: 1553 9335 900
Seq/Len: 25.88 155.58 7.56
MirrorTree (Pazo et al. 2001) 0.34
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 0.07 0.05 5.81
2 0.07 0.05 6.81
5 0.07 0.05 6.98
10 0.07 0.06 7.14
20 0.07 0.07 7.50
100 0.08 0.10 9.58
∞ 0.13 0.18 14.66
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
54_K 30_M 1.21 0.97 0.34
60_T 22_R 1.19 0.96 0.32
4_D 51_K 1.17 0.96 0.30
22_L 29_A 1.05 0.91 0.21
21_V 12_V 1.02 0.89 0.20
44_M 8_E 1.01 0.89 0.19
29_V 15_T 0.93 0.83 0.15
50_T 28_L 0.85 0.73 0.11
10_A 51_K 0.84 0.73 0.11
4_D 27_R 0.83 0.72 0.10
53_A 9_I 0.83 0.72 0.10
32_L 29_A 0.82 0.70 0.10
38_S 17_E 0.80 0.68 0.09
5_V 47_F 0.79 0.66 0.09
41_I 14_K 0.79 0.65 0.09
10_A 58_T 0.78 0.64 0.08
19_G 16_A 0.78 0.64 0.08
10_A 36_R 0.76 0.62 0.08
16_A 57_L 0.74 0.59 0.07
51_L 56_V 0.72 0.56 0.07
56_T 27_R 0.72 0.56 0.07
3_K 40_D 0.70 0.53 0.06
10_A 41_K 0.69 0.51 0.06
30_L 60_S 0.68 0.48 0.05
17_V 41_K 0.66 0.46 0.05
13_I 30_M 0.65 0.44 0.05
55_N 11_G 0.65 0.44 0.05
35_T 28_L 0.64 0.43 0.05
23_T 23_K 0.64 0.43 0.05
27_K 21_I 0.64 0.43 0.04
50_T 58_T 0.64 0.43 0.04
58_I 19_R 0.64 0.43 0.04
19_G 2_A 0.64 0.42 0.04
48_M 55_E 0.64 0.42 0.04
57_T 30_M 0.63 0.41 0.04
4_D 13_S 0.62 0.40 0.04
58_I 48_K 0.62 0.39 0.04
48_M 21_I 0.61 0.39 0.04
44_M 4_Q 0.61 0.38 0.04
19_G 3_K 0.61 0.38 0.04
30_L 18_E 0.61 0.38 0.04
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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