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OPENSEQ.org
1qdl
Genes: A B A+B
Length: 422 195 605
Sequences: 7061 14705 2757
Seq/Len: 16.73 75.41 4.56
MirrorTree (Pazo et al. 2001) 0.59
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 0.00 0.00 3.86
2 0.00 0.00 4.11
5 0.00 0.00 4.28
10 0.00 0.00 4.33
20 0.00 0.01 4.47
100 0.03 0.02 4.98
∞ 0.11 0.10 6.74
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
174_S 100_R 3.82 1.00 1.00
288_P 22_G 2.58 1.00 1.00
397_Y 104_V 2.36 1.00 1.00
283_G 19_Q 2.30 1.00 0.99
170_E 100_R 2.19 1.00 0.99
96_E 32_R 1.86 1.00 0.98
173_R 100_R 1.78 1.00 0.97
97_K 35_E 1.70 0.99 0.96
272_L 133_T 1.51 0.98 0.93
272_L 180_G 1.44 0.97 0.91
398_D 108_K 1.36 0.96 0.87
171_Y 56_G 1.27 0.94 0.82
176_Y 56_G 0.93 0.69 0.48
317_K 22_G 0.80 0.52 0.33
288_P 28_P 0.80 0.51 0.32
272_L 109_I 0.77 0.48 0.29
297_M 133_T 0.77 0.48 0.29
174_S 57_T 0.73 0.43 0.25
341_P 32_R 0.73 0.42 0.24
288_P 18_A 0.72 0.42 0.24
176_Y 63_D 0.72 0.41 0.24
173_R 104_V 0.71 0.40 0.23
359_A 133_T 0.69 0.37 0.20
325_V 158_E 0.67 0.34 0.18
335_V 133_T 0.67 0.34 0.18
178_F 181_T 0.62 0.29 0.15
167_E 97_K 0.62 0.29 0.15
278_A 48_R 0.62 0.28 0.14
289_G 23_E 0.62 0.28 0.14
283_G 22_G 0.61 0.27 0.14
296_L 179_V 0.60 0.26 0.13
316_L 96_A 0.58 0.24 0.12
167_E 45_D 0.58 0.24 0.11
330_F 83_V 0.55 0.21 0.10
314_G 96_A 0.55 0.21 0.10
296_L 133_T 0.55 0.21 0.10
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)
ID Seq/Len Name Options I_Prob Status
5366 3.29 1QDL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
5330 4.56 1qdl Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 1.00 Done - Shared
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