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OPENSEQ.org
1QDL
Genes: A B A+B
Length: 422 195 597
Sequences: 4709 16398 1963
Seq/Len: 11.16 84.09 3.29
MirrorTree (Pazo et al. 2001) 0.31
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 0.01 0.03 2.54
2 0.01 0.03 2.69
5 0.01 0.03 2.83
10 0.01 0.04 3.02
20 0.01 0.05 3.18
100 0.03 0.12 3.65
∞ 0.16 0.20 4.98
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 3.63 1.00 1.00
288_P 22_G 2.47 1.00 1.00
397_Y 104_V 2.09 1.00 0.99
170_E 100_R 2.08 1.00 0.99
283_G 19_Q 2.08 1.00 0.99
96_E 32_R 1.83 0.99 0.97
272_L 133_T 1.51 0.97 0.91
173_R 100_R 1.44 0.95 0.88
272_L 180_G 1.29 0.90 0.81
171_Y 56_G 1.28 0.90 0.79
398_D 108_K 1.23 0.87 0.76
176_Y 61_R 1.00 0.68 0.52
176_Y 56_G 0.94 0.60 0.45
288_P 18_A 0.86 0.50 0.34
299_V 189_Y 0.81 0.44 0.29
335_V 133_T 0.77 0.39 0.24
288_P 28_P 0.75 0.36 0.22
341_P 32_R 0.72 0.33 0.20
359_A 133_T 0.72 0.33 0.19
13_P 14_V 0.70 0.30 0.17
318_K 69_D 0.69 0.30 0.17
402_E 128_K 0.68 0.29 0.16
317_K 22_G 0.67 0.28 0.16
97_K 35_E 0.66 0.27 0.14
173_R 104_V 0.65 0.26 0.14
297_M 133_T 0.64 0.25 0.14
178_F 181_T 0.64 0.24 0.13
359_A 28_P 0.64 0.24 0.13
160_S 186_K 0.64 0.24 0.13
312_V 83_V 0.62 0.23 0.12
163_R 124_Y 0.62 0.23 0.12
180_V 15_Y 0.62 0.23 0.12
88_S 123_Y 0.62 0.23 0.12
268_K 131_K 0.61 0.22 0.11
296_L 179_V 0.60 0.21 0.11
119_I 49_L 0.59 0.21 0.10
365_I 45_D 0.59 0.20 0.10
384_K 38_I 0.59 0.20 0.10
269_A 19_Q 0.59 0.20 0.10
67_L 174_F 0.59 0.20 0.10
236_V 51_I 0.58 0.20 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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