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OPENSEQ.org
16
Genes: A B A+B
Length: 330 107 400
Sequences: 34289 5387 350
Seq/Len: 103.91 50.35 0.88
MirrorTree (Pazo et al. 2001) 0.15
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 0.10 0.04
2 0.09 0.10 0.10
5 0.12 0.11 0.23
10 0.14 0.11 0.44
20 0.16 0.11 0.80
100 0.25 0.12 2.46
∞ 0.30 0.21 4.45
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
146_L 92_P 0.99 0.30 0.00
176_T 22_C 0.98 0.30 0.00
41_I 81_A 0.93 0.26 0.00
300_I 19_G 0.89 0.23 0.00
169_I 96_T 0.88 0.23 0.00
59_V 70_Q 0.87 0.22 0.00
109_V 89_G 0.86 0.22 0.00
142_G 24_V 0.86 0.22 0.00
64_F 103_L 0.85 0.21 0.00
208_Y 100_D 0.84 0.20 0.00
33_R 101_V 0.83 0.20 0.00
300_I 88_P 0.83 0.20 0.00
112_Y 78_P 0.82 0.19 0.00
116_G 19_G 0.81 0.19 0.00
127_V 78_P 0.81 0.18 0.00
233_A 93_P 0.80 0.18 0.00
89_I 8_S 0.80 0.18 0.00
103_W 100_D 0.78 0.17 0.00
297_M 57_R 0.78 0.17 0.00
90_L 35_K 0.78 0.17 0.00
42_G 51_G 0.77 0.17 0.00
285_P 61_E 0.76 0.16 0.00
241_I 57_R 0.75 0.16 0.00
47_G 22_C 0.74 0.15 0.00
78_I 17_K 0.74 0.15 0.00
133_I 81_A 0.74 0.15 0.00
133_I 7_I 0.74 0.15 0.00
275_V 93_P 0.73 0.14 0.00
45_R 78_P 0.72 0.14 0.00
309_G 60_E 0.72 0.14 0.00
89_I 18_R 0.72 0.14 0.00
169_I 19_G 0.72 0.14 0.00
61_V 63_V 0.72 0.14 0.00
284_I 46_F 0.69 0.13 0.00
118_L 67_S 0.69 0.13 0.00
70_R 57_R 0.69 0.13 0.00
111_D 86_G 0.69 0.13 0.00
257_P 79_D 0.68 0.13 0.00
109_V 32_D 0.68 0.12 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)
ID Seq/Len Name Options I_Prob Status
8696 0.88 16 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4726 1.03 1b6c Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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