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OPENSEQ.org
1B6C Complex
Genes: A B A+B
Length: 107 342 400
Sequences: 3008 9841 717
Seq/Len: 28.11 28.77 1.79
MirrorTree (Pazo et al. 2001) 0.11
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 0.05 0.05 0.02
2 0.05 0.06 0.03
5 0.06 0.08 0.05
10 0.06 0.09 0.12
20 0.06 0.10 0.19
100 0.07 0.15 0.62
∞ 0.16 0.24 1.60
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
30_L 56_G 0.88 0.37 0.00
43_N 93_L 0.86 0.34 0.00
8_S 317_N 0.79 0.28 0.00
81_A 227_I 0.77 0.26 0.00
57_R 169_A 0.74 0.24 0.00
24_V 250_I 0.74 0.24 0.00
39_S 137_T 0.73 0.23 0.00
20_Q 240_I 0.67 0.19 0.00
33_G 98_I 0.67 0.19 0.00
62_G 98_I 0.67 0.19 0.00
34_K 173_L 0.67 0.18 0.00
104_L 193_L 0.66 0.18 0.00
47_K 131_L 0.65 0.17 0.00
24_V 154_H 0.65 0.17 0.00
63_V 54_R 0.65 0.17 0.00
21_T 47_Q 0.64 0.17 0.00
79_D 270_L 0.64 0.17 0.00
104_L 308_K 0.63 0.16 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
7395 0.47 1B6C_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
0296 1.79 1B6C Complex Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0295 0.21 1B6C Complex Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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