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OPENSEQ.org
K1-Ta
Genes: A B A+B
Length: 333 439 765
Sequences: 3770 1037 210
Seq/Len: 11.32 2.36 0.27
MirrorTree (Pazo et al. 2001) 0.13
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 0.02 0.06 0.01
2 0.03 0.06 0.01
5 0.04 0.06 0.03
10 0.05 0.07 0.05
20 0.07 0.07 0.09
100 0.14 0.10 0.27
∞ 0.24 0.18 0.55
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
204_F 383_A 1.14 0.20 0.00
73_Y 171_I 1.14 0.20 0.00
130_Y 87_F 0.94 0.13 0.00
182_G 374_A 0.94 0.13 0.00
121_N 287_S 0.91 0.12 0.00
208_V 66_V 0.89 0.11 0.00
271_V 393_H 0.87 0.11 0.00
65_I 122_I 0.86 0.11 0.00
133_I 68_V 0.86 0.11 0.00
113_N 66_V 0.84 0.10 0.00
183_K 124_K 0.84 0.10 0.00
203_I 234_I 0.83 0.10 0.00
111_I 149_F 0.83 0.10 0.00
68_D 161_Y 0.81 0.09 0.00
49_Q 87_F 0.80 0.09 0.00
44_F 198_S 0.79 0.09 0.00
308_T 223_T 0.78 0.09 0.00
56_Q 9_V 0.78 0.09 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
1290 0.27 K1-Ta Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
1288 0.1 K1-Ta Δgene:(1, 20) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1286 0.1 K1-Ta Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1284 0.09 K1-Ta Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
1282 0.08 K1-Ta Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2013_03) Killed - Shared
1280 0.11 K1-Ta Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
1276 0.1 K1-Ta Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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