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OPENSEQ.org
K1-Tb
Genes: A B A+B
Length: 333 418 747
Sequences: 3770 1131 213
Seq/Len: 11.32 2.71 0.29
MirrorTree (Pazo et al. 2001) 0.14
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 0.05 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 0.10
100 0.14 0.10 0.28
∞ 0.24 0.18 0.58
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 363_A 1.23 0.25 0.00
73_Y 169_V 1.03 0.17 0.00
133_I 66_V 0.91 0.12 0.00
183_K 122_K 0.91 0.12 0.00
130_Y 85_F 0.86 0.11 0.00
308_T 221_T 0.86 0.11 0.00
143_D 122_K 0.84 0.11 0.00
182_G 354_S 0.82 0.10 0.00
203_I 232_T 0.82 0.10 0.00
113_N 64_I 0.81 0.10 0.00
206_I 221_T 0.81 0.10 0.00
121_N 275_T 0.81 0.10 0.00
233_K 85_F 0.79 0.09 0.00
178_T 232_T 0.79 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
1291 0.29 K1-Tb Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
1289 0.1 K1-Tb Δgene:(1, 20) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1287 0.1 K1-Tb Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1285 0.1 K1-Tb Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
1283 0.09 K1-Tb Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2013_03) Killed - Shared
1281 0.11 K1-Tb Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
1277 0.1 K1-Tb Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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