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OPENSEQ.org
2B3T
Genes: A B A+B
Length: 276 360 609
Sequences: 4434 3364 2061
Seq/Len: 16.07 9.34 3.38
MirrorTree (Pazo et al. 2001) 0.69
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 0.08 3.01
2 0.01 0.08 3.14
5 0.01 0.08 3.20
10 0.01 0.08 3.23
20 0.01 0.08 3.24
100 0.02 0.10 3.34
∞ 0.11 0.14 4.01
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
267_N 239_T 0.89 0.55 0.00
224_S 219_P 0.84 0.48 0.00
114_L 244_I 0.81 0.44 0.00
76_E 265_K 0.76 0.39 0.00
39_I 177_F 0.73 0.35 0.00
230_S 330_D 0.71 0.33 0.00
191_D 177_F 0.69 0.31 0.00
94_D 221_D 0.69 0.30 0.00
166_S 26_A 0.66 0.28 0.00
117_G 236_H 0.64 0.25 0.00
198_D 297_L 0.63 0.24 0.00
30_H 267_K 0.62 0.23 0.00
126_A 264_H 0.61 0.23 0.00
94_D 328_R 0.60 0.21 0.00
139_V 101_L 0.60 0.21 0.00
209_A 156_H 0.59 0.21 0.00
160_N 23_L 0.59 0.21 0.00
274_R 289_A 0.59 0.20 0.00
104_A 91_Q 0.57 0.20 0.00
190_Q 64_T 0.57 0.19 0.00
88_T 96_L 0.57 0.19 0.00
262_R 227_F 0.56 0.19 0.00
227_A 352_Q 0.55 0.18 0.00
187_I 98_V 0.55 0.18 0.00
187_I 56_Q 0.55 0.18 0.00
62_R 118_G 0.55 0.17 0.00
187_I 221_D 0.55 0.17 0.00
255_Y 118_G 0.55 0.17 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
12351 3.38 2B3T Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
1214 2.82 2b3t Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
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