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OPENSEQ.org
2b3t
Genes: A B A+B
Length: 276 360 630
Sequences: 2694 2899 1778
Seq/Len: 9.76 8.05 2.82
MirrorTree (Pazo et al. 2001) 0.53
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 0.00 0.00 1.77
2 0.00 0.00 1.88
5 0.00 0.00 1.91
10 0.00 0.00 1.92
20 0.00 0.01 1.95
100 0.02 0.04 2.06
∞ 0.10 0.22 2.80
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
40_L 159_Y 0.81 0.39 0.00
224_S 219_P 0.74 0.33 0.00
41_A 132_F 0.72 0.30 0.00
117_G 267_K 0.65 0.23 0.00
267_N 239_T 0.64 0.22 0.00
143_P 251_T 0.61 0.20 0.00
209_A 156_H 0.61 0.20 0.00
238_H 193_Q 0.60 0.20 0.00
94_D 315_G 0.60 0.19 0.00
180_I 348_H 0.60 0.19 0.00
5_H 68_M 0.59 0.18 0.00
239_G 236_H 0.59 0.18 0.00
25_E 229_S 0.59 0.18 0.00
123_I 327_Y 0.58 0.18 0.00
39_I 8_K 0.58 0.18 0.00
154_Q 90_E 0.58 0.18 0.00
133_D 174_R 0.58 0.17 0.00
138_A 66_Q 0.58 0.17 0.00
122_A 329_L 0.57 0.17 0.00
22_R 229_S 0.57 0.17 0.00
264_Y 229_S 0.57 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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