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tria_opmh

Genes: A B A+B
Length: 383 482 755
Sequences: 14856 13105 6029
Seq/Len: 38.79 27.19 7.99
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 3.26
2 0.03 0.00 6.01
5 0.04 0.02 6.63
10 0.06 0.04 6.78
20 0.08 0.06 6.97
100 0.14 0.14 7.71
0.21 0.21 8.77
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
138_K 392_I 2.23 1.00 0.99
134_A 396_V 1.70 1.00 0.97
139_G 182_K 1.63 1.00 0.95
138_K 173_E 1.50 0.99 0.93
139_G 175_F 1.35 0.99 0.87
140_Y 392_I 1.13 0.95 0.73
134_A 177_V 1.08 0.93 0.68
142_S 181_D 1.03 0.91 0.63
138_K 388_E 1.03 0.91 0.63
132_Q 398_T 0.97 0.87 0.56
132_Q 179_L 0.93 0.84 0.51
140_Y 173_E 0.81 0.71 0.36
140_Y 389_A 0.81 0.70 0.35
138_K 169_D 0.69 0.53 0.22
139_G 395_Q 0.66 0.47 0.19
139_G 166_R 0.64 0.45 0.17
143_Q 178_G 0.60 0.38 0.14
144_S 179_L 0.60 0.38 0.14
140_Y 170_Q 0.58 0.34 0.12
135_L 179_L 0.53 0.28 0.09
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
6902 7.99 tria_opmh Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
0899 5.5 TriA-OpmH (NP_248846-NP_253661) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.99 Done

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