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trib_opmh

Genes: A B A+B
Length: 356 482 752
Sequences: 16865 13105 6990
Seq/Len: 47.37 27.19 9.3
MirrorTree (Pazo et al. 2001) 0.64
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 0.03 0.00 3.90
2 0.03 0.00 7.31
5 0.05 0.02 8.00
10 0.06 0.04 8.16
20 0.08 0.06 8.34
100 0.15 0.14 9.06
0.22 0.21 10.08
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
126_R 392_I 2.26 1.00 0.99
122_E 396_V 1.72 1.00 0.97
127_S 182_K 1.70 1.00 0.96
126_R 173_E 1.63 1.00 0.96
127_S 175_F 1.51 1.00 0.93
122_E 177_V 1.23 0.98 0.81
126_R 388_E 1.10 0.95 0.71
128_V 392_I 1.09 0.95 0.70
130_A 181_D 0.98 0.90 0.57
120_Q 398_T 0.91 0.85 0.48
120_Q 179_L 0.89 0.83 0.46
128_V 173_E 0.88 0.82 0.44
128_V 389_A 0.81 0.74 0.36
127_S 395_Q 0.80 0.74 0.35
126_R 169_D 0.77 0.69 0.31
127_S 166_R 0.75 0.67 0.29
132_A 179_L 0.60 0.42 0.14
128_V 170_Q 0.59 0.40 0.13
133_R 179_L 0.59 0.40 0.13
242_P 286_Y 0.57 0.36 0.12
123_L 179_L 0.53 0.31 0.10
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
6901 9.3 trib_opmh Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
0900 5.66 TriB-OpmH (NP_248847-NP_253661) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.99 Done

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