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OPENSEQ.org
TriB-OpmH (NP_248847-NP_253661)
Genes: A B A+B
Length: 356 482 741
Sequences: 10372 7820 4193
Seq/Len: 29.13 16.22 5.66
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 2.34
2 0.03 0.00 4.42
5 0.04 0.01 4.80
10 0.05 0.03 4.91
20 0.07 0.05 5.00
100 0.13 0.12 5.47
∞ 0.20 0.18 6.14
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 2.25 1.00 0.99
122_E 396_V 1.79 1.00 0.97
127_S 182_K 1.67 1.00 0.96
126_R 173_E 1.52 0.99 0.93
127_S 175_F 1.36 0.97 0.87
128_V 392_I 1.33 0.97 0.86
120_Q 398_T 1.22 0.94 0.79
120_Q 179_L 1.10 0.89 0.69
130_A 181_D 1.10 0.89 0.69
126_R 388_E 1.02 0.84 0.60
122_E 177_V 0.99 0.81 0.57
126_R 169_D 0.85 0.66 0.40
128_V 173_E 0.82 0.62 0.36
133_R 393_G 0.81 0.60 0.34
127_S 166_R 0.81 0.60 0.34
128_V 389_A 0.79 0.57 0.32
127_S 395_Q 0.74 0.49 0.26
132_A 179_L 0.71 0.45 0.23
128_V 170_Q 0.69 0.43 0.21
123_L 179_L 0.63 0.34 0.16
123_L 398_T 0.61 0.32 0.14
242_P 286_Y 0.57 0.26 0.11
131_Q 178_G 0.55 0.24 0.10
123_L 403_D 0.53 0.23 0.09
174_V 147_V 0.53 0.22 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
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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