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OPENSEQ.org
TriA-OpmH (NP_248846-NP_253661)
Genes: A B A+B
Length: 383 482 742
Sequences: 9936 7820 4080
Seq/Len: 25.94 16.22 5.5
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 2.18
2 0.03 0.00 4.18
5 0.04 0.01 4.53
10 0.05 0.03 4.63
20 0.06 0.05 4.72
100 0.13 0.12 5.17
∞ 0.20 0.18 5.81
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 2.26 1.00 0.99
134_A 396_V 1.83 1.00 0.98
139_G 182_K 1.71 1.00 0.96
138_K 173_E 1.52 0.99 0.93
139_G 175_F 1.40 0.98 0.89
140_Y 392_I 1.34 0.97 0.86
132_Q 398_T 1.21 0.94 0.79
132_Q 179_L 1.11 0.89 0.70
142_S 181_D 1.09 0.88 0.68
138_K 388_E 1.07 0.87 0.66
134_A 177_V 0.96 0.77 0.53
138_K 169_D 0.94 0.75 0.50
140_Y 389_A 0.81 0.59 0.34
145_E 393_G 0.81 0.59 0.34
140_Y 170_Q 0.77 0.53 0.29
140_Y 173_E 0.77 0.53 0.29
144_S 179_L 0.76 0.52 0.29
139_G 395_Q 0.76 0.51 0.28
139_G 166_R 0.74 0.49 0.26
135_L 403_D 0.67 0.38 0.19
95_V 237_A 0.64 0.35 0.17
135_L 398_T 0.58 0.27 0.12
254_P 286_Y 0.56 0.25 0.11
143_Q 178_G 0.56 0.25 0.10
135_L 179_L 0.55 0.24 0.10
138_K 176_D 0.55 0.23 0.10
138_K 396_V 0.55 0.23 0.10
336_I 239_N 0.54 0.23 0.09
336_I 213_L 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
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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