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OPENSEQ.org
MTase P08957_P05719
Genes: A B A+B
Length: 529 464 899
Sequences: 1768 1252 494
Seq/Len: 3.34 2.7 0.55
MirrorTree (Pazo et al. 2001) 0.66
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 0.37
2 0.00 0.01 0.43
5 0.00 0.01 0.48
10 0.01 0.01 0.49
20 0.01 0.01 0.50
100 0.02 0.01 0.51
∞ 0.07 0.05 0.59
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
337_I 147_I 0.98 0.22 0.00
229_C 121_F 0.92 0.19 0.00
263_V 333_Y 0.88 0.17 0.00
453_E 288_L 0.88 0.17 0.00
388_G 195_R 0.87 0.17 0.00
65_Q 17_T 0.85 0.15 0.00
233_D 286_G 0.84 0.15 0.00
225_A 386_E 0.84 0.15 0.00
171_V 172_L 0.83 0.15 0.00
341_P 420_G 0.82 0.15 0.00
354_V 418_F 0.82 0.14 0.00
455_I 184_A 0.81 0.14 0.00
166_Q 184_A 0.80 0.14 0.00
139_A 193_L 0.78 0.13 0.00
110_M 334_I 0.78 0.13 0.00
59_L 360_I 0.76 0.12 0.00
293_M 211_E 0.76 0.12 0.00
225_A 227_N 0.76 0.12 0.00
229_C 107_F 0.76 0.12 0.00
453_E 75_P 0.74 0.12 0.00
263_V 355_S 0.74 0.12 0.00
148_Q 186_F 0.74 0.12 0.00
455_I 163_A 0.74 0.12 0.00
326_R 15_V 0.73 0.11 0.00
110_M 17_T 0.72 0.11 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)
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