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OPENSEQ.org
2nuu_L_D
Genes: A B A+B
Length: 112 415 509
Sequences: 2544 4078 1443
Seq/Len: 22.71 9.83 2.83
MirrorTree (Pazo et al. 2001) 0.26
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 0.04 0.02 2.68
2 0.06 0.04 2.72
5 0.06 0.04 2.72
10 0.06 0.05 2.73
20 0.06 0.05 2.74
100 0.07 0.06 2.84
∞ 0.19 0.13 3.23
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
85_K 397_E 1.43 0.93 0.54
8_I 251_I 0.94 0.55 0.15
79_K 314_L 0.76 0.34 0.07
99_V 307_G 0.74 0.32 0.07
75_D 369_A 0.70 0.28 0.06
44_E 258_E 0.68 0.26 0.05
107_A 381_I 0.68 0.26 0.05
108_D 126_G 0.67 0.25 0.05
96_L 78_G 0.65 0.24 0.04
96_L 292_G 0.65 0.24 0.04
110_A 76_A 0.65 0.23 0.04
16_V 360_Q 0.65 0.23 0.04
15_D 406_N 0.65 0.23 0.04
99_V 71_Y 0.65 0.23 0.04
45_L 44_L 0.64 0.23 0.04
18_E 133_R 0.64 0.23 0.04
93_V 252_L 0.63 0.22 0.04
48_G 47_G 0.63 0.22 0.04
8_I 316_R 0.62 0.21 0.04
109_E 336_I 0.62 0.21 0.04
112_L 296_I 0.62 0.21 0.04
59_V 384_K 0.61 0.20 0.04
76_I 39_L 0.61 0.20 0.04
8_I 135_S 0.61 0.20 0.04
40_K 259_W 0.61 0.20 0.04
42_H 272_S 0.61 0.20 0.04
16_V 44_L 0.61 0.20 0.04
15_D 396_E 0.61 0.20 0.04
76_I 193_K 0.61 0.20 0.04
100_I 168_L 0.61 0.20 0.04
65_I 294_L 0.61 0.20 0.04
61_I 395_P 0.60 0.20 0.04
40_K 374_W 0.60 0.20 0.04
91_I 365_L 0.60 0.20 0.04
90_K 126_G 0.60 0.19 0.03
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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