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OPENSEQ.org
NarL-1-130 and NarX-380-to 598
Genes: A B A+B
Length: 134 211 332
Sequences: 84246 12389 9670
Seq/Len: 628.7 58.72 29.13
MirrorTree (Pazo et al. 2001) 0.79
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 0.01 0.01 25.29
2 0.02 0.02 26.07
5 0.02 0.03 26.77
10 0.03 0.04 27.32
20 0.04 0.06 28.03
100 0.12 0.11 30.14
∞ 0.20 0.20 30.91
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
110_D 59_R 1.94 1.00 0.98
29_A 31_M 1.46 1.00 0.91
113_P 27_S 1.42 1.00 0.90
114_E 31_M 1.32 0.99 0.85
22_V 24_M 1.30 0.99 0.84
18_L 20_S 1.19 0.98 0.77
30_P 35_A 1.06 0.95 0.64
25_L 28_C 1.00 0.92 0.57
15_H 17_Q 0.93 0.88 0.49
24_Q 28_C 0.87 0.83 0.41
28_M 28_C 0.86 0.82 0.41
88_V 16_A 0.85 0.82 0.40
20_T 46_Q 0.83 0.79 0.36
17_M 21_C 0.78 0.73 0.31
110_D 55_W 0.75 0.68 0.27
27_S 39_S 0.74 0.68 0.27
18_L 21_C 0.72 0.65 0.24
114_E 30_Q 0.69 0.59 0.21
110_D 52_N 0.69 0.59 0.21
88_V 62_L 0.68 0.57 0.20
112_E 48_R 0.66 0.54 0.18
28_M 32_Q 0.66 0.54 0.18
88_V 17_Q 0.65 0.52 0.17
110_D 56_A 0.65 0.52 0.17
24_Q 43_L 0.62 0.47 0.15
88_V 20_S 0.62 0.47 0.15
21_G 24_M 0.60 0.43 0.13
112_E 52_N 0.59 0.42 0.13
112_E 27_S 0.59 0.42 0.13
89_S 58_L 0.56 0.38 0.11
20_T 25_Q 0.55 0.35 0.10
60_L 17_Q 0.55 0.35 0.10
117_L 31_M 0.53 0.33 0.09
94_D 71_E 0.52 0.31 0.08
28_M 31_M 0.51 0.29 0.08
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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