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OPENSEQ.org
nrps_8it
Genes: A B A+B
Length: 174 376 539
Sequences: 8505 38754 738
Seq/Len: 48.88 103.07 1.37
MirrorTree (Pazo et al. 2001) 0.14
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 0.08 0.12
2 0.01 0.10 0.21
5 0.01 0.14 0.41
10 0.01 0.17 0.76
20 0.02 0.19 1.34
100 0.05 0.24 3.97
∞ 0.17 0.30 7.89
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
25_L 55_E 0.98 0.40 0.00
140_M 236_L 0.94 0.36 0.00
104_F 163_R 0.91 0.34 0.00
139_N 213_W 0.91 0.33 0.00
108_L 120_E 0.82 0.25 0.00
62_G 28_S 0.81 0.25 0.00
16_V 203_R 0.80 0.24 0.00
102_S 114_T 0.78 0.23 0.00
73_A 21_Y 0.77 0.22 0.00
162_T 21_Y 0.76 0.21 0.00
13_K 335_D 0.76 0.21 0.00
10_F 139_I 0.75 0.21 0.00
107_Y 20_T 0.74 0.20 0.00
138_L 40_I 0.74 0.20 0.00
57_P 95_L 0.73 0.19 0.00
102_S 237_R 0.71 0.18 0.00
15_P 62_A 0.71 0.18 0.00
106_V 121_D 0.70 0.18 0.00
106_V 248_L 0.70 0.18 0.00
160_I 306_N 0.70 0.18 0.00
135_T 239_V 0.70 0.17 0.00
53_V 122_T 0.70 0.17 0.00
149_L 140_I 0.70 0.17 0.00
165_K 154_R 0.69 0.17 0.00
25_L 203_R 0.69 0.17 0.00
131_A 68_A 0.68 0.17 0.00
61_E 87_E 0.68 0.16 0.00
18_F 22_S 0.67 0.16 0.00
1_I 48_V 0.67 0.16 0.00
11_D 10_V 0.67 0.16 0.00
41_A 141_T 0.67 0.16 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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