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OPENSEQ.org
PhyR-NepR
Genes: A B A+B
Length: 141 42 173
Sequences: 9151 222 112
Seq/Len: 64.9 5.29 0.65
MirrorTree (Pazo et al. 2001) 0.01
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.00 0.01
2 0.02 0.00 0.01
5 0.02 0.00 0.02
10 0.05 0.00 0.03
20 0.06 0.00 0.05
100 0.08 0.00 0.20
∞ 0.13 0.02 0.61
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
54_V 28_F 1.13 0.35 0.00
97_R 23_P 1.12 0.34 0.00
124_V 35_A 1.12 0.34 0.00
35_A 9_G 1.11 0.33 0.00
35_A 36_E 1.10 0.32 0.00
117_L 4_R 1.08 0.31 0.00
7_L 36_E 1.06 0.30 0.00
73_V 28_F 1.02 0.27 0.00
22_T 26_D 1.00 0.26 0.00
131_A 34_K 0.99 0.25 0.00
117_L 18_E 0.98 0.24 0.00
124_V 30_A 0.97 0.24 0.00
47_D 21_N 0.94 0.22 0.00
70_Q 8_I 0.93 0.21 0.00
112_E 33_R 0.92 0.21 0.00
48_A 22_E 0.90 0.20 0.00
129_G 9_G 0.89 0.19 0.00
5_A 21_N 0.88 0.19 0.00
6_R 31_I 0.87 0.18 0.00
85_A 35_A 0.85 0.17 0.00
100_F 19_V 0.84 0.17 0.00
90_M 13_R 0.84 0.17 0.00
103_T 35_A 0.84 0.17 0.00
114_A 12_L 0.82 0.16 0.00
49_N 18_E 0.82 0.16 0.00
50_L 31_I 0.81 0.15 0.00
49_N 23_P 0.81 0.15 0.00
54_V 12_L 0.81 0.15 0.00
35_A 11_K 0.81 0.15 0.00
126_R 22_E 0.81 0.15 0.00
12_P 32_L 0.80 0.15 0.00
115_Q 18_E 0.80 0.15 0.00
47_D 36_E 0.79 0.15 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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