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OPENSEQ.org
rrn5 uaf30
Genes: A B A+B
Length: 101 228 297
Sequences: 2338 273 63
Seq/Len: 23.15 1.2 0.21
MirrorTree (Pazo et al. 2001) 0.30
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 0.05 0.01 0.00
2 0.05 0.01 0.00
5 0.06 0.01 0.00
10 0.06 0.01 0.00
20 0.07 0.01 0.02
100 0.10 0.01 0.06
∞ 0.15 0.01 0.19
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
70_D 19_D 1.46 0.31 0.00
65_R 24_T 1.38 0.27 0.00
86_E 180_T 1.28 0.22 0.00
62_A 161_N 1.20 0.19 0.00
14_D 118_P 1.16 0.17 0.00
41_P 43_Q 1.12 0.16 0.00
79_S 22_T 1.10 0.16 0.00
55_L 160_P 1.08 0.15 0.00
66_K 74_E 1.07 0.15 0.00
37_R 143_E 1.06 0.14 0.00
34_D 186_H 1.05 0.14 0.00
6_I 19_D 1.04 0.14 0.00
17_E 151_Y 1.03 0.14 0.00
27_R 45_K 1.02 0.13 0.00
16_E 47_I 1.01 0.13 0.00
14_D 9_T 1.01 0.13 0.00
44_S 162_N 1.00 0.13 0.00
17_E 85_E 0.99 0.12 0.00
89_L 151_Y 0.99 0.12 0.00
13_W 152_I 0.98 0.12 0.00
43_K 172_L 0.98 0.12 0.00
66_K 24_T 0.97 0.12 0.00
12_D 131_A 0.97 0.12 0.00
6_I 37_A 0.96 0.12 0.00
67_A 18_M 0.96 0.12 0.00
40_L 181_N 0.95 0.11 0.00
16_E 24_T 0.95 0.11 0.00
37_R 24_T 0.94 0.11 0.00
88_K 154_A 0.94 0.11 0.00
42_R 170_E 0.93 0.11 0.00
32_R 165_E 0.93 0.11 0.00
35_E 163_K 0.93 0.11 0.00
48_I 23_V 0.93 0.11 0.00
44_S 173_E 0.91 0.10 0.00
32_R 189_L 0.90 0.10 0.00
43_K 152_I 0.90 0.10 0.00
37_R 198_K 0.90 0.10 0.00
66_K 132_S 0.90 0.10 0.00
48_I 17_D 0.90 0.10 0.00
19_N 24_T 0.89 0.10 0.00
37_R 39_D 0.89 0.10 0.00
90_S 75_N 0.89 0.10 0.00
45_A 33_K 0.89 0.10 0.00
41_P 39_D 0.89 0.10 0.00
14_D 14_L 0.88 0.10 0.00
78_M 83_T 0.88 0.10 0.00
19_N 136_E 0.87 0.10 0.00
35_E 31_A 0.87 0.10 0.00
25_L 83_T 0.87 0.10 0.00
92_T 120_S 0.87 0.10 0.00
40_L 139_L 0.87 0.10 0.00
21_F 188_I 0.86 0.09 0.00
29_S 152_I 0.86 0.09 0.00
44_S 154_A 0.86 0.09 0.00
76_Y 45_K 0.85 0.09 0.00
25_L 175_I 0.85 0.09 0.00
40_L 9_T 0.85 0.09 0.00
44_S 91_R 0.85 0.09 0.00
43_K 73_K 0.85 0.09 0.00
41_P 126_L 0.85 0.09 0.00
69_D 42_S 0.85 0.09 0.00
7_S 44_G 0.85 0.09 0.00
43_K 7_Y 0.84 0.09 0.00
79_S 19_D 0.84 0.09 0.00
77_E 113_T 0.83 0.09 0.00
40_L 167_L 0.83 0.09 0.00
42_R 19_D 0.83 0.09 0.00
34_D 37_A 0.83 0.09 0.00
90_S 24_T 0.83 0.09 0.00
55_L 20_L 0.82 0.09 0.00
89_L 44_G 0.82 0.09 0.00
38_S 171_K 0.82 0.09 0.00
73_P 138_E 0.81 0.08 0.00
78_M 172_L 0.81 0.08 0.00
66_K 58_V 0.81 0.08 0.00
68_G 134_L 0.81 0.08 0.00
89_L 126_L 0.80 0.08 0.00
45_A 27_K 0.80 0.08 0.00
30_I 105_T 0.80 0.08 0.00
86_E 21_E 0.80 0.08 0.00
75_A 26_K 0.80 0.08 0.00
59_S 191_S 0.80 0.08 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)
ID Seq/Len Name Options I_Prob Status
9618 0.21 rrn5 uaf30 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9617 0.01 rrn5 uaf30 Δgene:(1, 20) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
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