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OPENSEQ.org
rfa2 cut, pol30
Genes: A B A+B
Length: 184 258 433
Sequences: 346 9808 81
Seq/Len: 1.88 38.02 0.19
MirrorTree (Pazo et al. 2001) 0.13
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 0.03 0.00 0.00
2 0.03 0.00 0.00
5 0.03 0.00 0.00
10 0.03 0.00 0.00
20 0.03 0.00 0.01
100 0.03 0.01 0.03
∞ 0.05 0.01 0.18
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
66_E 70_M 1.39 0.26 0.00
44_V 38_Q 1.33 0.23 0.00
38_V 152_S 1.32 0.23 0.00
16_I 62_C 1.27 0.21 0.00
153_P 60_Y 1.25 0.20 0.00
58_I 70_M 1.21 0.18 0.00
44_V 57_F 1.18 0.17 0.00
60_D 57_F 1.17 0.17 0.00
47_I 101_L 1.16 0.17 0.00
47_I 60_Y 1.15 0.16 0.00
44_V 137_L 1.11 0.15 0.00
58_I 231_S 1.08 0.14 0.00
116_K 103_F 1.08 0.14 0.00
38_V 54_V 1.08 0.14 0.00
65_I 204_D 1.08 0.14 0.00
66_E 23_V 1.07 0.14 0.00
10_P 20_K 1.03 0.13 0.00
42_G 45_V 1.03 0.13 0.00
126_I 35_I 1.03 0.13 0.00
150_M 227_I 1.02 0.13 0.00
68_R 52_I 1.02 0.12 0.00
101_G 222_S 1.01 0.12 0.00
38_V 108_K 1.01 0.12 0.00
7_T 237_F 0.99 0.12 0.00
40_F 242_K 0.98 0.12 0.00
28_F 11_L 0.98 0.11 0.00
164_S 141_S 0.97 0.11 0.00
103_V 248_F 0.96 0.11 0.00
16_I 138_S 0.96 0.11 0.00
41_V 12_F 0.96 0.11 0.00
31_H 52_I 0.96 0.11 0.00
137_L 244_G 0.95 0.11 0.00
38_V 175_I 0.95 0.11 0.00
7_T 198_E 0.95 0.11 0.00
38_V 176_G 0.93 0.10 0.00
37_H 137_L 0.93 0.10 0.00
66_E 75_L 0.93 0.10 0.00
16_I 50_L 0.93 0.10 0.00
20_K 145_S 0.93 0.10 0.00
128_S 84_N 0.93 0.10 0.00
26_G 113_E 0.92 0.10 0.00
11_V 192_E 0.91 0.10 0.00
42_G 210_K 0.91 0.10 0.00
16_I 165_E 0.91 0.10 0.00
16_I 198_E 0.90 0.10 0.00
126_I 59_E 0.90 0.10 0.00
165_L 242_K 0.90 0.10 0.00
59_E 6_F 0.89 0.10 0.00
58_I 190_H 0.89 0.10 0.00
104_K 70_M 0.89 0.10 0.00
107_G 57_F 0.89 0.10 0.00
38_V 2_L 0.89 0.09 0.00
19_S 218_G 0.89 0.09 0.00
44_V 221_L 0.88 0.09 0.00
169_D 221_L 0.88 0.09 0.00
68_R 103_F 0.88 0.09 0.00
70_W 245_F 0.87 0.09 0.00
28_F 7_E 0.87 0.09 0.00
44_V 63_D 0.87 0.09 0.00
57_T 116_L 0.86 0.09 0.00
67_V 74_S 0.86 0.09 0.00
109_L 175_I 0.86 0.09 0.00
158_S 92_A 0.85 0.09 0.00
118_I 17_D 0.85 0.09 0.00
56_L 75_L 0.85 0.09 0.00
30_S 79_L 0.85 0.09 0.00
83_D 19_F 0.85 0.09 0.00
105_V 20_K 0.85 0.09 0.00
118_I 85_T 0.85 0.09 0.00
45_R 113_E 0.85 0.09 0.00
28_F 62_C 0.84 0.09 0.00
58_I 29_Q 0.84 0.09 0.00
9_T 162_I 0.83 0.08 0.00
38_V 164_K 0.83 0.08 0.00
146_A 72_L 0.83 0.08 0.00
45_R 24_Q 0.83 0.08 0.00
25_D 171_A 0.83 0.08 0.00
62_T 183_K 0.82 0.08 0.00
100_G 182_I 0.82 0.08 0.00
127_D 237_F 0.82 0.08 0.00
111_E 198_E 0.82 0.08 0.00
27_P 70_M 0.82 0.08 0.00
48_T 194_S 0.82 0.08 0.00
126_I 55_E 0.82 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
10242 0.19 rfa2 cut, pol30 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
10239 0.1 rfa2 cut, pol30 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
10235 0.11 rfa2 cut, pol30 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
10231 0.09 rfa2 cut, pol30 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
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