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OPENSEQ.org
S2SLF1_S3RNase
Genes: A B A+B
Length: 389 222 571
Sequences: 5325 1948 149
Seq/Len: 13.69 8.77 0.26
MirrorTree (Pazo et al. 2001) 0.06
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 0.20 0.01 0.05
2 0.24 0.01 0.06
5 0.26 0.01 0.07
10 0.28 0.01 0.07
20 0.29 0.01 0.08
100 0.31 0.01 0.14
∞ 0.34 0.01 0.24
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
240_I 204_D 1.47 0.36 0.00
241_L 119_S 1.35 0.29 0.00
200_T 159_G 1.25 0.24 0.00
173_R 176_L 1.21 0.22 0.00
170_K 112_Y 1.18 0.21 0.00
12_D 37_F 1.17 0.21 0.00
21_F 55_H 1.14 0.20 0.00
373_L 44_I 1.12 0.19 0.00
26_L 87_L 1.09 0.18 0.00
208_H 36_S 1.09 0.17 0.00
195_V 168_V 1.05 0.16 0.00
45_F 91_W 1.02 0.15 0.00
129_V 173_D 1.01 0.15 0.00
331_H 152_P 1.01 0.15 0.00
203_W 178_C 1.01 0.15 0.00
203_W 194_C 1.01 0.15 0.00
346_D 140_D 1.00 0.14 0.00
120_A 219_I 1.00 0.14 0.00
310_W 87_L 0.97 0.14 0.00
266_L 26_Y 0.96 0.13 0.00
49_H 28_Q 0.95 0.13 0.00
19_L 138_K 0.95 0.13 0.00
130_L 97_D 0.94 0.13 0.00
144_P 176_L 0.94 0.12 0.00
200_T 219_I 0.93 0.12 0.00
117_G 178_C 0.93 0.12 0.00
117_G 194_C 0.93 0.12 0.00
310_W 178_C 0.92 0.12 0.00
310_W 194_C 0.92 0.12 0.00
370_K 176_L 0.92 0.12 0.00
46_I 93_Q 0.91 0.12 0.00
20_T 140_D 0.91 0.12 0.00
118_L 36_S 0.90 0.12 0.00
117_G 188_L 0.90 0.12 0.00
236_M 76_S 0.90 0.12 0.00
331_H 124_D 0.90 0.11 0.00
310_W 112_Y 0.90 0.11 0.00
32_I 133_M 0.89 0.11 0.00
158_V 80_K 0.89 0.11 0.00
12_D 163_K 0.89 0.11 0.00
33_S 78_S 0.88 0.11 0.00
132_P 59_P 0.88 0.11 0.00
241_L 67_E 0.88 0.11 0.00
299_W 34_P 0.88 0.11 0.00
241_L 166_K 0.88 0.11 0.00
203_W 108_W 0.88 0.11 0.00
201_D 191_V 0.87 0.11 0.00
316_I 141_L 0.87 0.11 0.00
311_I 109_T 0.87 0.11 0.00
100_M 191_V 0.87 0.11 0.00
229_H 197_P 0.87 0.11 0.00
245_M 29_L 0.87 0.11 0.00
33_S 35_A 0.87 0.11 0.00
169_Y 199_A 0.86 0.11 0.00
203_W 91_W 0.86 0.11 0.00
132_P 57_L 0.86 0.11 0.00
12_D 81_D 0.86 0.10 0.00
19_L 30_V 0.86 0.10 0.00
21_F 107_L 0.86 0.10 0.00
45_F 116_G 0.86 0.10 0.00
331_H 166_K 0.85 0.10 0.00
224_Y 31_L 0.85 0.10 0.00
19_L 134_R 0.85 0.10 0.00
133_A 79_L 0.85 0.10 0.00
246_S 27_I 0.85 0.10 0.00
76_N 140_D 0.85 0.10 0.00
43_T 143_T 0.85 0.10 0.00
129_V 161_I 0.85 0.10 0.00
283_S 31_L 0.85 0.10 0.00
303_E 67_E 0.84 0.10 0.00
338_R 113_N 0.84 0.10 0.00
298_I 85_N 0.84 0.10 0.00
20_T 119_S 0.84 0.10 0.00
351_E 54_I 0.84 0.10 0.00
343_I 31_L 0.83 0.10 0.00
140_L 115_H 0.83 0.10 0.00
169_Y 119_S 0.83 0.10 0.00
243_F 55_H 0.83 0.10 0.00
241_L 168_V 0.83 0.10 0.00
22_P 150_I 0.83 0.10 0.00
45_F 112_Y 0.83 0.10 0.00
129_V 191_V 0.83 0.10 0.00
143_S 90_H 0.83 0.10 0.00
46_I 31_L 0.82 0.10 0.00
117_G 129_F 0.82 0.10 0.00
111_L 176_L 0.82 0.10 0.00
169_Y 183_K 0.82 0.10 0.00
275_E 83_I 0.82 0.10 0.00
12_D 153_G 0.82 0.10 0.00
42_S 176_L 0.82 0.10 0.00
45_F 178_C 0.82 0.10 0.00
45_F 194_C 0.82 0.10 0.00
171_V 24_F 0.82 0.10 0.00
321_I 113_N 0.82 0.10 0.00
100_M 161_I 0.82 0.10 0.00
40_I 128_Y 0.82 0.09 0.00
112_I 147_T 0.81 0.09 0.00
171_V 53_T 0.81 0.09 0.00
197_D 176_L 0.81 0.09 0.00
132_P 178_C 0.81 0.09 0.00
132_P 194_C 0.81 0.09 0.00
18_L 129_F 0.81 0.09 0.00
318_P 132_A 0.81 0.09 0.00
298_I 191_V 0.81 0.09 0.00
203_W 33_W 0.81 0.09 0.00
331_H 65_R 0.81 0.09 0.00
250_F 138_K 0.81 0.09 0.00
34_K 152_P 0.80 0.09 0.00
299_W 116_G 0.80 0.09 0.00
131_N 178_C 0.80 0.09 0.00
131_N 194_C 0.80 0.09 0.00
160_F 127_A 0.80 0.09 0.00
132_P 115_H 0.80 0.09 0.00
43_T 188_L 0.79 0.09 0.00
310_W 108_W 0.79 0.09 0.00
117_G 112_Y 0.79 0.09 0.00
117_G 108_W 0.79 0.09 0.00
229_H 20_V 0.79 0.09 0.00
230_W 108_W 0.79 0.09 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
7848 0.26 S2SLF1_S3RNase Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7847 0.09 S2SLF1_S3RNase_10JHfull Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7841 0.07 S2SLF1_S3RNase_4 Δgene:(1, 100) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
7838 0.07 S2SLF1_S3RNase_10 Δgene:(1, 100) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
7837 0.09 S2SLF1_S3RNase Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7833 0.05 S2SLF1_S3RNase Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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