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OPENSEQ.org
slf-rnase
Genes: A B A+B
Length: 389 221 573
Sequences: 2850 862 88
Seq/Len: 7.33 3.9 0.15
MirrorTree (Pazo et al. 2001) -0.01
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 0.20 0.03 0.02
2 0.23 0.03 0.03
5 0.27 0.04 0.03
10 0.28 0.04 0.04
20 0.29 0.04 0.05
100 0.32 0.04 0.07
∞ 0.38 0.05 0.14
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
134_T 150_P 1.56 0.29 0.00
171_V 85_L 1.44 0.24 0.00
301_M 154_H 1.36 0.21 0.00
18_L 209_C 1.32 0.19 0.00
245_M 148_I 1.29 0.18 0.00
116_D 188_E 1.29 0.18 0.00
120_A 125_A 1.27 0.18 0.00
297_H 40_P 1.26 0.17 0.00
45_F 203_C 1.25 0.17 0.00
193_I 85_L 1.25 0.17 0.00
310_W 110_Y 1.24 0.17 0.00
316_I 146_H 1.21 0.16 0.00
32_I 131_I 1.20 0.16 0.00
39_L 163_I 1.20 0.15 0.00
117_G 89_W 1.19 0.15 0.00
117_G 114_G 1.19 0.15 0.00
117_G 127_F 1.19 0.15 0.00
117_G 176_C 1.19 0.15 0.00
18_L 203_C 1.19 0.15 0.00
21_F 105_L 1.19 0.15 0.00
243_F 182_G 1.18 0.15 0.00
240_I 85_L 1.17 0.15 0.00
334_L 191_I 1.16 0.14 0.00
342_L 142_T 1.15 0.14 0.00
121_L 91_Q 1.13 0.14 0.00
35_A 85_L 1.12 0.13 0.00
316_I 31_L 1.11 0.13 0.00
226_E 217_T 1.10 0.13 0.00
310_W 89_W 1.10 0.13 0.00
310_W 114_G 1.10 0.13 0.00
310_W 127_F 1.10 0.13 0.00
310_W 176_C 1.10 0.13 0.00
347_L 217_T 1.10 0.13 0.00
16_L 142_T 1.09 0.13 0.00
45_F 116_C 1.09 0.12 0.00
308_E 48_S 1.08 0.12 0.00
117_G 192_C 1.08 0.12 0.00
117_G 106_W 1.07 0.12 0.00
33_S 206_S 1.05 0.12 0.00
117_G 33_W 1.05 0.12 0.00
203_W 126_Y 1.04 0.11 0.00
23_V 111_N 1.04 0.11 0.00
310_W 186_L 1.02 0.11 0.00
203_W 89_W 1.01 0.11 0.00
203_W 114_G 1.01 0.11 0.00
203_W 127_F 1.01 0.11 0.00
203_W 176_C 1.01 0.11 0.00
117_G 116_C 1.01 0.11 0.00
226_E 188_E 1.01 0.11 0.00
195_V 187_N 1.00 0.11 0.00
160_F 61_K 0.99 0.10 0.00
22_P 148_I 0.99 0.10 0.00
310_W 192_C 0.99 0.10 0.00
201_D 81_I 0.98 0.10 0.00
34_K 201_H 0.98 0.10 0.00
310_W 106_W 0.98 0.10 0.00
299_W 186_L 0.98 0.10 0.00
116_D 136_K 0.97 0.10 0.00
229_H 60_N 0.97 0.10 0.00
28_R 154_H 0.97 0.10 0.00
310_W 33_W 0.96 0.10 0.00
118_L 200_F 0.96 0.10 0.00
316_I 150_P 0.95 0.10 0.00
299_W 110_Y 0.95 0.10 0.00
23_V 123_Q 0.95 0.10 0.00
131_N 89_W 0.95 0.10 0.00
131_N 114_G 0.95 0.10 0.00
131_N 127_F 0.95 0.10 0.00
131_N 176_C 0.95 0.10 0.00
33_S 133_L 0.95 0.09 0.00
345_Y 75_R 0.95 0.09 0.00
168_Y 125_A 0.94 0.09 0.00
140_L 51_F 0.94 0.09 0.00
117_G 38_C 0.94 0.09 0.00
225_K 109_E 0.94 0.09 0.00
17_I 89_W 0.94 0.09 0.00
17_I 114_G 0.94 0.09 0.00
17_I 127_F 0.94 0.09 0.00
17_I 176_C 0.94 0.09 0.00
299_W 106_W 0.93 0.09 0.00
29_F 32_T 0.93 0.09 0.00
240_I 92_M 0.92 0.09 0.00
195_V 117_C 0.92 0.09 0.00
36_W 116_C 0.92 0.09 0.00
310_W 116_C 0.92 0.09 0.00
9_L 32_T 0.91 0.09 0.00
225_K 200_F 0.91 0.09 0.00
20_T 117_C 0.91 0.09 0.00
45_F 209_C 0.90 0.09 0.00
45_F 106_W 0.90 0.09 0.00
203_W 192_C 0.90 0.09 0.00
305_G 26_Y 0.89 0.09 0.00
224_Y 220_R 0.89 0.08 0.00
98_S 47_K 0.89 0.08 0.00
198_L 68_C 0.89 0.08 0.00
36_W 188_E 0.89 0.08 0.00
22_P 136_K 0.89 0.08 0.00
185_Y 27_F 0.89 0.08 0.00
140_L 38_C 0.89 0.08 0.00
316_I 29_L 0.89 0.08 0.00
245_M 85_L 0.88 0.08 0.00
195_V 78_E 0.88 0.08 0.00
117_G 55_G 0.88 0.08 0.00
203_W 106_W 0.88 0.08 0.00
138_R 123_Q 0.88 0.08 0.00
316_I 166_V 0.87 0.08 0.00
229_H 75_R 0.87 0.08 0.00
240_I 36_S 0.87 0.08 0.00
132_P 51_F 0.87 0.08 0.00
204_R 31_L 0.87 0.08 0.00
333_L 126_Y 0.87 0.08 0.00
29_F 137_L 0.87 0.08 0.00
239_V 21_S 0.87 0.08 0.00
203_W 33_W 0.86 0.08 0.00
117_G 126_Y 0.86 0.08 0.00
11_E 87_R 0.86 0.08 0.00
171_V 162_A 0.86 0.08 0.00
350_G 164_K 0.86 0.08 0.00
30_K 36_S 0.86 0.08 0.00
249_M 200_F 0.86 0.08 0.00
100_M 86_E 0.85 0.08 0.00
128_I 36_S 0.85 0.08 0.00
129_V 147_G 0.85 0.08 0.00
30_K 64_R 0.85 0.08 0.00
310_W 38_C 0.85 0.08 0.00
243_F 172_P 0.84 0.08 0.00
206_L 189_I 0.84 0.08 0.00
305_G 125_A 0.84 0.08 0.00
301_M 128_L 0.84 0.08 0.00
373_L 51_F 0.84 0.08 0.00
199_S 217_T 0.84 0.08 0.00
140_L 158_E 0.83 0.07 0.00
169_Y 125_A 0.83 0.07 0.00
298_I 217_T 0.83 0.07 0.00
13_L 80_N 0.83 0.07 0.00
230_W 128_L 0.83 0.07 0.00
330_N 104_P 0.83 0.07 0.00
26_L 194_N 0.83 0.07 0.00
203_W 116_C 0.82 0.07 0.00
277_F 129_L 0.82 0.07 0.00
310_W 85_L 0.82 0.07 0.00
117_G 110_Y 0.82 0.07 0.00
203_W 53_I 0.81 0.07 0.00
270_L 26_Y 0.81 0.07 0.00
36_W 203_C 0.81 0.07 0.00
334_L 189_I 0.81 0.07 0.00
170_K 106_W 0.81 0.07 0.00
167_N 182_G 0.81 0.07 0.00
10_P 112_R 0.81 0.07 0.00
171_V 190_G 0.81 0.07 0.00
51_N 30_V 0.81 0.07 0.00
119_I 24_F 0.81 0.07 0.00
171_V 206_S 0.81 0.07 0.00
32_I 33_W 0.81 0.07 0.00
117_G 203_C 0.81 0.07 0.00
284_N 29_L 0.81 0.07 0.00
206_L 66_E 0.81 0.07 0.00
24_K 164_K 0.81 0.07 0.00
205_E 29_L 0.81 0.07 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
13624 0.15 slf-rnase Δgene:(1, ∞) A:(1E-06, 2) B:(1E-06, 2) msa: HHblits (2015_06) 0.00 Done - Shared
10052 0.17 slf-rnase Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10049 0.15 slf-rnase Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9962 0.16 slf-rnase Δgene:(0, ∞) A:(1E-10, 2) B:(1E-10, 2) msa: HHblits (2015_06) 0.00 Done - Shared
9949 0.05 slf-rnase Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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