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OPENSEQ.org
sfb-rnase
Genes: A B A+B
Length: 363 159 516
Sequences: 2575 1557 88
Seq/Len: 7.09 9.79 0.17
MirrorTree (Pazo et al. 2001) 0.14
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 0.25 0.03 0.03
2 0.27 0.03 0.04
5 0.29 0.03 0.05
10 0.31 0.04 0.05
20 0.32 0.05 0.07
100 0.35 0.05 0.09
∞ 0.41 0.06 0.17
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
2_L 150_C 1.63 0.35 0.00
176_S 156_I 1.62 0.35 0.00
325_Y 156_I 1.42 0.25 0.00
49_L 58_S 1.42 0.25 0.00
29_F 144_C 1.32 0.21 0.00
103_G 47_W 1.28 0.20 0.00
103_G 55_G 1.28 0.20 0.00
103_G 118_C 1.28 0.20 0.00
182_W 57_C 1.27 0.19 0.00
67_E 50_E 1.24 0.18 0.00
206_G 129_E 1.23 0.18 0.00
29_F 150_C 1.22 0.17 0.00
281_W 47_W 1.22 0.17 0.00
281_W 55_G 1.22 0.17 0.00
281_W 118_C 1.22 0.17 0.00
304_N 130_V 1.18 0.16 0.00
281_W 51_W 1.17 0.16 0.00
180_D 132_F 1.15 0.15 0.00
103_G 35_W 1.14 0.15 0.00
159_T 111_K 1.14 0.15 0.00
17_C 58_S 1.13 0.15 0.00
46_L 71_S 1.12 0.14 0.00
29_F 57_C 1.11 0.14 0.00
43_H 106_I 1.11 0.14 0.00
29_F 35_W 1.11 0.14 0.00
123_P 54_H 1.10 0.14 0.00
304_N 31_L 1.08 0.13 0.00
308_M 72_Y 1.08 0.13 0.00
281_W 35_W 1.08 0.13 0.00
151_H 80_I 1.07 0.13 0.00
182_W 67_Y 1.07 0.13 0.00
122_N 35_W 1.06 0.13 0.00
2_L 144_C 1.05 0.12 0.00
97_I 79_N 1.04 0.12 0.00
5_L 114_P 1.04 0.12 0.00
46_L 140_K 1.03 0.12 0.00
20_W 57_C 1.03 0.12 0.00
103_G 133_C 1.02 0.12 0.00
183_K 88_S 1.02 0.12 0.00
17_C 108_T 1.01 0.12 0.00
236_P 129_E 1.01 0.12 0.00
230_F 20_F 1.00 0.11 0.00
281_W 31_L 0.99 0.11 0.00
182_W 47_W 0.99 0.11 0.00
182_W 55_G 0.99 0.11 0.00
182_W 118_C 0.99 0.11 0.00
1_I 51_W 0.99 0.11 0.00
157_Y 93_A 0.99 0.11 0.00
103_G 57_C 0.99 0.11 0.00
5_L 46_F 0.98 0.11 0.00
103_G 67_Y 0.98 0.11 0.00
335_I 50_E 0.98 0.11 0.00
359_L 64_Q 0.98 0.11 0.00
1_I 133_C 0.97 0.10 0.00
19_S 86_N 0.97 0.10 0.00
103_G 68_F 0.96 0.10 0.00
103_G 127_L 0.96 0.10 0.00
159_T 105_A 0.96 0.10 0.00
125_V 91_P 0.96 0.10 0.00
7_A 79_N 0.95 0.10 0.00
173_E 156_I 0.95 0.10 0.00
5_L 54_H 0.95 0.10 0.00
17_C 69_E 0.95 0.10 0.00
281_W 133_C 0.95 0.10 0.00
172_V 31_L 0.95 0.10 0.00
179_T 130_V 0.94 0.10 0.00
299_G 53_K 0.94 0.10 0.00
102_N 120_W 0.93 0.10 0.00
230_F 158_F 0.93 0.10 0.00
10_V 127_L 0.93 0.10 0.00
1_I 47_W 0.93 0.10 0.00
1_I 55_G 0.93 0.10 0.00
1_I 118_C 0.93 0.10 0.00
281_W 57_C 0.92 0.10 0.00
18_K 130_V 0.92 0.10 0.00
247_I 33_I 0.92 0.10 0.00
119_H 31_L 0.92 0.10 0.00
274_W 47_W 0.92 0.10 0.00
274_W 55_G 0.92 0.10 0.00
274_W 118_C 0.92 0.10 0.00
281_W 67_Y 0.92 0.10 0.00
133_M 31_L 0.91 0.09 0.00
88_P 98_K 0.90 0.09 0.00
123_P 47_W 0.90 0.09 0.00
123_P 55_G 0.90 0.09 0.00
123_P 118_C 0.90 0.09 0.00
281_W 68_F 0.90 0.09 0.00
286_P 71_S 0.90 0.09 0.00
29_F 47_W 0.90 0.09 0.00
29_F 55_G 0.90 0.09 0.00
29_F 118_C 0.90 0.09 0.00
1_I 3_P 0.90 0.09 0.00
279_K 129_E 0.90 0.09 0.00
284_L 5_I 0.89 0.09 0.00
224_D 133_C 0.89 0.09 0.00
206_G 47_W 0.89 0.09 0.00
206_G 55_G 0.89 0.09 0.00
206_G 118_C 0.89 0.09 0.00
106_C 57_C 0.89 0.09 0.00
274_W 127_L 0.89 0.09 0.00
148_F 127_L 0.89 0.09 0.00
180_D 97_W 0.89 0.09 0.00
18_K 142_I 0.89 0.09 0.00
172_V 130_V 0.88 0.09 0.00
127_K 107_K 0.88 0.09 0.00
181_S 46_F 0.88 0.09 0.00
103_G 129_E 0.88 0.09 0.00
204_F 77_S 0.87 0.09 0.00
305_K 20_F 0.87 0.09 0.00
126_R 83_I 0.86 0.09 0.00
183_K 17_G 0.86 0.08 0.00
158_K 55_G 0.86 0.08 0.00
158_K 118_C 0.86 0.08 0.00
158_K 47_W 0.86 0.08 0.00
29_F 97_W 0.86 0.08 0.00
103_G 31_L 0.85 0.08 0.00
122_N 47_W 0.85 0.08 0.00
122_N 55_G 0.85 0.08 0.00
122_N 118_C 0.85 0.08 0.00
20_W 144_C 0.85 0.08 0.00
229_E 110_T 0.85 0.08 0.00
27_S 56_T 0.84 0.08 0.00
182_W 35_W 0.84 0.08 0.00
1_I 2_W 0.84 0.08 0.00
300_I 114_P 0.84 0.08 0.00
172_V 37_D 0.84 0.08 0.00
104_L 89_I 0.84 0.08 0.00
320_L 104_S 0.84 0.08 0.00
232_E 129_E 0.84 0.08 0.00
157_Y 47_W 0.83 0.08 0.00
157_Y 55_G 0.83 0.08 0.00
157_Y 118_C 0.83 0.08 0.00
209_Y 20_F 0.83 0.08 0.00
46_L 38_V 0.83 0.08 0.00
206_G 67_Y 0.83 0.08 0.00
157_Y 51_W 0.83 0.08 0.00
256_L 106_I 0.83 0.08 0.00
285_C 39_E 0.83 0.08 0.00
29_F 133_C 0.82 0.08 0.00
155_N 75_W 0.82 0.08 0.00
120_I 113_T 0.82 0.08 0.00
308_M 76_K 0.82 0.08 0.00
102_N 129_E 0.82 0.08 0.00
148_F 107_K 0.82 0.08 0.00
101_S 127_L 0.82 0.08 0.00
131_P 54_H 0.82 0.08 0.00
252_Q 109_A 0.81 0.08 0.00
224_D 68_F 0.81 0.08 0.00
281_W 127_L 0.81 0.07 0.00
320_L 131_V 0.80 0.07 0.00
306_L 33_I 0.80 0.07 0.00
4_R 50_E 0.80 0.07 0.00
328_K 116_L 0.80 0.07 0.00
356_S 62_L 0.80 0.07 0.00
171_A 143_D 0.80 0.07 0.00
12_R 67_Y 0.80 0.07 0.00
175_Y 13_S 0.80 0.07 0.00
126_R 101_D 0.80 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.41 > 0.4) of paralogs.
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