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OPENSEQ.org
slf-rnase
Genes: A B A+B
Length: 389 221 563
Sequences: 5319 1855 85
Seq/Len: 13.67 8.39 0.15
MirrorTree (Pazo et al. 2001) 0.11
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 0.21 0.01 0.05
2 0.24 0.01 0.06
5 0.27 0.01 0.06
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 0.25
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
203_W 116_C 1.52 0.28 0.00
346_D 138_D 1.41 0.23 0.00
203_W 58_P 1.39 0.22 0.00
334_L 161_K 1.29 0.18 0.00
134_T 150_P 1.26 0.18 0.00
226_E 112_R 1.25 0.17 0.00
45_F 89_W 1.22 0.16 0.00
310_W 176_C 1.20 0.16 0.00
310_W 192_C 1.20 0.16 0.00
141_P 89_W 1.20 0.16 0.00
203_W 176_C 1.18 0.15 0.00
203_W 192_C 1.18 0.15 0.00
132_P 176_C 1.17 0.15 0.00
132_P 192_C 1.17 0.15 0.00
117_G 110_Y 1.16 0.14 0.00
18_L 203_C 1.16 0.14 0.00
275_E 105_L 1.15 0.14 0.00
33_S 133_L 1.15 0.14 0.00
229_H 195_P 1.14 0.14 0.00
194_D 65_L 1.14 0.14 0.00
17_I 114_G 1.14 0.14 0.00
270_L 189_I 1.12 0.13 0.00
173_R 174_L 1.11 0.13 0.00
299_W 126_Y 1.11 0.13 0.00
12_D 37_F 1.10 0.13 0.00
310_W 55_G 1.10 0.13 0.00
204_R 65_L 1.09 0.13 0.00
36_W 109_E 1.09 0.12 0.00
120_A 138_D 1.08 0.12 0.00
131_N 176_C 1.08 0.12 0.00
131_N 192_C 1.08 0.12 0.00
310_W 38_C 1.08 0.12 0.00
169_Y 203_C 1.08 0.12 0.00
310_W 114_G 1.08 0.12 0.00
18_L 34_P 1.08 0.12 0.00
244_D 106_W 1.07 0.12 0.00
203_W 55_G 1.07 0.12 0.00
26_L 186_L 1.07 0.12 0.00
369_Y 186_L 1.06 0.12 0.00
373_L 53_I 1.06 0.12 0.00
361_P 161_K 1.06 0.12 0.00
203_W 38_C 1.05 0.12 0.00
18_L 127_F 1.05 0.12 0.00
203_W 114_G 1.05 0.12 0.00
117_G 176_C 1.05 0.12 0.00
117_G 192_C 1.05 0.12 0.00
36_W 116_C 1.05 0.12 0.00
132_P 55_G 1.04 0.12 0.00
33_S 35_A 1.03 0.11 0.00
310_W 113_H 1.03 0.11 0.00
132_P 150_P 1.02 0.11 0.00
132_P 38_C 1.02 0.11 0.00
13_L 42_N 1.02 0.11 0.00
132_P 114_G 1.02 0.11 0.00
32_I 131_I 1.01 0.11 0.00
298_I 191_I 1.01 0.11 0.00
45_F 113_H 1.01 0.11 0.00
22_P 117_C 1.01 0.11 0.00
203_W 113_H 1.00 0.11 0.00
225_K 83_N 1.00 0.11 0.00
163_D 172_P 1.00 0.11 0.00
204_R 147_G 1.00 0.10 0.00
230_W 106_W 1.00 0.10 0.00
109_T 189_I 0.99 0.10 0.00
21_F 117_C 0.99 0.10 0.00
136_N 64_R 0.99 0.10 0.00
22_P 89_W 0.98 0.10 0.00
132_P 113_H 0.97 0.10 0.00
28_R 150_P 0.97 0.10 0.00
131_N 55_G 0.97 0.10 0.00
299_W 113_H 0.96 0.10 0.00
24_K 20_V 0.96 0.10 0.00
318_P 200_F 0.96 0.10 0.00
310_W 116_C 0.96 0.10 0.00
368_V 109_E 0.95 0.10 0.00
131_N 38_C 0.95 0.10 0.00
119_I 140_L 0.95 0.10 0.00
131_N 114_G 0.95 0.10 0.00
310_W 110_Y 0.95 0.10 0.00
171_V 52_T 0.95 0.10 0.00
310_W 57_W 0.94 0.09 0.00
310_W 106_W 0.94 0.09 0.00
244_D 54_H 0.94 0.09 0.00
30_K 86_E 0.94 0.09 0.00
300_V 155_T 0.94 0.09 0.00
18_L 38_C 0.94 0.09 0.00
310_W 85_L 0.94 0.09 0.00
256_P 85_L 0.94 0.09 0.00
12_D 56_L 0.93 0.09 0.00
117_G 55_G 0.93 0.09 0.00
277_F 92_M 0.92 0.09 0.00
310_W 58_P 0.92 0.09 0.00
203_W 110_Y 0.92 0.09 0.00
350_G 24_F 0.92 0.09 0.00
18_L 114_G 0.92 0.09 0.00
203_W 57_W 0.91 0.09 0.00
346_D 24_F 0.91 0.09 0.00
203_W 106_W 0.91 0.09 0.00
117_G 38_C 0.91 0.09 0.00
116_D 178_E 0.91 0.09 0.00
117_G 114_G 0.91 0.09 0.00
40_I 126_Y 0.91 0.09 0.00
118_L 36_S 0.91 0.09 0.00
270_L 191_I 0.91 0.09 0.00
200_T 180_I 0.91 0.09 0.00
310_W 89_W 0.91 0.09 0.00
241_L 152_T 0.90 0.09 0.00
172_V 167_T 0.90 0.09 0.00
170_K 113_H 0.90 0.09 0.00
225_K 167_T 0.90 0.09 0.00
141_P 113_H 0.90 0.09 0.00
23_V 130_A 0.90 0.09 0.00
170_K 189_I 0.90 0.09 0.00
117_G 127_F 0.90 0.09 0.00
131_N 113_H 0.90 0.09 0.00
313_K 85_L 0.90 0.09 0.00
32_I 29_L 0.90 0.09 0.00
166_S 29_L 0.89 0.08 0.00
45_F 106_W 0.89 0.08 0.00
12_D 68_C 0.89 0.08 0.00
29_F 150_P 0.89 0.08 0.00
36_W 58_P 0.89 0.08 0.00
132_P 110_Y 0.89 0.08 0.00
296_M 37_F 0.89 0.08 0.00
203_W 109_E 0.89 0.08 0.00
132_P 116_C 0.88 0.08 0.00
224_Y 157_G 0.88 0.08 0.00
233_T 74_S 0.88 0.08 0.00
310_W 51_F 0.88 0.08 0.00
154_S 198_D 0.88 0.08 0.00
310_W 33_W 0.88 0.08 0.00
254_K 154_H 0.88 0.08 0.00
98_S 112_R 0.88 0.08 0.00
40_I 132_R 0.87 0.08 0.00
203_W 89_W 0.87 0.08 0.00
195_V 170_K 0.87 0.08 0.00
132_P 106_W 0.87 0.08 0.00
169_Y 117_C 0.87 0.08 0.00
97_V 174_L 0.87 0.08 0.00
351_K 182_G 0.87 0.08 0.00
200_T 157_G 0.87 0.08 0.00
243_F 186_L 0.87 0.08 0.00
292_V 138_D 0.87 0.08 0.00
36_W 176_C 0.87 0.08 0.00
36_W 192_C 0.87 0.08 0.00
18_L 113_H 0.86 0.08 0.00
132_P 57_W 0.86 0.08 0.00
121_L 53_I 0.86 0.08 0.00
100_M 62_H 0.86 0.08 0.00
117_G 113_H 0.86 0.08 0.00
240_I 202_D 0.86 0.08 0.00
255_M 42_N 0.86 0.08 0.00
45_F 176_C 0.86 0.08 0.00
45_F 192_C 0.86 0.08 0.00
160_F 172_P 0.85 0.08 0.00
39_L 163_I 0.85 0.08 0.00
370_K 112_R 0.85 0.08 0.00
132_P 58_P 0.84 0.08 0.00
256_P 139_L 0.84 0.08 0.00
117_G 85_L 0.84 0.08 0.00
203_W 33_W 0.84 0.08 0.00
244_D 112_R 0.84 0.08 0.00
196_C 17_L 0.84 0.08 0.00
203_W 51_F 0.84 0.08 0.00
113_G 129_L 0.84 0.08 0.00
18_L 109_E 0.84 0.08 0.00
203_W 159_I 0.83 0.07 0.00
160_F 86_E 0.83 0.07 0.00
96_D 138_D 0.83 0.07 0.00
132_P 89_W 0.83 0.07 0.00
166_S 135_D 0.83 0.07 0.00
273_L 189_I 0.83 0.07 0.00
81_F 202_D 0.83 0.07 0.00
343_I 92_M 0.83 0.07 0.00
132_P 126_Y 0.83 0.07 0.00
355_L 117_C 0.83 0.07 0.00
195_V 100_S 0.83 0.07 0.00
225_K 87_R 0.82 0.07 0.00
310_W 172_P 0.82 0.07 0.00
299_W 109_E 0.82 0.07 0.00
294_D 77_K 0.82 0.07 0.00
13_L 125_A 0.82 0.07 0.00
161_G 189_I 0.82 0.07 0.00
10_P 150_P 0.82 0.07 0.00
195_V 166_V 0.82 0.07 0.00
310_W 203_C 0.82 0.07 0.00
40_I 174_L 0.82 0.07 0.00
131_N 116_C 0.81 0.07 0.00
375_S 146_H 0.81 0.07 0.00
131_N 110_Y 0.81 0.07 0.00
328_W 81_I 0.81 0.07 0.00
256_P 105_L 0.81 0.07 0.00
310_W 54_H 0.81 0.07 0.00
226_E 116_C 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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