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OPENSEQ.org
RsgA-Era
Genes: A B A+B
Length: 350 301 590
Sequences: 2498 2489 958
Seq/Len: 7.14 8.27 1.62
MirrorTree (Pazo et al. 2001) 0.63
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 0.03 0.04 0.00
2 0.03 0.04 0.00
5 0.03 0.04 0.01
10 0.03 0.04 0.01
20 0.03 0.04 0.03
100 0.04 0.04 0.22
∞ 0.09 0.04 1.47
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
330_H 171_K 1.21 0.68 0.01
295_G 92_V 1.12 0.59 0.01
265_I 49_G 1.11 0.58 0.01
264_V 152_V 1.10 0.57 0.01
218_V 50_I 1.04 0.50 0.01
223_L 162_V 0.99 0.45 0.00
222_S 161_N 0.98 0.44 0.00
234_I 181_P 0.97 0.43 0.00
156_I 96_V 0.97 0.43 0.00
221_S 238_E 0.94 0.40 0.00
202_E 254_I 0.94 0.40 0.00
332_I 254_I 0.92 0.38 0.00
329_Y 8_C 0.90 0.36 0.00
253_A 19_V 0.88 0.34 0.00
121_A 215_T 0.88 0.34 0.00
205_L 173_L 0.88 0.34 0.00
178_D 164_T 0.88 0.34 0.00
146_V 173_L 0.87 0.33 0.00
141_I 122_A 0.87 0.33 0.00
283_I 198_I 0.87 0.33 0.00
301_D 40_A 0.86 0.33 0.00
289_E 124_N 0.86 0.33 0.00
75_T 188_R 0.85 0.32 0.00
323_E 198_I 0.85 0.32 0.00
176_Q 92_V 0.85 0.31 0.00
194_T 59_I 0.84 0.30 0.00
188_L 151_I 0.84 0.30 0.00
314_E 7_Y 0.84 0.30 0.00
64_C 280_K 0.84 0.30 0.00
127_V 270_E 0.83 0.29 0.00
123_I 151_I 0.83 0.29 0.00
245_L 212_Y 0.82 0.29 0.00
337_A 33_I 0.82 0.28 0.00
313_R 185_I 0.81 0.28 0.00
309_G 11_I 0.81 0.28 0.00
183_I 242_Q 0.80 0.27 0.00
105_S 214_V 0.80 0.27 0.00
143_R 258_G 0.80 0.27 0.00
212_F 282_K 0.80 0.27 0.00
283_I 80_K 0.80 0.27 0.00
101_H 130_Q 0.80 0.27 0.00
204_A 162_V 0.79 0.26 0.00
243_S 96_V 0.79 0.26 0.00
238_D 128_N 0.78 0.25 0.00
73_L 45_H 0.78 0.25 0.00
329_Y 52_T 0.78 0.25 0.00
326_F 60_Y 0.78 0.25 0.00
101_H 257_I 0.77 0.25 0.00
202_E 246_V 0.77 0.25 0.00
327_E 214_V 0.77 0.25 0.00
281_E 137_P 0.77 0.25 0.00
49_G 13_I 0.77 0.25 0.00
239_I 298_V 0.77 0.24 0.00
253_A 218_I 0.77 0.24 0.00
226_A 293_R 0.77 0.24 0.00
188_L 293_R 0.77 0.24 0.00
256_Y 219_E 0.76 0.24 0.00
315_A 210_L 0.76 0.24 0.00
193_H 14_V 0.76 0.24 0.00
83_P 128_N 0.76 0.24 0.00
105_S 94_F 0.76 0.24 0.00
157_I 288_D 0.76 0.24 0.00
330_H 168_I 0.76 0.23 0.00
154_E 154_I 0.75 0.23 0.00
253_A 270_E 0.75 0.23 0.00
157_I 7_Y 0.75 0.23 0.00
50_M 278_W 0.75 0.23 0.00
332_I 161_N 0.74 0.23 0.00
162_I 218_I 0.74 0.23 0.00
258_F 122_A 0.74 0.23 0.00
208_R 50_I 0.74 0.22 0.00
221_S 96_V 0.73 0.22 0.00
284_T 256_T 0.73 0.22 0.00
143_R 295_L 0.73 0.22 0.00
192_S 126_V 0.73 0.22 0.00
203_E 264_D 0.73 0.22 0.00
131_A 75_N 0.73 0.22 0.00
189_M 59_I 0.73 0.21 0.00
198_L 59_I 0.73 0.21 0.00
137_S 34_S 0.73 0.21 0.00
264_V 33_I 0.73 0.21 0.00
137_S 80_K 0.73 0.21 0.00
256_Y 201_K 0.73 0.21 0.00
283_I 47_I 0.72 0.21 0.00
149_E 94_F 0.72 0.21 0.00
145_L 242_Q 0.72 0.21 0.00
147_A 97_E 0.72 0.21 0.00
330_H 61_V 0.72 0.21 0.00
242_N 94_F 0.72 0.21 0.00
307_D 124_N 0.72 0.21 0.00
238_D 8_C 0.72 0.21 0.00
212_F 153_P 0.72 0.21 0.00
78_R 231_I 0.72 0.21 0.00
239_I 6_S 0.72 0.21 0.00
235_L 242_Q 0.72 0.21 0.00
81_W 249_N 0.72 0.21 0.00
307_D 231_I 0.72 0.21 0.00
131_A 120_I 0.72 0.21 0.00
110_P 67_H 0.72 0.21 0.00
128_I 46_R 0.72 0.21 0.00
107_L 257_I 0.72 0.21 0.00
143_R 30_G 0.71 0.20 0.00
263_D 85_S 0.71 0.20 0.00
43_I 14_V 0.71 0.20 0.00
298_K 259_I 0.71 0.20 0.00
105_S 46_R 0.71 0.20 0.00
335_S 93_I 0.70 0.20 0.00
74_V 88_D 0.70 0.20 0.00
97_V 202_L 0.70 0.20 0.00
181_R 240_E 0.70 0.20 0.00
39_P 92_V 0.70 0.20 0.00
86_P 59_I 0.70 0.20 0.00
156_I 132_K 0.70 0.20 0.00
130_S 96_V 0.70 0.20 0.00
122_N 75_N 0.70 0.20 0.00
327_E 151_I 0.70 0.20 0.00
267_S 40_A 0.70 0.19 0.00
244_G 152_V 0.70 0.19 0.00
247_Q 122_A 0.70 0.19 0.00
272_E 212_Y 0.70 0.19 0.00
53_D 278_W 0.70 0.19 0.00
287_F 14_V 0.69 0.19 0.00
110_P 82_A 0.69 0.19 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)
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