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OPENSEQ.org
RadA-RecA2
Genes: A B A+B
Length: 458 348 739
Sequences: 1886 1825 952
Seq/Len: 4.12 5.24 1.29
MirrorTree (Pazo et al. 2001) 0.52
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 0.00 0.07 0.00
2 0.00 0.07 0.00
5 0.00 0.07 0.01
10 0.00 0.07 0.01
20 0.00 0.07 0.05
100 0.00 0.07 0.14
∞ 0.01 0.08 1.18
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
32_T 282_V 1.52 0.84 0.10
406_V 162_V 1.47 0.81 0.09
356_Y 227_E 1.25 0.65 0.05
111_V 156_D 1.25 0.64 0.05
8_F 17_K 1.16 0.55 0.04
102_I 16_E 1.15 0.55 0.04
214_I 287_S 1.10 0.50 0.03
403_V 283_Q 1.08 0.48 0.03
309_V 131_V 1.08 0.48 0.03
324_R 97_L 1.07 0.47 0.03
359_V 321_I 1.06 0.46 0.03
135_K 272_I 1.06 0.46 0.03
327_A 276_G 1.04 0.44 0.02
365_L 30_K 1.03 0.43 0.02
125_I 63_Y 1.03 0.43 0.02
179_V 51_I 1.02 0.42 0.02
197_C 301_E 1.00 0.40 0.02
386_P 138_I 0.96 0.36 0.02
90_K 113_L 0.96 0.36 0.02
173_V 60_I 0.96 0.36 0.02
180_Y 244_V 0.95 0.36 0.02
295_S 296_L 0.95 0.36 0.02
80_F 60_I 0.94 0.35 0.02
365_L 305_Q 0.94 0.34 0.02
363_V 4_R 0.93 0.34 0.02
122_V 251_P 0.93 0.33 0.02
367_E 289_Y 0.93 0.33 0.02
360_A 181_N 0.92 0.33 0.02
236_T 23_S 0.92 0.33 0.02
356_Y 100_V 0.92 0.33 0.02
336_S 254_R 0.91 0.32 0.01
323_P 296_L 0.91 0.32 0.01
148_L 292_E 0.91 0.32 0.01
173_V 62_V 0.90 0.31 0.01
237_V 86_G 0.90 0.31 0.01
375_V 77_A 0.89 0.30 0.01
26_G 54_Y 0.89 0.30 0.01
296_S 328_D 0.89 0.30 0.01
307_I 74_A 0.89 0.30 0.01
326_M 78_I 0.88 0.30 0.01
289_S 153_I 0.88 0.29 0.01
93_L 304_K 0.88 0.29 0.01
62_I 51_I 0.88 0.29 0.01
41_A 282_V 0.88 0.29 0.01
239_Y 15_I 0.87 0.29 0.01
121_S 282_V 0.87 0.29 0.01
311_I 217_S 0.87 0.28 0.01
378_I 317_I 0.87 0.28 0.01
332_H 197_V 0.87 0.28 0.01
204_I 103_Q 0.87 0.28 0.01
364_K 56_R 0.86 0.28 0.01
397_V 109_I 0.86 0.28 0.01
324_R 295_R 0.86 0.28 0.01
409_I 201_F 0.85 0.27 0.01
338_L 201_F 0.85 0.27 0.01
17_S 74_A 0.85 0.27 0.01
386_P 37_T 0.85 0.27 0.01
411_Q 193_I 0.85 0.27 0.01
183_D 244_V 0.84 0.27 0.01
418_K 221_L 0.84 0.27 0.01
33_M 312_D 0.84 0.26 0.01
320_F 201_F 0.84 0.26 0.01
296_S 148_V 0.83 0.26 0.01
394_I 219_V 0.83 0.25 0.01
345_R 301_E 0.83 0.25 0.01
83_V 134_G 0.83 0.25 0.01
237_V 267_S 0.83 0.25 0.01
250_I 271_E 0.82 0.25 0.01
8_F 312_D 0.82 0.25 0.01
384_D 63_Y 0.82 0.25 0.01
170_F 273_I 0.82 0.25 0.01
228_R 44_A 0.82 0.25 0.01
16_E 162_V 0.82 0.25 0.01
136_L 178_G 0.82 0.25 0.01
96_I 287_S 0.82 0.25 0.01
244_R 17_K 0.82 0.24 0.01
311_I 43_L 0.82 0.24 0.01
398_G 148_V 0.82 0.24 0.01
406_V 161_H 0.82 0.24 0.01
172_V 27_L 0.81 0.24 0.01
156_M 154_E 0.81 0.24 0.01
197_C 326_G 0.81 0.24 0.01
33_M 111_E 0.81 0.24 0.01
360_A 254_R 0.81 0.24 0.01
40_K 19_F 0.81 0.24 0.01
127_G 190_I 0.80 0.23 0.01
360_A 114_L 0.80 0.23 0.01
197_C 129_A 0.80 0.23 0.01
16_E 39_P 0.80 0.23 0.01
65_I 268_K 0.80 0.23 0.01
392_C 54_Y 0.80 0.23 0.01
172_V 217_S 0.80 0.23 0.01
318_T 3_D 0.79 0.23 0.01
78_G 282_V 0.79 0.23 0.01
184_I 62_V 0.79 0.23 0.01
318_T 114_L 0.79 0.23 0.01
54_Q 139_V 0.79 0.23 0.01
19_K 128_E 0.79 0.22 0.01
157_E 310_N 0.79 0.22 0.01
348_L 4_R 0.79 0.22 0.01
331_D 139_V 0.79 0.22 0.01
307_I 217_S 0.79 0.22 0.01
150_V 178_G 0.78 0.22 0.01
245_H 73_V 0.78 0.22 0.01
356_Y 186_I 0.78 0.22 0.01
237_V 259_D 0.78 0.22 0.01
286_E 150_K 0.78 0.22 0.01
383_R 43_L 0.78 0.22 0.01
271_E 136_V 0.78 0.22 0.01
88_V 26_K 0.78 0.22 0.01
304_T 178_G 0.78 0.22 0.01
384_D 229_L 0.78 0.22 0.01
112_S 242_I 0.78 0.22 0.01
295_S 193_I 0.78 0.22 0.01
18_P 323_E 0.78 0.21 0.01
327_A 12_L 0.77 0.21 0.01
194_V 162_V 0.77 0.21 0.01
138_A 35_I 0.77 0.21 0.01
418_K 162_V 0.77 0.21 0.01
2_A 217_S 0.77 0.21 0.01
331_D 280_D 0.77 0.21 0.01
109_L 88_A 0.77 0.21 0.01
309_V 283_Q 0.77 0.21 0.01
295_S 138_I 0.77 0.21 0.01
266_I 271_E 0.77 0.21 0.01
196_E 287_S 0.77 0.21 0.01
65_I 91_I 0.77 0.21 0.01
75_T 75_L 0.77 0.21 0.01
351_Q 177_S 0.76 0.21 0.01
188_P 132_R 0.76 0.21 0.01
275_T 136_V 0.76 0.21 0.01
309_V 141_V 0.76 0.20 0.01
198_T 249_V 0.76 0.20 0.01
397_V 219_V 0.76 0.20 0.01
265_G 153_I 0.76 0.20 0.01
244_R 56_R 0.76 0.20 0.01
415_E 24_I 0.76 0.20 0.01
398_G 24_I 0.76 0.20 0.01
186_S 187_A 0.76 0.20 0.01
102_I 300_R 0.76 0.20 0.01
122_V 88_A 0.75 0.20 0.01
246_H 300_R 0.75 0.20 0.01
224_I 188_I 0.75 0.20 0.01
345_R 114_L 0.75 0.20 0.01
326_M 183_S 0.75 0.20 0.01
418_K 261_M 0.75 0.20 0.01
152_S 43_L 0.75 0.20 0.01
409_I 181_N 0.75 0.20 0.01
185_T 287_S 0.75 0.20 0.01
190_S 80_E 0.74 0.20 0.01
65_I 291_Y 0.74 0.20 0.01
198_T 40_S 0.74 0.19 0.01
179_V 16_E 0.74 0.19 0.01
23_K 105_L 0.74 0.19 0.01
198_T 223_V 0.74 0.19 0.01
345_R 8_L 0.74 0.19 0.01
92_S 135_A 0.73 0.19 0.01
141_L 193_I 0.73 0.19 0.01
141_L 29_E 0.73 0.19 0.01
292_S 287_S 0.73 0.19 0.01
274_L 182_K 0.73 0.19 0.01
253_A 154_E 0.73 0.18 0.01
102_I 86_G 0.73 0.18 0.01
242_G 267_S 0.73 0.18 0.01
390_A 181_N 0.73 0.18 0.01
8_F 217_S 0.72 0.18 0.01
154_T 156_D 0.72 0.18 0.01
131_V 321_I 0.72 0.18 0.01
279_N 290_S 0.72 0.18 0.01
33_M 208_P 0.72 0.18 0.01
212_I 150_K 0.72 0.18 0.01
120_N 321_I 0.72 0.18 0.01
159_I 73_V 0.72 0.18 0.01
203_K 39_P 0.72 0.18 0.01
224_I 314_M 0.72 0.18 0.01
25_P 148_V 0.72 0.18 0.01
214_I 78_I 0.72 0.18 0.01
112_S 111_E 0.72 0.18 0.01
141_L 217_S 0.72 0.18 0.01
198_T 254_R 0.72 0.18 0.01
317_P 35_I 0.72 0.18 0.01
357_L 139_V 0.72 0.18 0.01
375_V 320_Q 0.72 0.18 0.01
400_T 197_V 0.71 0.18 0.01
151_L 276_G 0.71 0.18 0.01
188_P 107_V 0.71 0.17 0.01
150_V 269_E 0.71 0.17 0.01
328_T 10_M 0.71 0.17 0.01
123_L 266_I 0.71 0.17 0.01
195_R 241_K 0.71 0.17 0.01
335_V 254_R 0.71 0.17 0.01
376_I 282_V 0.71 0.17 0.01
238_L 200_M 0.71 0.17 0.01
188_P 63_Y 0.71 0.17 0.01
102_I 240_T 0.71 0.17 0.01
329_G 230_K 0.71 0.17 0.01
172_V 2_S 0.71 0.17 0.01
83_V 151_A 0.70 0.17 0.01
119_S 63_Y 0.70 0.17 0.01
217_H 218_S 0.70 0.17 0.01
96_I 317_I 0.70 0.17 0.01
176_I 24_I 0.70 0.17 0.01
2_A 261_M 0.70 0.17 0.01
299_A 193_I 0.70 0.17 0.01
356_Y 76_H 0.70 0.17 0.01
172_V 266_I 0.70 0.17 0.01
337_L 44_A 0.70 0.17 0.01
254_V 35_I 0.70 0.17 0.01
245_H 195_E 0.70 0.17 0.01
378_I 256_A 0.69 0.17 0.01
374_I 271_E 0.69 0.17 0.01
203_K 320_Q 0.69 0.17 0.01
218_V 302_N 0.69 0.17 0.01
96_I 38_V 0.69 0.16 0.01
398_G 16_E 0.69 0.16 0.01
18_P 154_E 0.69 0.16 0.01
337_L 35_I 0.69 0.16 0.01
136_L 261_M 0.69 0.16 0.01
63_T 35_I 0.69 0.16 0.01
293_A 203_N 0.69 0.16 0.01
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
10335 0.05 RadA-RecA2 Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
10334 0.09 RadA-RecA2 Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
10332 2.14 RadA-RecA2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
10330 1.28 RadA-RecA2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.23 Done - Shared
10329 0.05 RadA-RecA2 Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
10325 0.15 RadA-RecA2 Δgene:(1, 100) A:(1E-06, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.02 Done - Shared
10324 1.29 RadA-RecA2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.32 Done - Shared
10321 1.29 RadA-RecA2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.10 Done - Shared
10310 1.29 RadA-RecA2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.34 Done - Shared
10309 1.29 RadA-RecA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.06 Done - Shared
10303 2.14 infinite-E-80-Jack Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
10302 1.28 infinite-E-80-HHblist Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.11 Done - Shared
10301 1.29 infinite-E-60-HHblist Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.06 Done - Shared
10300 2.14 infinite- E-60 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
10298 0.2 RadA-RecA-interr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
10297 0.05 RadA-RecA-interr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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