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OPENSEQ.org
RadA-RecA2
Genes: A B A+B
Length: 458 348 788
Sequences: 4970 4470 1687
Seq/Len: 10.85 12.84 2.14
MirrorTree (Pazo et al. 2001) 0.55
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.01
10 0.00 0.00 0.04
20 0.00 0.00 0.09
100 0.00 0.00 0.30
∞ 0.00 0.00 2.09
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
16_E 39_P 1.14 0.69 0.01
40_K 19_F 1.12 0.67 0.01
138_A 8_L 1.11 0.66 0.01
356_Y 227_E 1.10 0.65 0.01
288_R 59_I 1.05 0.59 0.01
111_V 156_D 1.05 0.59 0.01
179_V 51_I 1.03 0.58 0.01
149_H 150_K 0.99 0.53 0.01
31_N 7_A 0.98 0.52 0.01
406_V 162_V 0.96 0.50 0.01
125_I 63_Y 0.93 0.47 0.01
23_K 105_L 0.92 0.46 0.01
295_S 296_L 0.92 0.45 0.01
38_I 217_S 0.90 0.43 0.01
367_E 289_Y 0.90 0.42 0.01
127_G 233_N 0.89 0.42 0.01
237_V 86_G 0.89 0.42 0.01
357_L 228_Q 0.88 0.41 0.01
296_S 244_V 0.87 0.40 0.01
368_P 326_G 0.86 0.39 0.01
88_V 26_K 0.86 0.39 0.01
236_T 113_L 0.86 0.39 0.01
112_S 185_T 0.86 0.38 0.01
163_I 326_G 0.85 0.38 0.01
309_V 283_Q 0.85 0.37 0.01
271_E 150_K 0.85 0.37 0.01
448_V 37_T 0.84 0.36 0.01
224_I 188_I 0.84 0.36 0.01
324_R 97_L 0.83 0.36 0.01
159_I 138_I 0.83 0.36 0.01
337_L 44_A 0.83 0.35 0.01
214_I 141_V 0.83 0.35 0.01
18_P 154_E 0.82 0.35 0.01
307_I 74_A 0.82 0.34 0.01
357_L 17_K 0.82 0.34 0.01
50_S 91_I 0.82 0.34 0.01
242_G 259_D 0.82 0.34 0.01
378_I 317_I 0.81 0.34 0.01
83_V 134_G 0.81 0.33 0.01
339_M 38_V 0.81 0.33 0.01
274_L 182_K 0.81 0.33 0.01
375_V 77_A 0.81 0.33 0.01
326_M 183_S 0.81 0.33 0.01
384_D 229_L 0.80 0.33 0.01
219_T 201_F 0.80 0.33 0.01
398_G 232_G 0.80 0.33 0.01
360_A 254_R 0.80 0.32 0.00
324_R 295_R 0.80 0.32 0.00
448_V 87_Q 0.80 0.32 0.00
327_A 104_K 0.80 0.32 0.00
112_S 108_N 0.79 0.32 0.00
329_G 230_K 0.79 0.31 0.00
279_N 290_S 0.79 0.31 0.00
397_V 319_E 0.78 0.31 0.00
194_V 54_Y 0.78 0.31 0.00
197_C 185_T 0.78 0.30 0.00
19_K 128_E 0.77 0.30 0.00
425_I 249_V 0.77 0.30 0.00
78_G 282_V 0.77 0.30 0.00
295_S 138_I 0.77 0.30 0.00
289_S 128_E 0.77 0.30 0.00
318_T 3_D 0.77 0.29 0.00
250_I 271_E 0.77 0.29 0.00
93_L 304_K 0.77 0.29 0.00
92_S 51_I 0.76 0.29 0.00
76_Q 217_S 0.76 0.29 0.00
199_A 59_I 0.76 0.28 0.00
156_M 177_S 0.76 0.28 0.00
56_V 281_I 0.76 0.28 0.00
55_T 317_I 0.76 0.28 0.00
309_V 131_V 0.76 0.28 0.00
246_H 300_R 0.75 0.28 0.00
360_A 181_N 0.75 0.28 0.00
356_Y 97_L 0.75 0.28 0.00
214_I 287_S 0.75 0.28 0.00
135_K 221_L 0.75 0.27 0.00
8_F 17_K 0.74 0.27 0.00
167_N 35_I 0.74 0.27 0.00
204_I 227_E 0.74 0.26 0.00
251_L 80_E 0.74 0.26 0.00
283_I 87_Q 0.74 0.26 0.00
398_G 148_V 0.73 0.26 0.00
332_H 197_V 0.73 0.26 0.00
93_L 300_R 0.73 0.26 0.00
204_I 103_Q 0.73 0.26 0.00
398_G 24_I 0.73 0.26 0.00
187_A 60_I 0.73 0.26 0.00
75_T 291_Y 0.72 0.25 0.00
413_V 292_E 0.72 0.25 0.00
336_S 148_V 0.72 0.25 0.00
386_P 141_V 0.72 0.25 0.00
326_M 128_E 0.72 0.25 0.00
348_L 293_E 0.72 0.25 0.00
384_D 63_Y 0.72 0.25 0.00
212_I 285_S 0.72 0.25 0.00
197_C 326_G 0.71 0.24 0.00
90_K 113_L 0.71 0.24 0.00
381_S 228_Q 0.71 0.24 0.00
173_V 33_T 0.71 0.24 0.00
45_R 60_I 0.71 0.24 0.00
237_V 267_S 0.71 0.24 0.00
450_E 201_F 0.71 0.24 0.00
16_E 310_N 0.71 0.24 0.00
403_V 59_I 0.71 0.24 0.00
146_P 39_P 0.71 0.24 0.00
291_G 114_L 0.71 0.24 0.00
334_R 12_L 0.70 0.24 0.00
102_I 16_E 0.70 0.24 0.00
356_Y 33_T 0.70 0.24 0.00
32_T 111_E 0.70 0.23 0.00
188_P 132_R 0.70 0.23 0.00
318_T 223_V 0.70 0.23 0.00
266_I 271_E 0.70 0.23 0.00
30_W 177_S 0.70 0.23 0.00
233_M 131_V 0.70 0.23 0.00
173_V 43_L 0.70 0.23 0.00
152_S 113_L 0.70 0.23 0.00
212_I 150_K 0.70 0.23 0.00
41_A 141_V 0.70 0.23 0.00
442_V 262_Y 0.69 0.23 0.00
194_V 162_V 0.69 0.23 0.00
398_G 16_E 0.69 0.23 0.00
418_K 221_L 0.69 0.23 0.00
234_V 86_G 0.69 0.23 0.00
364_K 315_L 0.69 0.23 0.00
197_C 301_E 0.69 0.22 0.00
130_S 232_G 0.69 0.22 0.00
327_A 128_E 0.69 0.22 0.00
237_V 259_D 0.69 0.22 0.00
251_L 23_S 0.69 0.22 0.00
194_V 40_S 0.69 0.22 0.00
164_Q 91_I 0.69 0.22 0.00
331_D 274_D 0.69 0.22 0.00
448_V 203_N 0.68 0.22 0.00
141_L 217_S 0.68 0.22 0.00
439_G 141_V 0.68 0.22 0.00
365_L 30_K 0.68 0.22 0.00
122_V 251_P 0.68 0.22 0.00
66_E 203_N 0.68 0.22 0.00
152_S 43_L 0.68 0.22 0.00
266_I 227_E 0.68 0.22 0.00
301_M 289_Y 0.68 0.22 0.00
102_I 86_G 0.68 0.22 0.00
356_Y 100_V 0.68 0.22 0.00
405_R 153_I 0.68 0.21 0.00
29_A 254_R 0.68 0.21 0.00
254_V 74_A 0.67 0.21 0.00
392_C 54_Y 0.67 0.21 0.00
406_V 312_D 0.67 0.21 0.00
214_I 5_Q 0.67 0.21 0.00
21_M 104_K 0.67 0.21 0.00
245_H 193_I 0.67 0.21 0.00
428_A 59_I 0.67 0.21 0.00
184_I 296_L 0.67 0.21 0.00
211_P 78_I 0.67 0.21 0.00
414_K 193_I 0.67 0.21 0.00
134_T 134_G 0.67 0.21 0.00
423_R 134_G 0.67 0.21 0.00
159_I 322_R 0.67 0.21 0.00
434_W 272_I 0.67 0.21 0.00
196_E 287_S 0.67 0.21 0.00
335_V 254_R 0.67 0.21 0.00
243_E 304_K 0.67 0.21 0.00
32_T 282_V 0.67 0.21 0.00
28_G 285_S 0.66 0.20 0.00
14_G 263_G 0.66 0.20 0.00
239_Y 15_I 0.66 0.20 0.00
446_A 217_S 0.66 0.20 0.00
218_V 302_N 0.66 0.20 0.00
335_V 276_G 0.66 0.20 0.00
342_L 249_V 0.66 0.20 0.00
198_T 40_S 0.66 0.20 0.00
428_A 307_L 0.66 0.20 0.00
172_V 184_K 0.66 0.20 0.00
121_S 282_V 0.66 0.20 0.00
297_I 284_K 0.66 0.20 0.00
309_V 24_I 0.66 0.20 0.00
116_S 234_D 0.66 0.20 0.00
122_V 88_A 0.66 0.20 0.00
351_Q 177_S 0.66 0.20 0.00
345_R 114_L 0.66 0.20 0.00
173_V 138_I 0.66 0.20 0.00
297_I 139_V 0.66 0.20 0.00
288_R 148_V 0.66 0.20 0.00
385_T 317_I 0.66 0.20 0.00
419_L 54_Y 0.65 0.20 0.00
181_Q 51_I 0.65 0.20 0.00
131_V 321_I 0.65 0.20 0.00
324_R 228_Q 0.65 0.20 0.00
96_I 110_E 0.65 0.20 0.00
277_V 49_L 0.65 0.20 0.00
112_S 242_I 0.65 0.20 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
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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