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OPENSEQ.org
RadA-RecA-interr
Genes: A B A+B
Length: 458 348 790
Sequences: 12167 4770 160
Seq/Len: 26.57 13.71 0.2
MirrorTree (Pazo et al. 2001) 0.06
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 0.02 0.00 0.00
2 0.02 0.00 0.01
5 0.02 0.00 0.05
10 0.02 0.00 0.10
20 0.03 0.00 0.20
100 0.04 0.00 0.69
∞ 0.11 0.01 2.79
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
214_I 156_D 1.92 0.56 0.00
311_I 162_V 1.56 0.35 0.00
452_L 83_Q 1.40 0.27 0.00
158_Y 268_K 1.40 0.27 0.00
251_L 23_S 1.36 0.25 0.00
234_V 86_G 1.32 0.23 0.00
274_L 229_L 1.31 0.23 0.00
234_V 203_N 1.26 0.21 0.00
448_V 321_I 1.25 0.20 0.00
427_P 15_I 1.24 0.20 0.00
447_N 154_E 1.21 0.19 0.00
357_L 201_F 1.20 0.19 0.00
350_L 151_A 1.20 0.19 0.00
439_G 276_G 1.17 0.17 0.00
142_G 173_L 1.16 0.17 0.00
356_Y 99_P 1.14 0.17 0.00
448_V 217_S 1.14 0.17 0.00
8_F 268_K 1.13 0.16 0.00
422_K 276_G 1.12 0.16 0.00
446_A 289_Y 1.11 0.16 0.00
446_A 26_K 1.11 0.16 0.00
377_S 218_S 1.10 0.15 0.00
274_L 235_V 1.10 0.15 0.00
210_I 138_I 1.10 0.15 0.00
212_I 193_I 1.09 0.15 0.00
214_I 193_I 1.08 0.15 0.00
441_E 295_R 1.08 0.15 0.00
33_M 182_K 1.08 0.15 0.00
427_P 11_A 1.08 0.15 0.00
337_L 321_I 1.08 0.15 0.00
197_C 83_Q 1.08 0.14 0.00
65_I 128_E 1.07 0.14 0.00
233_M 275_L 1.07 0.14 0.00
12_S 60_I 1.07 0.14 0.00
435_T 23_S 1.07 0.14 0.00
456_L 241_K 1.07 0.14 0.00
254_V 27_L 1.06 0.14 0.00
311_I 114_L 1.05 0.14 0.00
375_V 76_H 1.03 0.13 0.00
378_I 314_M 1.03 0.13 0.00
147_S 254_R 1.03 0.13 0.00
8_F 317_I 1.03 0.13 0.00
355_A 148_V 1.03 0.13 0.00
192_S 23_S 1.02 0.13 0.00
292_S 35_I 1.01 0.13 0.00
262_N 153_I 1.01 0.13 0.00
449_A 313_I 1.01 0.13 0.00
423_R 24_I 1.01 0.12 0.00
282_E 136_V 1.00 0.12 0.00
250_I 306_F 1.00 0.12 0.00
436_K 23_S 0.99 0.12 0.00
208_K 81_V 0.99 0.12 0.00
355_A 109_I 0.98 0.12 0.00
173_V 83_Q 0.98 0.12 0.00
190_S 296_L 0.98 0.12 0.00
397_V 34_R 0.98 0.12 0.00
436_K 39_P 0.98 0.12 0.00
455_S 295_R 0.98 0.12 0.00
210_I 103_Q 0.97 0.12 0.00
378_I 60_I 0.97 0.12 0.00
136_L 36_S 0.96 0.11 0.00
404_R 188_I 0.96 0.11 0.00
115_L 203_N 0.96 0.11 0.00
64_S 217_S 0.96 0.11 0.00
378_I 62_V 0.96 0.11 0.00
71_P 110_E 0.96 0.11 0.00
345_R 4_R 0.95 0.11 0.00
311_I 183_S 0.95 0.11 0.00
46_R 269_E 0.95 0.11 0.00
234_V 26_K 0.95 0.11 0.00
202_M 321_I 0.94 0.11 0.00
94_V 54_Y 0.94 0.11 0.00
304_T 282_V 0.94 0.11 0.00
365_L 114_L 0.93 0.11 0.00
448_V 59_I 0.93 0.11 0.00
264_M 276_G 0.93 0.11 0.00
277_V 80_E 0.93 0.11 0.00
291_G 217_S 0.93 0.11 0.00
278_L 219_V 0.93 0.11 0.00
36_E 300_R 0.92 0.10 0.00
313_A 317_I 0.92 0.10 0.00
390_A 35_I 0.91 0.10 0.00
156_M 4_R 0.91 0.10 0.00
211_P 47_T 0.91 0.10 0.00
382_F 249_V 0.91 0.10 0.00
405_R 73_V 0.91 0.10 0.00
23_K 148_V 0.90 0.10 0.00
111_V 201_F 0.90 0.10 0.00
357_L 301_E 0.90 0.10 0.00
270_R 178_G 0.90 0.10 0.00
365_L 280_D 0.90 0.10 0.00
61_P 203_N 0.90 0.10 0.00
405_R 272_I 0.90 0.10 0.00
406_V 113_L 0.90 0.10 0.00
250_I 228_Q 0.90 0.10 0.00
268_E 59_I 0.89 0.10 0.00
287_E 281_I 0.89 0.10 0.00
313_A 119_T 0.89 0.10 0.00
197_C 51_I 0.89 0.10 0.00
311_I 51_I 0.89 0.10 0.00
369_A 180_I 0.89 0.10 0.00
448_V 153_I 0.89 0.10 0.00
377_S 127_A 0.89 0.10 0.00
217_H 153_I 0.88 0.10 0.00
83_V 219_V 0.88 0.10 0.00
413_V 303_A 0.88 0.10 0.00
23_K 139_V 0.88 0.10 0.00
130_S 188_I 0.88 0.09 0.00
413_V 217_S 0.88 0.09 0.00
364_K 44_A 0.88 0.09 0.00
427_P 131_V 0.87 0.09 0.00
428_A 38_V 0.87 0.09 0.00
357_L 186_I 0.87 0.09 0.00
261_T 78_I 0.87 0.09 0.00
296_S 36_S 0.87 0.09 0.00
420_G 260_I 0.87 0.09 0.00
141_L 296_L 0.87 0.09 0.00
456_L 99_P 0.86 0.09 0.00
357_L 39_P 0.86 0.09 0.00
361_G 217_S 0.86 0.09 0.00
321_G 67_S 0.86 0.09 0.00
38_I 91_I 0.86 0.09 0.00
345_R 217_S 0.86 0.09 0.00
56_V 139_V 0.85 0.09 0.00
427_P 302_N 0.85 0.09 0.00
370_I 99_P 0.85 0.09 0.00
271_E 139_V 0.85 0.09 0.00
296_S 24_I 0.85 0.09 0.00
450_E 312_D 0.85 0.09 0.00
210_I 17_K 0.85 0.09 0.00
274_L 176_L 0.85 0.09 0.00
182_S 60_I 0.85 0.09 0.00
388_N 139_V 0.85 0.09 0.00
405_R 74_A 0.84 0.09 0.00
403_V 292_E 0.84 0.09 0.00
365_L 60_I 0.84 0.09 0.00
409_I 236_M 0.84 0.09 0.00
339_M 150_K 0.84 0.09 0.00
210_I 39_P 0.84 0.09 0.00
450_E 295_R 0.84 0.09 0.00
311_I 281_I 0.84 0.09 0.00
39_K 39_P 0.84 0.09 0.00
385_T 229_L 0.84 0.09 0.00
406_V 23_S 0.83 0.09 0.00
177_Q 38_V 0.83 0.09 0.00
446_A 296_L 0.83 0.09 0.00
295_S 289_Y 0.83 0.09 0.00
357_L 200_M 0.83 0.09 0.00
432_D 235_V 0.83 0.09 0.00
245_H 24_I 0.83 0.09 0.00
64_S 294_E 0.83 0.09 0.00
214_I 244_V 0.83 0.09 0.00
452_L 188_I 0.83 0.09 0.00
428_A 188_I 0.83 0.09 0.00
332_H 83_Q 0.83 0.09 0.00
335_V 223_V 0.82 0.08 0.00
406_V 12_L 0.82 0.08 0.00
429_A 59_I 0.82 0.08 0.00
345_R 28_G 0.82 0.08 0.00
403_V 262_Y 0.82 0.08 0.00
150_V 128_E 0.82 0.08 0.00
234_V 60_I 0.82 0.08 0.00
363_V 228_Q 0.82 0.08 0.00
233_M 139_V 0.82 0.08 0.00
456_L 90_F 0.82 0.08 0.00
234_V 187_A 0.82 0.08 0.00
385_T 108_N 0.82 0.08 0.00
398_G 158_G 0.82 0.08 0.00
8_F 238_N 0.82 0.08 0.00
454_T 141_V 0.82 0.08 0.00
286_E 148_V 0.81 0.08 0.00
60_S 127_A 0.81 0.08 0.00
254_V 74_A 0.81 0.08 0.00
451_A 178_G 0.81 0.08 0.00
60_S 141_V 0.81 0.08 0.00
375_V 311_K 0.81 0.08 0.00
378_I 63_Y 0.81 0.08 0.00
156_M 244_V 0.81 0.08 0.00
356_Y 227_E 0.81 0.08 0.00
411_Q 40_S 0.81 0.08 0.00
444_G 150_K 0.81 0.08 0.00
357_L 282_V 0.81 0.08 0.00
384_D 249_V 0.80 0.08 0.00
270_R 312_D 0.80 0.08 0.00
166_M 51_I 0.80 0.08 0.00
40_K 35_I 0.80 0.08 0.00
190_S 180_I 0.80 0.08 0.00
102_I 285_S 0.80 0.08 0.00
109_L 289_Y 0.80 0.08 0.00
173_V 114_L 0.80 0.08 0.00
91_G 11_A 0.80 0.08 0.00
58_K 139_V 0.80 0.08 0.00
168_P 35_I 0.80 0.08 0.00
12_S 29_E 0.80 0.08 0.00
349_L 156_D 0.80 0.08 0.00
388_N 316_M 0.80 0.08 0.00
186_S 148_V 0.80 0.08 0.00
176_I 275_L 0.80 0.08 0.00
254_V 76_H 0.79 0.08 0.00
348_L 4_R 0.79 0.08 0.00
66_E 197_V 0.79 0.08 0.00
389_P 8_L 0.79 0.08 0.00
424_M 97_L 0.79 0.08 0.00
455_S 234_D 0.79 0.08 0.00
347_G 85_G 0.79 0.08 0.00
173_V 240_T 0.79 0.08 0.00
196_E 317_I 0.79 0.08 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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