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OPENSEQ.org
FTSW vs PBP3
Genes: A B A+B
Length: 588 414 915
Sequences: 5960 2986 1906
Seq/Len: 10.14 7.21 2.08
MirrorTree (Pazo et al. 2001) 0.74
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 0.06 0.00 0.31
2 0.06 0.00 0.34
5 0.06 0.00 1.31
10 0.07 0.01 1.37
20 0.07 0.01 1.40
100 0.10 0.04 1.57
∞ 0.23 0.14 1.90
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
39_L 313_V 1.62 0.95 0.71
47_V 309_Y 1.41 0.88 0.54
43_A 309_Y 1.40 0.87 0.53
38_L 360_V 1.38 0.87 0.51
45_L 271_F 1.36 0.86 0.50
42_V 312_V 1.29 0.81 0.42
192_V 357_L 1.02 0.56 0.20
38_L 357_L 1.01 0.55 0.19
228_A 187_V 1.00 0.54 0.18
37_F 366_M 1.00 0.53 0.18
244_V 276_L 0.99 0.53 0.18
47_V 276_L 0.99 0.53 0.18
39_L 314_L 0.98 0.52 0.17
433_A 198_L 0.97 0.50 0.17
42_V 300_F 0.94 0.46 0.15
34_A 357_L 0.92 0.44 0.13
446_I 348_I 0.89 0.41 0.12
39_L 316_L 0.88 0.41 0.12
38_L 366_M 0.87 0.39 0.11
551_G 315_A 0.86 0.38 0.11
272_V 357_L 0.85 0.37 0.10
35_L 320_F 0.85 0.36 0.10
378_D 310_V 0.83 0.34 0.09
246_R 348_I 0.81 0.33 0.09
179_I 226_I 0.80 0.32 0.08
376_L 382_S 0.79 0.31 0.08
279_P 253_P 0.79 0.31 0.08
299_I 144_L 0.78 0.30 0.08
523_Q 107_W 0.78 0.30 0.07
150_Y 139_I 0.78 0.29 0.07
192_V 198_L 0.77 0.29 0.07
192_V 146_I 0.76 0.28 0.07
393_L 251_W 0.76 0.28 0.07
269_T 127_V 0.76 0.28 0.07
473_S 385_L 0.76 0.28 0.07
312_M 352_F 0.75 0.28 0.07
417_F 88_Y 0.75 0.27 0.07
449_V 146_I 0.75 0.27 0.07
203_Q 91_L 0.74 0.26 0.06
258_E 262_Y 0.73 0.26 0.06
491_I 247_V 0.73 0.25 0.06
481_G 48_L 0.72 0.25 0.06
139_L 231_S 0.72 0.25 0.06
228_A 155_S 0.72 0.25 0.06
481_G 235_L 0.72 0.24 0.06
113_L 382_S 0.72 0.24 0.06
356_L 139_I 0.71 0.24 0.06
113_L 139_I 0.71 0.24 0.06
468_V 357_L 0.71 0.24 0.06
38_L 316_L 0.71 0.24 0.05
269_T 316_L 0.71 0.23 0.05
47_V 299_I 0.70 0.23 0.05
137_I 98_I 0.70 0.23 0.05
562_N 158_C 0.70 0.23 0.05
45_L 304_G 0.70 0.23 0.05
60_R 266_Q 0.69 0.23 0.05
31_I 353_S 0.69 0.22 0.05
374_S 354_F 0.69 0.22 0.05
236_I 277_W 0.69 0.22 0.05
467_V 195_Q 0.69 0.22 0.05
37_F 93_F 0.69 0.22 0.05
385_L 108_Q 0.69 0.22 0.05
236_I 84_R 0.68 0.22 0.05
319_Q 111_S 0.68 0.22 0.05
551_G 218_K 0.68 0.22 0.05
328_V 122_L 0.68 0.21 0.05
491_I 256_D 0.68 0.21 0.05
134_G 98_I 0.68 0.21 0.05
121_L 310_V 0.68 0.21 0.05
399_G 365_G 0.68 0.21 0.04
526_F 124_I 0.68 0.21 0.04
319_Q 382_S 0.67 0.21 0.04
446_I 211_M 0.67 0.21 0.04
68_S 309_Y 0.67 0.21 0.04
166_R 383_S 0.67 0.21 0.04
383_F 374_L 0.67 0.21 0.04
139_L 58_I 0.67 0.20 0.04
90_A 391_I 0.67 0.20 0.04
282_N 239_A 0.67 0.20 0.04
177_H 146_I 0.67 0.20 0.04
263_V 288_L 0.66 0.20 0.04
517_G 374_L 0.66 0.20 0.04
422_M 376_L 0.66 0.20 0.04
268_N 393_M 0.66 0.20 0.04
299_I 218_K 0.66 0.20 0.04
159_I 360_V 0.66 0.20 0.04
33_L 389_T 0.66 0.20 0.04
355_V 336_I 0.66 0.20 0.04
57_G 286_Q 0.66 0.20 0.04
42_V 364_A 0.66 0.20 0.04
462_S 94_I 0.66 0.20 0.04
376_L 93_F 0.65 0.19 0.04
350_L 296_T 0.65 0.19 0.04
32_L 186_L 0.65 0.19 0.04
41_R 60_F 0.64 0.19 0.04
338_G 57_A 0.64 0.19 0.04
419_Y 273_R 0.64 0.18 0.04
380_Y 309_Y 0.64 0.18 0.04
236_I 99_T 0.63 0.18 0.04
435_I 120_I 0.63 0.18 0.04
395_G 225_I 0.63 0.18 0.04
426_L 86_G 0.63 0.18 0.04
367_L 250_F 0.63 0.18 0.04
434_T 215_A 0.63 0.18 0.04
35_L 218_K 0.63 0.18 0.04
428_L 152_T 0.63 0.18 0.04
75_T 86_G 0.63 0.18 0.04
97_E 303_I 0.63 0.18 0.04
139_L 146_I 0.63 0.18 0.04
91_I 135_A 0.63 0.17 0.04
317_A 92_A 0.63 0.17 0.04
446_I 267_S 0.62 0.17 0.03
294_M 232_A 0.62 0.17 0.03
412_R 393_M 0.62 0.17 0.03
471_M 326_A 0.62 0.17 0.03
236_I 358_V 0.62 0.17 0.03
491_I 141_L 0.62 0.17 0.03
248_L 154_L 0.62 0.17 0.03
38_L 364_A 0.62 0.17 0.03
248_L 309_Y 0.62 0.17 0.03
530_V 360_V 0.62 0.17 0.03
481_G 233_V 0.62 0.17 0.03
557_V 332_K 0.61 0.17 0.03
79_G 373_T 0.61 0.17 0.03
156_L 213_F 0.61 0.17 0.03
480_G 198_L 0.61 0.17 0.03
67_V 186_L 0.61 0.17 0.03
380_Y 342_G 0.61 0.17 0.03
413_A 242_Y 0.61 0.17 0.03
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
12988 1.53 FtsW PBP3 Complex Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.97 Done - Shared
10910 2.08 FTSW vs PBP3 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.71 Done
6907 1.53 ftsi-ftsw Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.97 Done
3872 3.53 FTSW_PBP3 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
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