May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
FTSW_PBP3
Genes: A B A+B
Length: 588 414 931
Sequences: 12255 6178 3290
Seq/Len: 20.84 14.92 3.53
MirrorTree (Pazo et al. 2001) 0.83
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 0.06 0.03 1.05
2 0.07 0.04 1.13
5 0.08 0.04 3.03
10 0.10 0.06 3.20
20 0.11 0.07 3.28
100 0.16 0.11 3.80
∞ 0.23 0.23 4.51
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 2.40 1.00 1.00
42_V 312_V 1.83 0.99 0.97
43_A 309_Y 1.53 0.97 0.92
47_V 276_L 1.48 0.96 0.90
34_A 357_L 1.48 0.96 0.90
37_F 366_M 1.37 0.94 0.85
35_L 320_F 1.33 0.93 0.83
38_L 360_V 1.31 0.92 0.82
38_L 357_L 1.25 0.90 0.78
47_V 309_Y 1.24 0.89 0.77
60_R 266_Q 1.17 0.85 0.71
42_V 364_A 1.05 0.74 0.58
39_L 316_L 1.00 0.70 0.53
38_L 366_M 0.93 0.61 0.43
50_P 275_E 0.89 0.56 0.38
42_V 300_F 0.87 0.54 0.37
38_L 361_G 0.84 0.49 0.33
31_I 353_S 0.81 0.46 0.29
376_L 382_S 0.80 0.44 0.28
45_L 271_F 0.78 0.42 0.26
38_L 364_A 0.76 0.39 0.24
46_Q 309_Y 0.74 0.38 0.22
37_F 223_I 0.72 0.35 0.20
471_M 216_G 0.72 0.35 0.20
57_G 286_Q 0.69 0.32 0.18
367_L 119_I 0.69 0.31 0.17
28_C 324_F 0.69 0.31 0.17
28_C 320_F 0.68 0.30 0.17
60_R 286_Q 0.67 0.29 0.16
236_I 332_K 0.66 0.28 0.15
399_G 365_G 0.65 0.27 0.14
151_I 61_I 0.64 0.26 0.13
487_K 183_G 0.63 0.25 0.13
192_V 232_A 0.62 0.24 0.12
39_L 309_Y 0.62 0.24 0.12
236_I 315_A 0.62 0.24 0.12
299_I 317_L 0.62 0.24 0.12
27_L 214_L 0.62 0.24 0.12
26_L 119_I 0.62 0.24 0.12
113_L 114_M 0.61 0.23 0.12
419_Y 273_R 0.61 0.23 0.11
522_S 124_I 0.60 0.22 0.11
41_R 364_A 0.60 0.22 0.11
26_L 213_F 0.60 0.22 0.11
153_K 49_L 0.60 0.22 0.11
38_L 316_L 0.60 0.22 0.11
505_G 161_A 0.59 0.22 0.11
397_R 384_L 0.59 0.22 0.11
139_L 214_L 0.59 0.22 0.11
475_A 118_S 0.59 0.21 0.10
516_A 118_S 0.59 0.21 0.10
53_L 272_G 0.58 0.21 0.10
46_Q 304_G 0.58 0.20 0.10
87_P 376_L 0.57 0.20 0.09
276_A 217_A 0.57 0.20 0.09
210_R 373_T 0.57 0.19 0.09
20_I 342_G 0.56 0.19 0.09
461_E 117_G 0.56 0.19 0.09
198_K 93_F 0.56 0.19 0.09
63_R 164_L 0.56 0.19 0.09
28_C 327_M 0.56 0.19 0.09
298_T 301_A 0.56 0.19 0.09
281_Y 321_F 0.56 0.19 0.09
409_D 358_V 0.56 0.18 0.08
57_G 369_T 0.55 0.18 0.08
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
Page generated in 1.6925 seconds.