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: 414 588 932
Sequences: 5922 11507 3092
Seq/Len: 14.3 19.57 3.32
MirrorTree (Pazo et al. 2001) 0.84
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 0.03 1.00
2 0.02 0.04 1.07
5 0.02 0.05 2.85
10 0.03 0.06 3.01
20 0.03 0.08 3.09
100 0.06 0.11 3.59
∞ 0.13 0.18 4.33
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
313_V 39_L 2.34 1.00 0.99
312_V 42_V 1.84 0.99 0.97
309_Y 43_A 1.54 0.97 0.91
357_L 34_A 1.43 0.95 0.87
276_L 47_V 1.41 0.94 0.87
366_M 37_F 1.31 0.91 0.81
360_V 38_L 1.31 0.91 0.81
320_F 35_L 1.30 0.91 0.80
309_Y 47_V 1.26 0.89 0.77
357_L 38_L 1.25 0.88 0.77
266_Q 60_R 1.20 0.85 0.72
316_L 39_L 1.09 0.77 0.61
364_A 42_V 1.06 0.74 0.58
275_E 50_P 0.94 0.60 0.43
366_M 38_L 0.93 0.59 0.42
216_G 471_M 0.90 0.56 0.39
353_S 31_I 0.86 0.51 0.34
271_F 45_L 0.86 0.51 0.34
232_A 192_V 0.86 0.51 0.34
300_F 42_V 0.79 0.42 0.26
361_G 38_L 0.79 0.41 0.26
309_Y 39_L 0.78 0.40 0.25
286_Q 57_G 0.77 0.39 0.23
309_Y 46_Q 0.75 0.36 0.21
324_F 28_C 0.74 0.36 0.21
315_A 236_I 0.74 0.36 0.21
223_I 37_F 0.74 0.35 0.21
382_S 376_L 0.71 0.32 0.18
320_F 28_C 0.70 0.32 0.18
317_L 299_I 0.70 0.31 0.18
91_L 235_S 0.70 0.31 0.18
364_A 38_L 0.69 0.30 0.16
382_S 319_Q 0.69 0.30 0.16
118_S 475_A 0.69 0.29 0.16
286_Q 60_R 0.65 0.26 0.14
119_I 367_L 0.65 0.26 0.14
98_I 108_D 0.65 0.26 0.13
273_R 419_Y 0.65 0.25 0.13
262_Y 446_I 0.64 0.25 0.13
161_A 370_A 0.64 0.25 0.13
342_G 20_I 0.63 0.24 0.12
233_V 35_L 0.63 0.24 0.12
351_W 283_P 0.63 0.24 0.12
397_I 40_G 0.62 0.23 0.12
124_I 522_S 0.62 0.23 0.12
242_Y 319_Q 0.62 0.23 0.12
272_G 53_L 0.62 0.23 0.11
373_T 499_K 0.62 0.23 0.11
304_G 46_Q 0.61 0.23 0.11
267_S 421_L 0.61 0.22 0.11
213_F 26_L 0.60 0.22 0.11
301_A 298_T 0.60 0.22 0.11
365_G 399_G 0.60 0.22 0.10
316_L 38_L 0.60 0.21 0.10
301_A 272_V 0.60 0.21 0.10
360_V 42_V 0.60 0.21 0.10
211_M 549_V 0.59 0.21 0.10
213_F 156_L 0.59 0.21 0.10
117_G 338_G 0.59 0.20 0.10
317_L 40_G 0.59 0.20 0.10
102_L 26_L 0.59 0.20 0.10
214_L 27_L 0.58 0.20 0.10
327_M 28_C 0.58 0.20 0.09
183_G 487_K 0.58 0.20 0.09
164_L 63_R 0.58 0.20 0.09
282_G 361_N 0.58 0.20 0.09
114_M 33_L 0.57 0.19 0.09
364_A 41_R 0.57 0.19 0.09
203_V 519_A 0.57 0.19 0.09
346_C 24_F 0.57 0.19 0.09
262_Y 31_I 0.57 0.19 0.09
146_I 460_P 0.57 0.18 0.09
117_G 340_E 0.56 0.18 0.08
104_M 558_L 0.56 0.18 0.08
76_N 192_V 0.56 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
6268 1.53 FtsW-FtsI Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.98 Done - Shared
2407 3.07 ftsw-pbp3 d5 Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done
2387 1.09 ftsw-pbp3 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.18 Done
2382 3.32 ftsw-pbp3 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.99 Done
Page generated in 0.1259 seconds.