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OPENSEQ.org
ftsw-pbp3 d5
Genes: A B A+B
Length: 414 588 931
Sequences: 5922 11507 2856
Seq/Len: 14.3 19.57 3.07
MirrorTree (Pazo et al. 2001) 0.88
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 2.56 1.00 1.00
312_V 42_V 1.91 0.99 0.98
309_Y 43_A 1.67 0.98 0.94
357_L 34_A 1.52 0.96 0.91
276_L 47_V 1.46 0.95 0.88
366_M 37_F 1.38 0.93 0.84
320_F 35_L 1.36 0.92 0.83
309_Y 47_V 1.29 0.89 0.79
357_L 38_L 1.21 0.85 0.72
360_V 38_L 1.19 0.83 0.70
266_Q 60_R 1.10 0.76 0.61
364_A 42_V 1.03 0.69 0.53
316_L 39_L 0.97 0.62 0.46
232_A 192_V 0.92 0.56 0.40
366_M 38_L 0.91 0.55 0.39
275_E 50_P 0.89 0.52 0.36
309_Y 46_Q 0.87 0.50 0.34
216_G 471_M 0.87 0.49 0.33
353_S 31_I 0.85 0.47 0.32
300_F 42_V 0.82 0.43 0.28
360_V 42_V 0.80 0.41 0.26
286_Q 57_G 0.78 0.39 0.24
324_F 28_C 0.78 0.39 0.24
315_A 236_I 0.78 0.38 0.24
286_Q 60_R 0.76 0.36 0.22
223_I 37_F 0.75 0.35 0.21
361_G 38_L 0.75 0.35 0.21
262_Y 446_I 0.75 0.35 0.21
271_F 45_L 0.73 0.33 0.19
373_T 210_R 0.73 0.32 0.19
382_S 376_L 0.72 0.32 0.18
373_T 499_K 0.71 0.31 0.18
320_F 28_C 0.71 0.30 0.17
119_I 367_L 0.70 0.30 0.17
272_G 53_L 0.70 0.30 0.17
301_A 266_D 0.70 0.30 0.17
317_L 299_I 0.70 0.29 0.17
364_A 41_R 0.69 0.29 0.16
118_S 475_A 0.68 0.28 0.15
382_S 319_Q 0.68 0.28 0.15
309_Y 39_L 0.68 0.27 0.15
309_Y 498_A 0.65 0.25 0.13
200_T 530_V 0.65 0.24 0.13
214_L 27_L 0.64 0.24 0.12
124_I 33_L 0.64 0.24 0.12
282_G 361_N 0.64 0.23 0.12
342_G 20_I 0.64 0.23 0.12
141_L 124_L 0.63 0.23 0.12
59_G 127_R 0.63 0.23 0.12
156_L 356_L 0.63 0.23 0.12
273_R 419_Y 0.63 0.23 0.12
164_L 63_R 0.63 0.23 0.11
98_I 108_D 0.63 0.23 0.11
376_L 87_P 0.62 0.22 0.11
346_C 24_F 0.61 0.21 0.11
243_R 363_G 0.61 0.21 0.10
365_G 399_G 0.60 0.20 0.10
117_G 340_E 0.60 0.20 0.10
103_P 343_D 0.60 0.20 0.10
317_L 32_L 0.60 0.20 0.10
120_I 224_T 0.60 0.20 0.10
183_G 487_K 0.60 0.20 0.10
124_I 522_S 0.59 0.20 0.10
364_A 38_L 0.59 0.20 0.10
394_L 449_V 0.59 0.20 0.09
87_V 340_E 0.59 0.19 0.09
94_I 378_D 0.59 0.19 0.09
316_L 38_L 0.58 0.19 0.09
288_L 219_E 0.58 0.19 0.09
317_L 39_L 0.58 0.19 0.09
210_A 459_F 0.58 0.19 0.09
139_I 45_L 0.58 0.18 0.09
114_M 33_L 0.57 0.18 0.09
107_W 523_Q 0.57 0.18 0.08
226_I 485_A 0.57 0.18 0.08
310_V 502_G 0.57 0.18 0.08
285_V 60_R 0.57 0.18 0.08
146_I 460_P 0.57 0.18 0.08
93_F 198_K 0.57 0.18 0.08
213_F 156_L 0.57 0.18 0.08
91_L 235_S 0.57 0.18 0.08
373_T 182_T 0.57 0.18 0.08
94_I 29_G 0.57 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
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