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OPENSEQ.org
FtsW_PBP1b
Genes: A B A+B
Length: 414 844 1164
Sequences: 6194 619 353
Seq/Len: 14.96 0.73 0.3
MirrorTree (Pazo et al. 2001) 0.52
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 0.03 0.00 0.00
2 0.04 0.00 0.00
5 0.04 0.00 0.00
10 0.06 0.00 0.00
20 0.07 0.00 0.01
100 0.11 0.00 0.07
∞ 0.23 0.00 0.28
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
358_V 664_A 1.30 0.29 0.00
141_L 737_S 1.27 0.28 0.00
139_I 763_I 1.27 0.28 0.00
304_G 595_K 1.15 0.22 0.00
247_V 243_I 1.15 0.22 0.00
187_V 279_S 1.13 0.21 0.00
117_G 243_I 1.12 0.20 0.00
302_I 524_P 1.11 0.20 0.00
192_L 617_T 1.09 0.19 0.00
53_F 526_I 1.07 0.18 0.00
376_L 762_D 1.06 0.18 0.00
139_I 642_S 1.03 0.17 0.00
291_L 350_L 1.03 0.17 0.00
121_L 531_T 1.02 0.16 0.00
242_Y 225_L 1.02 0.16 0.00
302_I 498_Y 1.01 0.16 0.00
262_Y 554_D 1.01 0.16 0.00
301_A 488_V 1.01 0.16 0.00
357_L 531_T 1.01 0.16 0.00
256_D 498_Y 1.00 0.16 0.00
109_R 297_M 1.00 0.16 0.00
144_L 331_S 1.00 0.15 0.00
120_I 476_V 0.99 0.15 0.00
191_L 225_L 0.99 0.15 0.00
55_L 268_L 0.99 0.15 0.00
231_S 647_D 0.98 0.15 0.00
288_L 315_Y 0.98 0.15 0.00
352_F 598_V 0.97 0.15 0.00
384_L 142_P 0.97 0.15 0.00
92_A 743_Y 0.97 0.14 0.00
358_V 478_D 0.96 0.14 0.00
193_L 596_L 0.95 0.14 0.00
87_V 643_V 0.95 0.14 0.00
293_E 499_N 0.95 0.14 0.00
377_I 671_L 0.94 0.14 0.00
204_L 762_D 0.94 0.14 0.00
235_L 763_I 0.93 0.13 0.00
301_A 690_Y 0.93 0.13 0.00
307_L 265_A 0.92 0.13 0.00
119_I 742_I 0.92 0.13 0.00
123_M 590_T 0.92 0.13 0.00
154_L 349_L 0.91 0.13 0.00
344_L 317_G 0.91 0.13 0.00
94_I 627_T 0.91 0.13 0.00
117_G 388_Q 0.91 0.13 0.00
349_G 297_M 0.90 0.12 0.00
367_L 618_P 0.90 0.12 0.00
91_L 473_A 0.90 0.12 0.00
272_G 501_A 0.90 0.12 0.00
314_L 526_I 0.90 0.12 0.00
176_R 484_V 0.90 0.12 0.00
301_A 708_T 0.90 0.12 0.00
310_V 57_R 0.90 0.12 0.00
379_Y 275_N 0.90 0.12 0.00
327_M 531_T 0.89 0.12 0.00
154_L 613_A 0.89 0.12 0.00
201_V 258_A 0.89 0.12 0.00
127_V 657_Q 0.89 0.12 0.00
102_L 94_R 0.89 0.12 0.00
376_L 415_M 0.89 0.12 0.00
97_I 644_I 0.89 0.12 0.00
301_A 492_E 0.89 0.12 0.00
393_M 472_T 0.89 0.12 0.00
323_A 471_E 0.88 0.12 0.00
323_A 714_D 0.88 0.12 0.00
190_V 387_D 0.88 0.12 0.00
250_F 626_Q 0.88 0.12 0.00
384_L 274_K 0.88 0.12 0.00
59_G 243_I 0.88 0.12 0.00
82_A 396_A 0.88 0.12 0.00
323_A 219_S 0.87 0.12 0.00
194_A 79_L 0.87 0.12 0.00
349_G 339_V 0.87 0.12 0.00
90_I 763_I 0.87 0.12 0.00
44_Y 283_S 0.87 0.12 0.00
217_A 265_A 0.87 0.12 0.00
200_T 314_V 0.87 0.12 0.00
323_A 124_M 0.87 0.12 0.00
161_A 729_Q 0.87 0.12 0.00
59_G 737_S 0.87 0.12 0.00
116_L 122_N 0.87 0.12 0.00
340_F 762_D 0.87 0.12 0.00
256_D 225_L 0.87 0.12 0.00
141_L 230_L 0.87 0.12 0.00
109_R 622_A 0.87 0.12 0.00
394_L 775_V 0.87 0.12 0.00
223_I 721_T 0.87 0.12 0.00
192_L 577_T 0.86 0.11 0.00
229_G 683_G 0.86 0.11 0.00
310_V 452_K 0.86 0.11 0.00
61_I 164_S 0.86 0.11 0.00
61_I 428_D 0.86 0.11 0.00
250_F 225_L 0.86 0.11 0.00
130_S 703_N 0.86 0.11 0.00
283_N 490_G 0.86 0.11 0.00
361_G 498_Y 0.86 0.11 0.00
388_S 743_Y 0.86 0.11 0.00
309_Y 742_I 0.86 0.11 0.00
307_L 640_L 0.85 0.11 0.00
99_T 556_R 0.85 0.11 0.00
163_Y 202_I 0.85 0.11 0.00
303_I 553_D 0.85 0.11 0.00
397_I 484_V 0.85 0.11 0.00
303_I 279_S 0.85 0.11 0.00
310_V 737_S 0.85 0.11 0.00
377_I 674_M 0.85 0.11 0.00
307_L 674_M 0.85 0.11 0.00
199_G 278_L 0.85 0.11 0.00
301_A 673_T 0.85 0.11 0.00
117_G 620_E 0.85 0.11 0.00
113_T 134_R 0.85 0.11 0.00
315_A 142_P 0.85 0.11 0.00
376_L 479_R 0.85 0.11 0.00
54_G 386_I 0.84 0.11 0.00
376_L 720_I 0.84 0.11 0.00
152_T 702_T 0.84 0.11 0.00
121_L 773_N 0.84 0.11 0.00
256_D 301_Y 0.84 0.11 0.00
301_A 531_T 0.84 0.11 0.00
327_M 371_E 0.84 0.11 0.00
362_A 421_E 0.84 0.11 0.00
366_M 108_G 0.84 0.11 0.00
207_T 265_A 0.84 0.11 0.00
97_I 243_I 0.84 0.11 0.00
154_L 620_E 0.84 0.11 0.00
330_G 667_A 0.83 0.11 0.00
377_I 484_V 0.83 0.11 0.00
157_F 613_A 0.83 0.11 0.00
119_I 49_K 0.83 0.11 0.00
393_M 451_E 0.83 0.11 0.00
299_I 343_S 0.83 0.10 0.00
98_I 55_K 0.83 0.10 0.00
397_I 741_S 0.83 0.10 0.00
291_L 202_I 0.83 0.10 0.00
252_N 670_T 0.83 0.10 0.00
218_K 658_A 0.83 0.10 0.00
322_V 256_L 0.83 0.10 0.00
230_I 380_L 0.83 0.10 0.00
393_M 475_V 0.82 0.10 0.00
209_L 324_I 0.82 0.10 0.00
370_K 355_K 0.82 0.10 0.00
91_L 484_V 0.82 0.10 0.00
389_T 154_M 0.82 0.10 0.00
175_L 617_T 0.82 0.10 0.00
191_L 284_Y 0.82 0.10 0.00
141_L 684_R 0.82 0.10 0.00
301_A 387_D 0.82 0.10 0.00
91_L 571_R 0.82 0.10 0.00
59_G 149_A 0.82 0.10 0.00
253_P 317_G 0.81 0.10 0.00
128_V 468_S 0.81 0.10 0.00
357_L 610_L 0.81 0.10 0.00
309_Y 630_S 0.81 0.10 0.00
162_N 243_I 0.81 0.10 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
13000 0.01 FTSW PBP1b complex Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6263 0.02 FtsW_PBP1B Δgene:(1, 100) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed
4024 0.3 FtsW_PBP1b Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4022 0.09 FtsW_PBP1b Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3935 0.02 FtsW_PBP1b Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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