May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
WbaP_RfbX
Genes: A B A+B
Length: 476 430 885
Sequences: 2789 25347 1399
Seq/Len: 5.86 58.95 1.58
MirrorTree (Pazo et al. 2001) 0.27
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 0.00 0.01 0.10
2 0.00 0.02 0.18
5 0.01 0.03 0.46
10 0.01 0.05 1.07
20 0.02 0.08 1.54
100 0.04 0.15 1.95
∞ 0.11 0.22 2.53
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
369_I 199_V 1.07 0.53 0.00
306_V 311_L 0.99 0.44 0.00
334_S 378_I 0.89 0.35 0.00
64_V 104_L 0.89 0.34 0.00
314_I 70_Q 0.88 0.34 0.00
384_L 203_S 0.88 0.34 0.00
19_I 351_G 0.87 0.33 0.00
431_V 388_G 0.85 0.31 0.00
376_I 251_V 0.85 0.31 0.00
394_D 87_I 0.85 0.31 0.00
148_K 60_A 0.85 0.31 0.00
287_C 95_F 0.83 0.29 0.00
23_I 27_G 0.81 0.28 0.00
151_I 98_I 0.81 0.27 0.00
376_I 239_L 0.80 0.26 0.00
301_Y 323_I 0.79 0.26 0.00
19_I 405_L 0.78 0.25 0.00
325_K 394_F 0.78 0.25 0.00
300_I 408_I 0.78 0.25 0.00
313_A 355_C 0.77 0.24 0.00
369_I 361_D 0.77 0.24 0.00
310_G 399_G 0.77 0.24 0.00
313_A 331_F 0.76 0.23 0.00
314_I 86_Y 0.76 0.23 0.00
178_F 179_I 0.75 0.23 0.00
315_Y 103_A 0.73 0.21 0.00
454_T 196_Y 0.73 0.21 0.00
425_M 287_P 0.72 0.21 0.00
149_T 243_V 0.72 0.21 0.00
378_K 98_I 0.72 0.21 0.00
390_V 69_L 0.72 0.20 0.00
167_S 325_L 0.72 0.20 0.00
286_V 323_I 0.71 0.20 0.00
391_L 50_L 0.71 0.20 0.00
87_L 141_S 0.71 0.20 0.00
301_Y 31_A 0.71 0.20 0.00
369_I 359_W 0.70 0.20 0.00
161_A 35_Y 0.70 0.20 0.00
315_Y 257_T 0.70 0.19 0.00
128_V 13_I 0.70 0.19 0.00
127_L 240_L 0.70 0.19 0.00
64_V 225_I 0.69 0.19 0.00
313_A 229_R 0.69 0.19 0.00
301_Y 236_L 0.69 0.19 0.00
330_Y 351_G 0.69 0.18 0.00
226_W 402_G 0.69 0.18 0.00
213_L 23_I 0.69 0.18 0.00
128_V 83_Y 0.69 0.18 0.00
371_A 199_V 0.69 0.18 0.00
282_T 28_V 0.69 0.18 0.00
314_I 13_I 0.69 0.18 0.00
240_V 63_F 0.69 0.18 0.00
462_L 317_V 0.69 0.18 0.00
238_V 351_G 0.68 0.18 0.00
292_L 289_C 0.68 0.18 0.00
378_K 304_M 0.68 0.18 0.00
388_F 267_T 0.68 0.18 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
13680 1.58 WbaP_RfbX Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
13679 0 WbaP_RfbX Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.0949 seconds.