May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
yubA-yubB
Genes: A B A+B
Length: 388 276 585
Sequences: 5320 3169 1511
Seq/Len: 13.71 11.48 2.58
MirrorTree (Pazo et al. 2001) 0.26
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 0.07 0.02
2 0.00 0.07 0.02
5 0.00 0.07 0.06
10 0.01 0.07 0.09
20 0.01 0.07 0.12
100 0.03 0.08 0.44
∞ 0.14 0.11 2.28
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
254_I 157_Y 0.99 0.58 0.00
124_D 239_V 0.92 0.50 0.00
348_I 10_A 0.86 0.44 0.00
306_I 235_I 0.85 0.42 0.00
128_N 266_I 0.83 0.40 0.00
183_I 266_I 0.83 0.40 0.00
94_I 11_I 0.81 0.38 0.00
287_I 169_L 0.81 0.38 0.00
97_I 28_G 0.80 0.36 0.00
137_N 237_A 0.79 0.35 0.00
72_V 237_A 0.79 0.35 0.00
47_I 102_V 0.77 0.33 0.00
183_I 28_G 0.77 0.33 0.00
97_I 33_V 0.76 0.33 0.00
263_L 15_V 0.76 0.33 0.00
168_T 232_V 0.76 0.32 0.00
51_L 245_V 0.76 0.32 0.00
92_L 250_R 0.76 0.32 0.00
59_I 152_L 0.75 0.32 0.00
92_L 7_F 0.74 0.30 0.00
61_T 245_V 0.74 0.30 0.00
110_E 266_I 0.74 0.30 0.00
85_S 270_I 0.73 0.30 0.00
266_I 153_D 0.73 0.29 0.00
146_M 106_V 0.73 0.29 0.00
264_A 204_M 0.72 0.28 0.00
128_N 14_I 0.72 0.28 0.00
242_F 70_D 0.72 0.28 0.00
301_V 99_V 0.71 0.28 0.00
360_I 58_L 0.71 0.28 0.00
192_I 97_I 0.71 0.28 0.00
298_L 7_F 0.71 0.27 0.00
367_W 161_I 0.71 0.27 0.00
209_K 266_I 0.70 0.27 0.00
273_V 151_T 0.70 0.27 0.00
332_I 215_L 0.70 0.26 0.00
232_S 165_L 0.70 0.26 0.00
335_L 182_I 0.69 0.26 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
11069 0.14 yubA-yubB_morestringent Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
11064 2.58 yubA-yubB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
Page generated in 0.1068 seconds.