May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
YidC-Sol YfgMM
Genes: A B A+B
Length: 321 442 714
Sequences: 1608 10879 845
Seq/Len: 5.01 24.61 1.18
MirrorTree (Pazo et al. 2001) 0.21
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 0.07 0.10 0.00
2 0.07 0.11 0.00
5 0.07 0.15 0.01
10 0.07 0.16 0.03
20 0.07 0.19 0.06
100 0.07 0.21 0.20
∞ 0.07 0.27 1.11
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
304_V 367_Y 1.35 0.70 0.01
142_V 59_V 1.09 0.47 0.00
204_E 408_V 1.07 0.44 0.00
107_Y 373_I 1.02 0.40 0.00
304_V 47_K 1.00 0.38 0.00
273_P 365_A 1.00 0.38 0.00
273_P 25_I 1.00 0.38 0.00
294_A 352_M 0.99 0.37 0.00
203_D 248_A 0.97 0.35 0.00
275_Q 31_V 0.96 0.34 0.00
37_I 350_E 0.94 0.33 0.00
44_L 372_T 0.94 0.32 0.00
241_I 400_V 0.91 0.30 0.00
258_G 137_S 0.88 0.28 0.00
141_F 281_A 0.86 0.26 0.00
270_L 23_I 0.86 0.26 0.00
157_Q 343_K 0.85 0.26 0.00
241_I 362_L 0.84 0.25 0.00
108_N 46_F 0.84 0.25 0.00
108_N 208_A 0.83 0.24 0.00
241_I 96_R 0.83 0.24 0.00
238_T 373_I 0.83 0.24 0.00
241_I 32_A 0.83 0.24 0.00
291_D 101_E 0.81 0.22 0.00
141_F 371_L 0.80 0.22 0.00
278_A 224_L 0.79 0.21 0.00
222_I 365_A 0.78 0.21 0.00
55_V 405_V 0.78 0.20 0.00
155_N 4_L 0.77 0.20 0.00
37_I 112_L 0.77 0.20 0.00
252_T 302_S 0.77 0.20 0.00
37_I 23_I 0.77 0.20 0.00
51_R 25_I 0.76 0.19 0.00
141_F 239_H 0.76 0.19 0.00
48_I 181_D 0.75 0.19 0.00
147_D 208_A 0.75 0.19 0.00
37_I 216_A 0.75 0.19 0.00
142_V 23_I 0.75 0.19 0.00
155_N 145_K 0.75 0.19 0.00
36_L 108_L 0.75 0.19 0.00
67_L 46_F 0.75 0.19 0.00
68_N 4_L 0.74 0.18 0.00
119_G 371_L 0.74 0.18 0.00
74_Q 122_V 0.74 0.18 0.00
151_N 4_L 0.73 0.18 0.00
150_V 278_Q 0.73 0.18 0.00
245_D 59_V 0.73 0.17 0.00
75_L 30_I 0.73 0.17 0.00
33_Q 363_L 0.73 0.17 0.00
125_V 372_T 0.73 0.17 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)
Page generated in 0.1832 seconds.