May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
CheYFliY
Genes: A B A+B
Length: 120 378 465
Sequences: 89189 1134 812
Seq/Len: 743.24 3 1.75
MirrorTree (Pazo et al. 2001) 0.25
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 0.10 0.21 0.51
2 0.13 0.21 0.62
5 0.16 0.22 0.73
10 0.19 0.22 0.97
20 0.23 0.22 1.25
100 0.32 0.27 1.63
∞ 0.34 0.27 1.79
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
7_I 189_V 0.99 0.47 0.00
9_D 321_L 0.94 0.42 0.00
47_S 329_I 0.93 0.41 0.00
47_S 9_D 0.90 0.38 0.00
118_T 126_A 0.89 0.37 0.00
111_V 221_L 0.89 0.36 0.00
49_D 95_T 0.88 0.36 0.00
71_Q 243_K 0.87 0.35 0.00
95_Q 302_I 0.86 0.34 0.00
70_K 53_A 0.86 0.34 0.00
18_I 364_V 0.84 0.32 0.00
115_I 83_F 0.84 0.32 0.00
4_R 141_A 0.84 0.32 0.00
75_Q 238_T 0.83 0.31 0.00
8_V 66_I 0.83 0.31 0.00
3_H 287_E 0.82 0.30 0.00
52_T 57_S 0.81 0.29 0.00
38_Q 209_Y 0.81 0.29 0.00
7_I 274_Q 0.81 0.29 0.00
71_Q 271_A 0.80 0.29 0.00
96_A 92_V 0.80 0.29 0.00
35_N 65_D 0.80 0.28 0.00
111_V 209_Y 0.80 0.28 0.00
51_V 310_L 0.80 0.28 0.00
63_I 122_D 0.79 0.28 0.00
18_I 71_V 0.79 0.28 0.00
71_Q 269_K 0.79 0.27 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
9390 1.88 CheYFliY Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.05 Done - Shared
9388 0.07 CheYFliY Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
9377 1.75 CheYFliY Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
Page generated in 0.2627 seconds.