May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
HisF_HisH_aCrePar
Genes: A B A+B
Length: 251 191 430
Sequences: 4748 2926 2262
Seq/Len: 18.92 15.32 5.26
MirrorTree (Pazo et al. 2001) 0.55
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 0.50 0.00 4.47
2 0.55 0.00 4.81
5 0.56 0.00 4.96
10 0.58 0.00 5.00
20 0.58 0.01 5.01
100 0.59 0.01 5.12
∞ 0.64 0.02 5.56
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
122_G 175_G 0.71 0.43 0.00
105_T 11_V 0.70 0.42 0.00
169_I 151_L 0.65 0.35 0.00
6_I 155_Y 0.63 0.33 0.00
69_R 134_Y 0.63 0.32 0.00
105_T 17_V 0.58 0.27 0.00
102_S 166_G 0.57 0.25 0.00
224_A 182_I 0.56 0.24 0.00
100_K 45_L 0.56 0.24 0.00
205_A 21_L 0.55 0.23 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.59 > 0.4) of paralogs.
Page generated in 0.0553 seconds.