May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
HisF_HisH_aCrePae
Genes: A B A+B
Length: 253 190 422
Sequences: 4826 13843 2275
Seq/Len: 19.08 72.86 5.39
MirrorTree (Pazo et al. 2001) 0.46
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 0.51 0.03 4.37
2 0.58 0.03 4.75
5 0.60 0.04 4.97
10 0.62 0.04 5.02
20 0.63 0.05 5.14
100 0.63 0.11 5.72
∞ 0.67 0.20 6.87
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
103_V 9_T 0.70 0.43 0.00
70_K 42_V 0.70 0.43 0.00
88_S 115_H 0.67 0.38 0.00
212_H 126_G 0.66 0.37 0.00
77_S 22_R 0.65 0.36 0.00
8_I 154_Y 0.63 0.34 0.00
65_F 109_I 0.63 0.33 0.00
107_T 16_V 0.60 0.30 0.00
107_T 10_V 0.60 0.29 0.00
102_K 44_L 0.60 0.29 0.00
6_R 124_A 0.58 0.27 0.00
224_V 105_K 0.57 0.26 0.00
104_S 165_G 0.56 0.25 0.00
226_A 181_I 0.56 0.25 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 (0.63 > 0.4) of paralogs.
Page generated in 0.0574 seconds.