May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
elftr222
Genes: A B A+B
Length: 449 318 732
Sequences: 3477 16392 1235
Seq/Len: 7.74 51.55 1.69
MirrorTree (Pazo et al. 2001) 0.11
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 0.04 0.01
2 0.00 0.05 0.03
5 0.00 0.08 0.07
10 0.00 0.12 0.16
20 0.02 0.16 0.32
100 0.03 0.28 0.94
∞ 0.16 0.32 1.61
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
277_V 199_V 0.95 0.42 0.00
377_K 95_N 0.92 0.39 0.00
260_M 137_N 0.91 0.38 0.00
274_T 169_I 0.88 0.35 0.00
255_V 202_V 0.81 0.29 0.00
190_F 93_L 0.75 0.24 0.00
268_F 114_S 0.74 0.23 0.00
344_G 220_A 0.70 0.20 0.00
308_I 248_N 0.70 0.20 0.00
371_S 304_Y 0.68 0.18 0.00
307_D 213_S 0.67 0.18 0.00
206_E 91_L 0.64 0.16 0.00
255_V 288_C 0.63 0.15 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
0536 1.69 elftr222 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0533 0.33 eftr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
Page generated in 0.1217 seconds.