May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_K_cIV_cyoc2_2_Ecoli
Genes: A B A+B
Length: 100 204 292
Sequences: 5077 4744 2886
Seq/Len: 50.77 23.25 9.88
MirrorTree (Pazo et al. 2001) 0.48
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 0.00 0.03 0.12
2 0.00 0.03 2.16
5 0.01 0.03 5.10
10 0.01 0.04 5.71
20 0.02 0.04 5.96
100 0.03 0.05 6.55
∞ 0.07 0.08 9.49
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
73_A 75_L 1.13 0.97 0.16
65_A 64_F 1.01 0.93 0.11
92_I 26_I 0.93 0.88 0.08
67_S 135_F 0.92 0.88 0.08
73_A 96_S 0.84 0.80 0.06
44_L 74_F 0.83 0.78 0.06
44_L 23_G 0.81 0.77 0.06
44_L 62_D 0.80 0.75 0.05
30_F 78_F 0.79 0.73 0.05
43_A 167_R 0.76 0.70 0.04
70_A 64_F 0.76 0.69 0.04
67_S 198_V 0.75 0.68 0.04
33_I 117_I 0.74 0.66 0.04
68_L 100_S 0.72 0.64 0.04
88_Q 52_N 0.72 0.64 0.04
74_S 118_Y 0.71 0.62 0.04
68_L 74_F 0.71 0.62 0.04
18_G 86_A 0.70 0.60 0.04
41_A 37_C 0.69 0.59 0.03
73_A 64_F 0.68 0.57 0.03
94_S 68_F 0.67 0.56 0.03
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
2763 9.88 cI_K_cIV_cyoc2_2_Ecoli Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
2762 9.81 cI_K_cIV_cyoc2_Ecoli Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
2760 2.92 cI_K_cIV_cyoc20_Ecoli Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2751 9.4 cI_K_cIV_cyoc_Ecoli Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
Page generated in 0.039 seconds.