May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
Sec Y - PpiD (E coli) 30
Genes: A B A+B
Length: 437 102 517
Sequences: 2573 6898 1156
Seq/Len: 5.89 67.63 2.24
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 0.01 0.04 0.00
2 0.01 0.06 0.00
5 0.01 0.06 0.01
10 0.01 0.07 0.01
20 0.01 0.08 0.03
100 0.02 0.11 0.39
∞ 0.03 0.20 2.14
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
158_V 75_L 1.05 0.61 0.00
28_V 75_L 1.05 0.61 0.00
217_L 59_T 0.92 0.46 0.00
31_I 8_Y 0.90 0.44 0.00
375_L 68_G 0.88 0.42 0.00
362_I 72_K 0.87 0.41 0.00
380_I 8_Y 0.86 0.39 0.00
27_I 21_A 0.82 0.35 0.00
35_I 6_T 0.81 0.35 0.00
126_F 66_N 0.81 0.34 0.00
83_S 4_Q 0.81 0.34 0.00
186_I 15_T 0.79 0.32 0.00
339_A 38_E 0.77 0.31 0.00
326_F 39_K 0.77 0.30 0.00
132_A 11_I 0.76 0.30 0.00
75_A 24_D 0.76 0.29 0.00
369_L 85_F 0.76 0.29 0.00
69_S 80_K 0.75 0.29 0.00
42_A 34_A 0.75 0.28 0.00
240_I 34_A 0.75 0.28 0.00
379_F 34_A 0.74 0.27 0.00
45_L 49_G 0.73 0.27 0.00
386_F 28_K 0.72 0.26 0.00
37_I 6_T 0.72 0.26 0.00
220_A 17_D 0.71 0.25 0.00
24_G 24_D 0.71 0.25 0.00
217_L 88_V 0.70 0.24 0.00
276_A 87_I 0.70 0.24 0.00
322_I 35_L 0.70 0.24 0.00
221_V 22_V 0.70 0.24 0.00
43_A 66_N 0.70 0.24 0.00
360_K 21_A 0.69 0.23 0.00
337_E 39_K 0.69 0.23 0.00
157_V 51_D 0.68 0.23 0.00
111_K 36_A 0.68 0.22 0.00
380_I 80_K 0.68 0.22 0.00
37_I 82_S 0.68 0.22 0.00
430_K 30_G 0.68 0.22 0.00
315_L 92_D 0.68 0.22 0.00
303_S 8_Y 0.67 0.21 0.00
160_L 15_T 0.66 0.21 0.00
337_E 17_D 0.66 0.21 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
13316 2.24 Sec Y - PpiD (E coli) 30 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13281 2.16 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.02 Done - Shared
13273 0 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed - Shared
13272 0 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed - Shared
13270 0 Sec Y - PpiD (E coli) 20 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
13265 0.02 Sec Y - PpiD (E coli) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.1373 seconds.