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OPENSEQ.org
Sec Y - PpiD (E coli) 20
Genes: A B A+B
Length: 437 102 517
Sequences: 2581 6378 1117
Seq/Len: 5.91 62.53 2.16
MirrorTree (Pazo et al. 2001) 0.12
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 0.05 0.00
5 0.01 0.06 0.00
10 0.01 0.07 0.01
20 0.01 0.08 0.02
100 0.02 0.10 0.37
∞ 0.03 0.19 2.07
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
27_I 21_A 1.16 0.71 0.02
130_G 69_L 1.15 0.70 0.01
380_I 8_Y 1.03 0.58 0.01
158_V 75_L 0.98 0.53 0.01
217_L 88_V 0.97 0.52 0.01
126_F 66_N 0.94 0.47 0.01
157_V 51_D 0.86 0.38 0.01
69_S 80_K 0.84 0.37 0.01
42_A 34_A 0.84 0.37 0.01
288_S 14_K 0.84 0.37 0.01
360_K 21_A 0.82 0.35 0.01
128_S 25_E 0.80 0.32 0.01
91_L 11_I 0.80 0.32 0.01
240_I 34_A 0.80 0.32 0.01
78_I 13_T 0.79 0.32 0.01
192_V 75_L 0.79 0.32 0.01
339_A 47_R 0.79 0.31 0.01
35_I 6_T 0.77 0.29 0.01
362_I 13_T 0.77 0.29 0.01
418_T 95_A 0.76 0.29 0.01
362_I 72_K 0.76 0.29 0.01
365_V 63_E 0.75 0.28 0.01
20_L 87_I 0.74 0.27 0.01
35_I 58_A 0.74 0.27 0.01
374_A 80_K 0.74 0.27 0.01
186_I 15_T 0.74 0.27 0.01
379_F 79_I 0.73 0.26 0.01
242_V 63_E 0.73 0.26 0.01
91_L 36_A 0.73 0.26 0.01
380_I 80_K 0.73 0.26 0.01
299_L 79_I 0.73 0.26 0.01
339_A 38_E 0.72 0.25 0.00
162_T 39_K 0.72 0.25 0.00
420_M 45_S 0.71 0.25 0.00
326_F 39_K 0.71 0.24 0.00
221_V 75_L 0.71 0.24 0.00
322_I 35_L 0.70 0.23 0.00
101_I 67_A 0.69 0.23 0.00
74_F 75_L 0.69 0.23 0.00
193_A 22_V 0.69 0.23 0.00
349_V 7_R 0.69 0.23 0.00
69_S 39_K 0.69 0.23 0.00
56_I 62_D 0.69 0.22 0.00
179_I 28_K 0.68 0.22 0.00
379_F 34_A 0.68 0.22 0.00
287_A 69_L 0.68 0.22 0.00
331_L 22_V 0.67 0.21 0.00
119_G 17_D 0.67 0.21 0.00
18_R 38_E 0.67 0.21 0.00
88_I 71_E 0.67 0.21 0.00
154_F 18_E 0.66 0.21 0.00
386_F 28_K 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
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