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OPENSEQ.org
phoPQ
Genes: A B A+B
Length: 223 486 696
Sequences: 37839 25909 13822
Seq/Len: 169.68 53.31 19.86
MirrorTree (Pazo et al. 2001) 0.97
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 0.01 0.01 19.50
2 0.02 0.02 20.20
5 0.05 0.03 20.78
10 0.08 0.04 21.37
20 0.12 0.06 22.11
100 0.24 0.17 24.71
∞ 0.29 0.22 25.79
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
12_L 284_A 3.33 1.00 1.00
15_H 288_S 2.89 1.00 1.00
104_H 291_R 2.63 1.00 1.00
14_H 302_D 2.17 1.00 0.99
11_L 310_Q 1.57 1.00 0.95
19_Q 292_S 1.50 1.00 0.93
11_L 309_E 1.39 0.99 0.90
11_L 306_V 1.36 0.99 0.89
9_N 285_V 1.33 0.99 0.88
12_L 285_V 1.17 0.97 0.78
82_E 326_S 1.15 0.97 0.76
80_A 280_K 1.14 0.97 0.75
14_H 306_V 1.13 0.97 0.74
15_H 289_T 1.09 0.96 0.70
18_V 303_A 1.06 0.95 0.68
106_E 295_S 1.06 0.95 0.67
23_A 295_S 1.03 0.94 0.65
105_I 291_R 1.02 0.93 0.63
100_T 280_K 1.00 0.93 0.61
53_G 439_R 1.00 0.92 0.60
9_N 313_R 0.99 0.92 0.59
22_D 296_E 0.98 0.91 0.58
19_Q 295_S 0.97 0.91 0.57
11_L 285_V 0.90 0.85 0.48
103_F 284_A 0.89 0.85 0.47
84_W 291_R 0.85 0.81 0.42
9_N 281_T 0.85 0.81 0.42
15_H 285_V 0.81 0.77 0.37
22_D 295_S 0.80 0.76 0.36
53_G 436_D 0.78 0.73 0.33
12_L 288_S 0.77 0.72 0.32
195_G 431_R 0.70 0.60 0.24
80_A 281_T 0.69 0.59 0.23
81_R 273_T 0.69 0.59 0.23
53_G 281_T 0.69 0.58 0.22
79_T 274_D 0.68 0.58 0.22
188_H 258_L 0.68 0.57 0.22
18_V 292_S 0.67 0.55 0.20
105_I 292_S 0.66 0.54 0.20
188_H 310_Q 0.66 0.54 0.20
104_H 312_S 0.66 0.53 0.19
105_I 295_S 0.66 0.53 0.19
106_E 291_R 0.66 0.53 0.19
21_Q 299_S 0.64 0.50 0.17
63_I 272_L 0.62 0.48 0.17
191_D 310_Q 0.62 0.46 0.16
7_E 285_V 0.61 0.46 0.15
7_E 289_T 0.61 0.45 0.15
191_D 278_S 0.60 0.44 0.15
53_G 432_G 0.60 0.43 0.14
54_L 322_L 0.58 0.41 0.13
186_E 290_L 0.58 0.40 0.13
18_V 302_D 0.58 0.40 0.13
12_L 281_T 0.57 0.39 0.12
104_H 287_Q 0.57 0.38 0.12
81_R 281_T 0.56 0.37 0.12
18_V 289_T 0.55 0.36 0.11
87_K 281_T 0.55 0.35 0.11
11_L 289_T 0.55 0.35 0.11
188_H 278_S 0.55 0.35 0.11
79_T 268_Y 0.54 0.34 0.10
7_E 324_R 0.54 0.33 0.10
171_K 220_P 0.53 0.32 0.10
192_V 392_K 0.52 0.31 0.09
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
10955 3.84 PhoPQ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.98 Done - Shared
5226 3.46 phoPQ (A, all) (B, all)_delta1-2 Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done
5215 30.85 phoPQ (A, 1-110) (B, 265-475)_delta1-2 Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done
1239 3.38 PQ Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 1.00 Done
0685 19.86 phoPQ Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 1.00 Done
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