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OPENSEQ.org
phoPQ (A, 1-110) (B, 265-475)_delta1-2
Genes: A B A+B
Length: 223 486 696
Sequences: 55049 37188 21473
Seq/Len: 246.86 76.52 30.85
MirrorTree (Pazo et al. 2001) 0.98
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 0.09 0.07 29.20
2 0.10 0.08 30.29
5 0.13 0.10 31.17
10 0.16 0.12 31.98
20 0.19 0.14 33.04
100 0.27 0.21 36.52
∞ 0.29 0.24 37.97
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
15_H 288_S 2.84 1.00 1.00
12_L 284_A 2.84 1.00 1.00
104_H 291_R 2.27 1.00 0.99
14_H 302_D 2.26 1.00 0.99
11_L 310_Q 1.54 1.00 0.94
11_L 309_E 1.51 1.00 0.93
11_L 306_V 1.49 1.00 0.93
19_Q 292_S 1.30 0.99 0.86
9_N 285_V 1.25 0.98 0.83
14_H 306_V 1.16 0.97 0.76
22_D 296_E 1.13 0.97 0.74
106_E 295_S 1.07 0.95 0.68
82_E 326_S 1.07 0.95 0.68
15_H 289_T 1.05 0.94 0.66
105_I 291_R 1.03 0.94 0.64
11_L 285_V 1.02 0.93 0.63
18_V 303_A 1.01 0.93 0.61
12_L 285_V 0.97 0.91 0.58
23_A 295_S 0.97 0.91 0.57
21_Q 299_S 0.94 0.89 0.53
22_D 295_S 0.91 0.86 0.49
100_T 280_K 0.89 0.85 0.47
15_H 285_V 0.87 0.83 0.44
103_F 284_A 0.82 0.78 0.38
104_H 312_S 0.82 0.78 0.38
18_V 292_S 0.81 0.77 0.37
9_N 313_R 0.80 0.75 0.35
19_Q 295_S 0.78 0.73 0.33
9_N 281_T 0.74 0.67 0.28
18_V 299_S 0.73 0.65 0.27
104_H 287_Q 0.69 0.60 0.23
12_L 288_S 0.69 0.59 0.23
106_E 291_R 0.69 0.58 0.22
11_L 289_T 0.65 0.53 0.19
53_G 439_R 0.62 0.47 0.16
80_A 280_K 0.62 0.47 0.16
105_I 292_S 0.62 0.47 0.16
81_R 273_T 0.61 0.46 0.15
18_V 302_D 0.57 0.39 0.13
15_H 292_S 0.57 0.39 0.12
22_D 299_S 0.57 0.38 0.12
84_W 291_R 0.56 0.38 0.12
53_G 436_D 0.54 0.34 0.10
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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