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OPENSEQ.org
PhoPQ
Genes: A B A+B
Length: 223 486 687
Sequences: 35860 4346 2641
Seq/Len: 160.81 8.94 3.84
MirrorTree (Pazo et al. 2001) 0.53
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 0.01 3.32
2 0.02 0.01 3.34
5 0.04 0.01 3.42
10 0.06 0.01 3.55
20 0.10 0.02 3.72
100 0.20 0.06 4.55
∞ 0.25 0.16 5.43
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
104_H 291_R 2.03 1.00 0.98
12_L 284_A 1.93 1.00 0.98
15_H 288_S 1.41 0.96 0.87
14_H 306_V 1.25 0.91 0.77
100_T 280_K 1.18 0.87 0.71
82_E 326_S 1.12 0.83 0.66
9_N 313_R 1.11 0.82 0.64
11_L 285_V 1.05 0.77 0.58
19_Q 292_S 0.99 0.70 0.50
16_L 222_E 0.90 0.60 0.40
11_L 310_Q 0.90 0.60 0.39
151_T 449_A 0.89 0.58 0.38
15_H 289_T 0.87 0.56 0.36
112_M 292_S 0.82 0.49 0.30
153_F 260_S 0.82 0.49 0.30
100_T 209_L 0.81 0.49 0.29
194_M 336_E 0.81 0.48 0.29
36_A 18_L 0.80 0.47 0.28
12_L 281_T 0.79 0.46 0.27
105_I 291_R 0.79 0.45 0.26
14_H 289_T 0.78 0.45 0.26
151_T 40_Y 0.78 0.44 0.26
87_K 314_I 0.77 0.43 0.25
179_Y 378_D 0.77 0.43 0.25
116_M 250_L 0.76 0.42 0.24
189_T 269_R 0.75 0.41 0.23
5_V 360_V 0.74 0.40 0.22
11_L 289_T 0.74 0.39 0.22
14_H 302_D 0.74 0.39 0.22
34_K 359_G 0.74 0.39 0.22
9_N 285_V 0.74 0.39 0.22
148_I 363_S 0.73 0.38 0.21
149_K 338_H 0.73 0.38 0.21
77_V 457_E 0.73 0.38 0.21
171_K 315_S 0.72 0.37 0.20
9_N 257_L 0.72 0.36 0.20
93_A 435_V 0.71 0.36 0.20
178_L 276_T 0.71 0.36 0.19
29_D 212_V 0.71 0.35 0.19
174_L 246_E 0.71 0.35 0.19
77_V 59_F 0.70 0.34 0.18
12_L 288_S 0.70 0.34 0.18
53_G 274_D 0.69 0.33 0.17
153_F 442_Q 0.68 0.32 0.17
36_A 281_T 0.68 0.32 0.17
157_I 83_P 0.68 0.32 0.17
16_L 87_L 0.68 0.32 0.17
106_E 291_R 0.68 0.32 0.17
190_I 241_P 0.68 0.32 0.17
12_L 313_R 0.68 0.32 0.16
100_T 452_I 0.68 0.31 0.16
189_T 247_L 0.67 0.31 0.16
5_V 288_S 0.67 0.31 0.16
145_D 421_P 0.67 0.31 0.16
153_F 444_V 0.67 0.31 0.16
194_M 474_V 0.67 0.31 0.16
18_V 292_S 0.67 0.31 0.16
17_K 421_P 0.67 0.31 0.16
75_I 253_N 0.67 0.30 0.16
12_L 274_D 0.67 0.30 0.15
213_V 52_L 0.67 0.30 0.15
173_S 386_V 0.66 0.30 0.15
108_V 268_Y 0.66 0.30 0.15
166_G 239_L 0.66 0.29 0.15
23_A 447_A 0.65 0.29 0.14
180_P 266_D 0.65 0.29 0.14
36_A 216_W 0.65 0.29 0.14
6_V 239_L 0.65 0.28 0.14
210_I 398_V 0.65 0.28 0.14
180_P 464_E 0.65 0.28 0.14
66_W 453_T 0.65 0.28 0.14
12_L 452_I 0.65 0.28 0.14
167_K 228_V 0.64 0.28 0.14
162_I 258_L 0.64 0.28 0.14
174_L 70_L 0.64 0.28 0.14
15_H 306_V 0.64 0.27 0.14
106_E 295_S 0.64 0.27 0.13
47_I 179_D 0.64 0.27 0.13
29_D 203_L 0.63 0.27 0.13
132_F 104_W 0.63 0.27 0.13
91_L 393_Y 0.63 0.27 0.13
12_L 81_Q 0.63 0.27 0.13
33_A 433_Q 0.63 0.26 0.13
201_I 17_F 0.63 0.26 0.13
104_H 287_Q 0.63 0.26 0.13
207_Q 398_V 0.63 0.26 0.13
190_I 173_L 0.62 0.26 0.12
213_V 290_L 0.62 0.26 0.12
196_R 268_Y 0.62 0.25 0.12
93_A 291_R 0.62 0.25 0.12
199_K 275_L 0.62 0.25 0.12
80_A 281_T 0.62 0.25 0.12
45_P 375_E 0.62 0.25 0.12
12_L 299_S 0.62 0.25 0.12
9_N 292_S 0.61 0.25 0.12
204_Q 205_L 0.61 0.25 0.12
168_V 321_Y 0.61 0.24 0.12
83_S 280_K 0.61 0.24 0.12
168_V 352_N 0.61 0.24 0.12
128_S 19_L 0.61 0.24 0.11
135_D 34_M 0.61 0.24 0.11
196_R 451_E 0.61 0.24 0.11
93_A 205_L 0.61 0.24 0.11
151_T 51_L 0.61 0.24 0.11
88_V 322_L 0.60 0.24 0.11
15_H 378_D 0.60 0.23 0.11
87_K 392_K 0.60 0.23 0.11
115_L 232_E 0.60 0.23 0.11
202_Q 372_F 0.60 0.23 0.11
40_L 298_M 0.60 0.23 0.11
81_R 214_A 0.60 0.23 0.11
171_K 326_S 0.60 0.23 0.11
60_L 239_L 0.60 0.23 0.11
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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