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OPENSEQ.org
phoPQ (A, all) (B, all)_delta1-2
Genes: A B A+B
Length: 223 486 685
Sequences: 35860 4346 2370
Seq/Len: 160.81 8.94 3.46
MirrorTree (Pazo et al. 2001) 0.74
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
12_L 284_A 2.70 1.00 1.00
104_H 291_R 2.38 1.00 0.99
15_H 288_S 1.73 0.99 0.96
14_H 306_V 1.42 0.95 0.88
19_Q 292_S 1.34 0.93 0.84
9_N 313_R 1.28 0.91 0.80
100_T 280_K 1.25 0.89 0.78
82_E 326_S 1.23 0.88 0.76
11_L 285_V 1.23 0.88 0.76
11_L 310_Q 1.14 0.82 0.68
36_A 18_L 1.13 0.81 0.67
15_H 289_T 1.09 0.78 0.63
105_I 291_R 1.08 0.77 0.62
106_E 295_S 1.07 0.76 0.61
151_T 40_Y 1.00 0.69 0.52
9_N 285_V 0.98 0.67 0.50
162_I 258_L 0.98 0.66 0.50
106_E 291_R 0.96 0.65 0.48
112_M 292_S 0.95 0.63 0.46
14_H 289_T 0.93 0.61 0.44
14_H 302_D 0.93 0.61 0.44
174_L 246_E 0.91 0.58 0.41
77_V 59_F 0.89 0.56 0.39
179_Y 378_D 0.89 0.56 0.39
189_T 247_L 0.88 0.55 0.38
153_F 444_V 0.88 0.55 0.38
178_L 276_T 0.88 0.54 0.37
105_I 292_S 0.87 0.54 0.37
87_K 314_I 0.86 0.52 0.36
153_F 271_T 0.86 0.52 0.36
92_S 253_N 0.86 0.52 0.36
53_G 274_D 0.86 0.52 0.35
153_F 260_S 0.86 0.52 0.35
9_N 257_L 0.86 0.51 0.35
80_A 281_T 0.85 0.51 0.34
189_T 269_R 0.85 0.51 0.34
100_T 209_L 0.84 0.49 0.33
16_L 222_E 0.83 0.49 0.32
12_L 281_T 0.83 0.48 0.32
50_V 448_V 0.82 0.47 0.31
171_K 315_S 0.82 0.47 0.31
12_L 81_Q 0.82 0.47 0.31
88_V 322_L 0.82 0.46 0.30
199_K 275_L 0.82 0.46 0.30
93_A 291_R 0.79 0.43 0.27
166_G 239_L 0.79 0.43 0.27
194_M 336_E 0.79 0.43 0.27
151_T 449_A 0.78 0.42 0.27
171_K 326_S 0.77 0.41 0.25
5_V 288_S 0.77 0.41 0.25
221_E 447_A 0.77 0.40 0.25
161_L 19_L 0.77 0.40 0.25
196_R 268_Y 0.76 0.39 0.24
151_T 51_L 0.76 0.39 0.24
93_A 435_V 0.76 0.39 0.24
220_F 247_L 0.75 0.38 0.23
11_L 289_T 0.74 0.37 0.23
15_H 306_V 0.74 0.37 0.23
53_G 439_R 0.74 0.37 0.22
72_S 223_A 0.73 0.36 0.22
12_L 313_R 0.73 0.36 0.22
49_I 121_E 0.73 0.36 0.21
5_V 360_V 0.73 0.36 0.21
149_K 338_H 0.73 0.36 0.21
5_V 318_I 0.73 0.35 0.21
145_D 453_T 0.73 0.35 0.21
47_I 422_L 0.73 0.35 0.21
18_V 292_S 0.73 0.35 0.21
64_R 396_E 0.73 0.35 0.21
171_K 202_N 0.72 0.35 0.20
157_I 46_K 0.72 0.34 0.20
197_L 284_A 0.72 0.34 0.20
195_G 268_Y 0.72 0.34 0.20
77_V 457_E 0.72 0.34 0.20
153_F 442_Q 0.72 0.34 0.20
180_P 266_D 0.72 0.34 0.20
75_I 32_Y 0.71 0.34 0.20
190_I 176_V 0.71 0.34 0.20
162_I 283_L 0.71 0.33 0.19
33_A 436_D 0.71 0.33 0.19
108_V 268_Y 0.71 0.33 0.19
174_L 409_L 0.70 0.33 0.19
9_N 303_A 0.70 0.32 0.18
76_L 224_L 0.70 0.32 0.18
33_A 433_Q 0.70 0.32 0.18
9_N 210_L 0.70 0.32 0.18
12_L 285_V 0.70 0.32 0.18
127_I 175_I 0.69 0.31 0.18
104_H 287_Q 0.69 0.31 0.18
173_S 386_V 0.69 0.31 0.18
116_M 250_L 0.69 0.31 0.18
190_I 173_L 0.69 0.31 0.17
177_Q 290_L 0.69 0.31 0.17
88_V 327_M 0.68 0.30 0.17
75_I 441_G 0.68 0.30 0.17
12_L 288_S 0.68 0.30 0.17
15_H 378_D 0.68 0.30 0.17
165_N 22_A 0.68 0.30 0.17
114_A 257_L 0.68 0.30 0.17
196_R 381_E 0.68 0.30 0.17
115_L 232_E 0.68 0.29 0.16
16_L 286_L 0.68 0.29 0.16
102_P 277_H 0.67 0.29 0.16
75_I 49_F 0.67 0.29 0.16
161_L 400_I 0.67 0.29 0.16
190_I 241_P 0.67 0.28 0.16
36_A 98_A 0.67 0.28 0.16
12_L 452_I 0.67 0.28 0.16
201_I 17_F 0.67 0.28 0.16
194_M 159_V 0.67 0.28 0.15
5_V 262_R 0.67 0.28 0.15
90_V 447_A 0.66 0.28 0.15
157_I 452_I 0.66 0.28 0.15
132_F 108_M 0.66 0.28 0.15
171_K 321_Y 0.66 0.28 0.15
99_V 266_D 0.66 0.28 0.15
167_K 228_V 0.66 0.28 0.15
194_M 173_L 0.66 0.28 0.15
171_K 270_T 0.66 0.28 0.15
179_Y 276_T 0.66 0.28 0.15
157_I 83_P 0.66 0.27 0.15
7_E 285_V 0.66 0.27 0.15
210_I 398_V 0.66 0.27 0.15
196_R 318_I 0.66 0.27 0.15
156_T 274_D 0.66 0.27 0.15
64_R 474_V 0.66 0.27 0.15
16_L 162_N 0.66 0.27 0.15
103_F 446_L 0.66 0.27 0.15
168_V 352_N 0.66 0.27 0.15
24_G 250_L 0.65 0.27 0.15
84_W 291_R 0.65 0.27 0.14
190_I 270_T 0.65 0.27 0.14
48_A 450_R 0.65 0.27 0.14
60_L 239_L 0.65 0.27 0.14
12_L 299_S 0.65 0.27 0.14
188_H 258_L 0.65 0.27 0.14
87_K 355_Y 0.65 0.27 0.14
11_L 258_L 0.65 0.26 0.14
36_A 126_V 0.65 0.26 0.14
196_R 310_Q 0.65 0.26 0.14
49_I 341_A 0.65 0.26 0.14
99_V 64_K 0.64 0.26 0.14
23_A 447_A 0.64 0.26 0.14
46_D 220_P 0.64 0.26 0.14
192_V 393_Y 0.64 0.26 0.14
81_R 214_A 0.64 0.25 0.13
72_S 342_P 0.64 0.25 0.13
118_R 385_N 0.64 0.25 0.13
75_I 393_Y 0.64 0.25 0.13
189_T 456_Y 0.64 0.25 0.13
84_W 381_E 0.63 0.25 0.13
105_I 236_R 0.63 0.25 0.13
175_M 268_Y 0.63 0.25 0.13
132_F 352_N 0.63 0.25 0.13
210_I 428_I 0.63 0.25 0.13
213_V 52_L 0.63 0.25 0.13
135_D 34_M 0.63 0.25 0.13
147_V 338_H 0.63 0.25 0.13
168_V 321_Y 0.63 0.25 0.13
6_V 239_L 0.63 0.24 0.13
169_V 24_V 0.63 0.24 0.13
12_L 274_D 0.62 0.24 0.13
115_L 227_E 0.62 0.24 0.13
34_K 359_G 0.62 0.24 0.12
192_V 257_L 0.62 0.24 0.12
21_Q 93_G 0.62 0.24 0.12
18_V 302_D 0.62 0.24 0.12
28_D 244_T 0.62 0.24 0.12
194_M 412_V 0.62 0.24 0.12
179_Y 221_I 0.62 0.24 0.12
75_I 189_Y 0.62 0.24 0.12
151_T 279_L 0.62 0.24 0.12
9_N 228_V 0.62 0.24 0.12
194_M 474_V 0.62 0.24 0.12
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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