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OPENSEQ.org
ParA-ParB
Genes: A B A+B
Length: 267 304 532
Sequences: 16068 2887 2100
Seq/Len: 60.18 9.5 3.95
MirrorTree (Pazo et al. 2001) 0.62
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 0.02 0.01 3.54
2 0.03 0.11 3.65
5 0.03 0.12 3.68
10 0.05 0.12 3.69
20 0.06 0.12 3.68
100 0.11 0.13 3.74
∞ 0.18 0.13 3.89
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
224_R 17_G 1.37 0.95 0.58
247_A 289_T 1.33 0.94 0.55
156_C 133_I 1.01 0.74 0.26
47_G 216_A 1.00 0.72 0.25
29_T 180_M 0.98 0.71 0.24
245_S 298_N 0.97 0.70 0.23
43_A 169_I 0.93 0.65 0.20
101_E 24_A 0.85 0.55 0.15
166_Q 55_N 0.84 0.54 0.14
91_A 203_A 0.84 0.53 0.14
124_P 156_E 0.84 0.53 0.14
172_E 84_I 0.81 0.49 0.13
209_H 287_Y 0.80 0.48 0.12
28_G 157_K 0.80 0.47 0.12
97_G 21_G 0.79 0.46 0.11
184_I 85_L 0.78 0.45 0.11
141_V 25_L 0.77 0.44 0.11
41_I 267_V 0.77 0.44 0.11
168_M 152_K 0.76 0.43 0.10
32_A 143_N 0.75 0.41 0.10
186_G 138_Q 0.75 0.41 0.10
159_F 286_T 0.74 0.40 0.09
51_T 290_L 0.74 0.40 0.09
158_F 226_V 0.74 0.39 0.09
197_S 284_T 0.73 0.39 0.09
41_I 228_E 0.73 0.39 0.09
195_R 117_P 0.73 0.39 0.09
226_S 177_A 0.73 0.38 0.09
51_T 179_T 0.72 0.38 0.09
256_I 128_V 0.72 0.38 0.09
50_S 42_G 0.72 0.37 0.08
158_F 207_A 0.71 0.37 0.08
147_A 225_S 0.71 0.37 0.08
158_F 205_A 0.71 0.37 0.08
91_A 211_D 0.70 0.35 0.08
127_Y 75_I 0.70 0.35 0.08
206_V 184_A 0.70 0.35 0.08
152_V 125_D 0.70 0.35 0.08
156_C 202_H 0.70 0.35 0.08
251_L 130_E 0.69 0.34 0.07
116_L 301_T 0.69 0.34 0.07
171_I 126_L 0.69 0.34 0.07
247_A 172_S 0.69 0.34 0.07
196_N 168_T 0.69 0.33 0.07
215_Y 287_Y 0.69 0.33 0.07
159_F 174_S 0.68 0.33 0.07
224_R 293_L 0.68 0.33 0.07
133_P 147_E 0.68 0.32 0.07
143_A 174_S 0.68 0.32 0.07
196_N 260_L 0.68 0.32 0.07
242_C 28_E 0.68 0.32 0.07
154_L 158_F 0.67 0.31 0.07
150_V 144_V 0.67 0.31 0.07
152_V 169_I 0.67 0.31 0.07
220_P 134_I 0.67 0.31 0.07
116_L 217_K 0.67 0.31 0.07
224_R 16_R 0.67 0.31 0.07
139_L 27_G 0.66 0.30 0.07
47_G 192_Y 0.66 0.30 0.06
226_S 75_I 0.65 0.29 0.06
189_L 87_R 0.65 0.29 0.06
68_L 209_A 0.65 0.29 0.06
51_T 134_I 0.65 0.29 0.06
184_I 67_D 0.65 0.29 0.06
6_L 66_E 0.65 0.29 0.06
69_M 274_I 0.65 0.29 0.06
166_Q 85_L 0.65 0.29 0.06
69_M 166_A 0.64 0.28 0.06
151_F 110_R 0.64 0.28 0.06
241_K 199_T 0.64 0.28 0.06
89_I 208_A 0.64 0.28 0.06
11_I 225_S 0.64 0.28 0.06
197_S 81_L 0.64 0.27 0.06
10_A 105_W 0.63 0.27 0.06
247_A 175_H 0.63 0.27 0.06
24_A 300_L 0.63 0.27 0.06
47_G 147_E 0.63 0.27 0.06
140_T 201_G 0.63 0.27 0.06
68_L 191_S 0.63 0.27 0.06
187_V 193_L 0.63 0.27 0.06
173_R 26_L 0.63 0.27 0.05
196_N 162_Q 0.62 0.26 0.05
250_K 109_Q 0.62 0.26 0.05
71_E 211_D 0.62 0.26 0.05
21_T 85_L 0.62 0.26 0.05
10_A 72_S 0.62 0.26 0.05
238_Y 151_Y 0.62 0.26 0.05
192_Y 44_S 0.62 0.26 0.05
8_V 132_G 0.62 0.26 0.05
231_F 129_L 0.62 0.26 0.05
214_V 170_G 0.62 0.26 0.05
96_S 78_K 0.62 0.26 0.05
184_I 75_I 0.61 0.25 0.05
12_A 254_D 0.61 0.25 0.05
152_V 46_E 0.61 0.25 0.05
41_I 46_E 0.61 0.25 0.05
187_V 296_L 0.61 0.25 0.05
165_T 27_G 0.61 0.25 0.05
66_D 299_R 0.61 0.25 0.05
204_K 251_R 0.61 0.25 0.05
205_D 141_D 0.61 0.25 0.05
196_N 287_Y 0.61 0.25 0.05
76_D 49_I 0.61 0.24 0.05
173_R 23_S 0.61 0.24 0.05
169_R 133_I 0.60 0.24 0.05
108_R 25_L 0.60 0.24 0.05
127_Y 66_E 0.60 0.24 0.05
129_L 76_R 0.60 0.24 0.05
47_G 189_V 0.60 0.24 0.05
242_C 130_E 0.60 0.24 0.05
49_C 166_A 0.60 0.24 0.05
37_R 231_A 0.60 0.24 0.05
92_D 137_V 0.60 0.24 0.05
222_N 287_Y 0.60 0.24 0.05
24_A 203_A 0.60 0.24 0.05
256_I 210_A 0.60 0.23 0.05
43_A 180_M 0.59 0.23 0.05
96_S 177_A 0.59 0.23 0.05
29_T 27_G 0.59 0.23 0.05
96_S 172_S 0.59 0.23 0.05
194_R 97_Q 0.59 0.23 0.05
238_Y 287_Y 0.59 0.23 0.05
218_V 91_D 0.59 0.23 0.05
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
8225 3.95 ParA-ParB Δgene:(1, 5) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.58 Done
6897 3.96 AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.67 Done - Shared
4212 4.73 CCparA-parB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
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