May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
PArB-ParA CC
Genes: A B A+B
Length: 304 267 532
Sequences: 2888 14735 2104
Seq/Len: 9.5 55.19 3.95
MirrorTree (Pazo et al. 2001) 0.61
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 0.02 3.55
2 0.11 0.03 3.64
5 0.12 0.03 3.68
10 0.12 0.05 3.67
20 0.12 0.06 3.68
100 0.13 0.10 3.73
∞ 0.13 0.18 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
289_T 247_A 1.37 0.95 0.60
17_G 224_R 1.36 0.95 0.59
133_I 156_C 0.97 0.69 0.23
180_M 29_T 0.96 0.68 0.23
216_A 47_G 0.95 0.68 0.22
298_N 245_S 0.91 0.63 0.19
169_I 43_A 0.89 0.60 0.18
24_A 101_E 0.84 0.53 0.15
21_G 97_G 0.84 0.53 0.14
156_E 124_P 0.81 0.49 0.13
25_L 141_V 0.81 0.49 0.13
55_N 166_Q 0.79 0.46 0.12
290_L 51_T 0.78 0.45 0.11
138_Q 186_G 0.77 0.44 0.11
157_K 28_G 0.77 0.43 0.11
203_A 91_A 0.76 0.43 0.11
286_T 159_F 0.76 0.43 0.11
84_I 172_E 0.76 0.42 0.10
42_G 50_S 0.75 0.41 0.10
75_I 127_Y 0.74 0.40 0.10
184_A 206_V 0.74 0.40 0.10
284_T 197_S 0.73 0.39 0.09
152_K 168_M 0.72 0.38 0.09
179_T 51_T 0.72 0.38 0.09
128_V 256_I 0.72 0.37 0.09
177_A 226_S 0.71 0.37 0.09
301_T 116_L 0.71 0.36 0.08
287_Y 209_H 0.71 0.36 0.08
85_L 184_I 0.71 0.36 0.08
125_D 152_V 0.71 0.36 0.08
267_V 41_I 0.71 0.36 0.08
49_I 76_D 0.69 0.34 0.08
169_I 152_V 0.69 0.34 0.08
117_P 195_R 0.69 0.34 0.08
191_S 68_L 0.69 0.34 0.08
228_E 41_I 0.69 0.33 0.07
207_A 158_F 0.69 0.33 0.07
143_N 32_A 0.69 0.33 0.07
211_D 91_A 0.68 0.33 0.07
172_S 247_A 0.68 0.33 0.07
16_R 224_R 0.68 0.33 0.07
293_L 224_R 0.68 0.32 0.07
225_S 147_A 0.68 0.32 0.07
66_E 6_L 0.67 0.31 0.07
217_K 116_L 0.67 0.31 0.07
205_A 158_F 0.66 0.30 0.07
26_L 173_R 0.66 0.30 0.07
175_H 247_A 0.66 0.30 0.07
109_Q 250_K 0.66 0.30 0.07
141_D 205_D 0.66 0.30 0.07
85_L 21_T 0.65 0.29 0.06
147_E 133_P 0.65 0.29 0.06
168_T 196_N 0.65 0.29 0.06
130_E 251_L 0.65 0.29 0.06
110_R 151_F 0.65 0.29 0.06
81_L 197_S 0.64 0.28 0.06
28_E 242_C 0.64 0.28 0.06
193_L 187_V 0.64 0.28 0.06
126_L 171_I 0.64 0.28 0.06
166_A 69_M 0.64 0.28 0.06
274_I 69_M 0.64 0.28 0.06
192_Y 47_G 0.64 0.28 0.06
287_Y 215_Y 0.64 0.28 0.06
78_K 96_S 0.64 0.28 0.06
158_F 154_L 0.64 0.28 0.06
211_D 71_E 0.64 0.28 0.06
202_H 156_C 0.64 0.28 0.06
290_L 28_G 0.63 0.27 0.06
226_V 158_F 0.63 0.27 0.06
144_V 150_V 0.63 0.27 0.06
209_A 68_L 0.63 0.27 0.06
44_S 192_Y 0.63 0.27 0.06
254_D 12_A 0.63 0.27 0.06
155_M 187_V 0.63 0.27 0.06
72_S 10_A 0.62 0.26 0.06
208_A 89_I 0.62 0.26 0.06
75_I 226_S 0.62 0.26 0.05
137_V 92_D 0.62 0.26 0.05
27_G 139_L 0.62 0.26 0.05
174_S 143_A 0.62 0.26 0.05
46_E 152_V 0.62 0.26 0.05
85_L 166_Q 0.61 0.25 0.05
275_D 78_A 0.61 0.25 0.05
141_D 27_L 0.61 0.25 0.05
64_R 259_E 0.61 0.25 0.05
134_I 220_P 0.61 0.25 0.05
67_D 151_F 0.61 0.25 0.05
133_I 169_R 0.61 0.25 0.05
260_L 196_N 0.61 0.25 0.05
98_I 67_V 0.61 0.25 0.05
200_A 188_V 0.61 0.25 0.05
171_K 231_F 0.61 0.25 0.05
189_V 47_G 0.61 0.24 0.05
23_S 173_R 0.60 0.24 0.05
186_P 154_L 0.60 0.24 0.05
151_Y 238_Y 0.60 0.24 0.05
65_E 219_I 0.60 0.24 0.05
174_S 159_F 0.60 0.24 0.05
180_M 43_A 0.60 0.24 0.05
290_L 143_A 0.60 0.24 0.05
70_D 194_R 0.60 0.23 0.05
170_G 214_V 0.60 0.23 0.05
231_A 37_R 0.59 0.23 0.05
67_D 184_I 0.59 0.23 0.05
234_R 24_A 0.59 0.23 0.05
27_G 158_F 0.59 0.23 0.05
130_E 242_C 0.59 0.23 0.05
108_A 153_P 0.59 0.23 0.05
284_T 94_D 0.59 0.23 0.05
109_Q 124_P 0.59 0.23 0.05
134_I 51_T 0.59 0.23 0.05
234_R 258_R 0.59 0.23 0.05
261_E 218_V 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
8032 3.89 PArB-ParA CC Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.68 Done
8031 3.94 PArB-ParA CC Δgene:(1, 20) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.69 Done
8030 3.96 PArB-ParA CC Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2015_06) 0.63 Done
6327 3.95 PArB-ParA CC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.60 Done - Shared
Page generated in 1.0941 seconds.