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OPENSEQ.org
PArB-ParA CC
Genes: A B A+B
Length: 304 267 532
Sequences: 2905 17234 2106
Seq/Len: 9.56 64.55 3.96
MirrorTree (Pazo et al. 2001) 0.63
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 0.03 3.55
2 0.11 0.03 3.65
5 0.12 0.04 3.67
10 0.12 0.06 3.68
20 0.12 0.07 3.69
100 0.13 0.12 3.75
∞ 0.13 0.18 3.93
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 1.39 0.96 0.63
17_G 224_R 1.35 0.94 0.60
298_N 245_S 0.98 0.71 0.25
133_I 156_C 0.98 0.70 0.25
216_A 47_G 0.95 0.68 0.23
180_M 29_T 0.90 0.60 0.19
156_E 124_P 0.89 0.59 0.18
169_I 43_A 0.87 0.57 0.17
24_A 101_E 0.86 0.56 0.17
21_G 97_G 0.80 0.48 0.13
25_L 141_V 0.80 0.48 0.13
203_A 91_A 0.79 0.47 0.12
55_N 166_Q 0.79 0.46 0.12
157_K 28_G 0.78 0.45 0.12
267_V 41_I 0.77 0.44 0.12
42_G 50_S 0.76 0.42 0.11
138_Q 186_G 0.76 0.42 0.11
290_L 51_T 0.75 0.41 0.10
128_V 256_I 0.74 0.40 0.10
84_I 172_E 0.74 0.39 0.10
152_K 168_M 0.72 0.38 0.09
284_T 197_S 0.72 0.38 0.09
286_T 159_F 0.72 0.37 0.09
228_E 41_I 0.72 0.37 0.09
179_T 51_T 0.72 0.37 0.09
287_Y 209_H 0.71 0.36 0.09
301_T 116_L 0.70 0.35 0.09
85_L 184_I 0.70 0.35 0.08
125_D 152_V 0.70 0.35 0.08
143_N 32_A 0.70 0.35 0.08
184_A 206_V 0.68 0.33 0.08
208_A 89_I 0.68 0.32 0.08
16_R 224_R 0.68 0.32 0.07
174_S 143_A 0.67 0.32 0.07
207_A 158_F 0.67 0.32 0.07
117_P 195_R 0.67 0.31 0.07
75_I 127_Y 0.67 0.31 0.07
110_R 151_F 0.67 0.31 0.07
75_I 226_S 0.67 0.31 0.07
141_D 205_D 0.67 0.31 0.07
126_L 171_I 0.67 0.31 0.07
130_E 251_L 0.67 0.31 0.07
175_H 247_A 0.66 0.31 0.07
226_V 158_F 0.66 0.30 0.07
205_A 158_F 0.66 0.30 0.07
299_R 66_D 0.66 0.30 0.07
274_I 69_M 0.66 0.30 0.07
172_S 247_A 0.66 0.30 0.07
85_L 21_T 0.66 0.30 0.07
168_T 196_N 0.66 0.30 0.07
225_S 147_A 0.65 0.30 0.07
177_A 226_S 0.65 0.30 0.07
66_E 6_L 0.65 0.29 0.07
28_E 242_C 0.65 0.29 0.07
155_M 187_V 0.65 0.29 0.07
65_E 219_I 0.65 0.29 0.07
217_K 116_L 0.65 0.29 0.07
287_Y 215_Y 0.65 0.29 0.07
147_E 133_P 0.65 0.29 0.07
49_I 76_D 0.65 0.29 0.07
64_R 259_E 0.65 0.29 0.07
169_I 152_V 0.65 0.29 0.07
27_G 139_L 0.65 0.29 0.06
109_Q 250_K 0.64 0.28 0.06
234_R 24_A 0.64 0.28 0.06
191_S 68_L 0.64 0.28 0.06
254_D 12_A 0.64 0.28 0.06
293_L 224_R 0.64 0.28 0.06
202_H 156_C 0.64 0.28 0.06
158_F 154_L 0.64 0.28 0.06
44_S 192_Y 0.64 0.28 0.06
211_D 71_E 0.64 0.28 0.06
26_L 173_R 0.64 0.28 0.06
174_S 159_F 0.63 0.27 0.06
166_A 69_M 0.63 0.27 0.06
81_L 197_S 0.63 0.27 0.06
78_K 96_S 0.63 0.27 0.06
134_I 220_P 0.62 0.26 0.06
141_D 27_L 0.62 0.26 0.06
209_A 68_L 0.62 0.26 0.06
85_L 166_Q 0.62 0.26 0.06
200_A 188_V 0.61 0.25 0.06
192_Y 47_G 0.61 0.25 0.06
75_I 184_I 0.61 0.25 0.06
23_S 173_R 0.61 0.25 0.06
144_V 150_V 0.61 0.25 0.06
46_E 152_V 0.61 0.25 0.06
166_A 259_E 0.61 0.25 0.06
193_L 187_V 0.61 0.25 0.06
137_V 92_D 0.61 0.25 0.05
67_D 184_I 0.61 0.25 0.05
133_I 169_R 0.60 0.24 0.05
296_L 25_I 0.60 0.24 0.05
260_L 196_N 0.60 0.24 0.05
170_G 214_V 0.60 0.24 0.05
151_Y 238_Y 0.60 0.24 0.05
130_E 242_C 0.60 0.24 0.05
134_I 51_T 0.60 0.24 0.05
189_V 47_G 0.60 0.24 0.05
237_P 204_K 0.60 0.24 0.05
67_D 151_F 0.60 0.24 0.05
109_Q 124_P 0.60 0.24 0.05
210_A 181_R 0.60 0.24 0.05
300_L 24_A 0.60 0.24 0.05
53_Q 242_C 0.60 0.23 0.05
162_Q 196_N 0.60 0.23 0.05
275_D 78_A 0.59 0.23 0.05
211_D 91_A 0.59 0.23 0.05
97_Q 194_R 0.59 0.23 0.05
201_G 140_T 0.59 0.23 0.05
50_E 257_S 0.59 0.23 0.05
132_G 8_V 0.59 0.23 0.05
27_G 165_T 0.59 0.23 0.05
171_K 231_F 0.59 0.23 0.05
261_E 218_V 0.59 0.23 0.05
87_R 189_L 0.59 0.23 0.05
69_E 35_G 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
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