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OPENSEQ.org
AB
Genes: A B A+B
Length: 267 304 532
Sequences: 14735 2888 2106
Seq/Len: 55.19 9.5 3.96
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 0.02 0.01 3.55
2 0.03 0.11 3.65
5 0.03 0.12 3.67
10 0.05 0.12 3.67
20 0.06 0.12 3.69
100 0.10 0.13 3.73
∞ 0.18 0.13 3.90
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 1.41 0.96 0.67
247_A 289_T 1.36 0.95 0.63
245_S 298_N 0.94 0.66 0.24
43_A 169_I 0.93 0.65 0.23
156_C 133_I 0.92 0.64 0.22
47_G 216_A 0.92 0.64 0.22
29_T 180_M 0.90 0.62 0.21
101_E 24_A 0.85 0.55 0.17
97_G 21_G 0.82 0.50 0.15
141_V 25_L 0.81 0.49 0.14
41_I 267_V 0.81 0.48 0.14
28_G 157_K 0.80 0.47 0.14
124_P 156_E 0.79 0.47 0.14
209_H 287_Y 0.78 0.45 0.13
256_I 128_V 0.76 0.42 0.12
159_F 286_T 0.75 0.41 0.11
91_A 203_A 0.75 0.41 0.11
51_T 290_L 0.75 0.41 0.11
172_E 84_I 0.75 0.41 0.11
50_S 42_G 0.75 0.41 0.11
197_S 284_T 0.74 0.41 0.11
224_R 16_R 0.74 0.40 0.11
184_I 85_L 0.74 0.40 0.11
166_Q 55_N 0.74 0.40 0.11
226_S 177_A 0.73 0.39 0.10
6_L 66_E 0.73 0.39 0.10
186_G 138_Q 0.73 0.39 0.10
206_V 184_A 0.72 0.37 0.10
41_I 228_E 0.72 0.37 0.10
116_L 301_T 0.71 0.36 0.10
192_Y 44_S 0.71 0.36 0.09
168_M 152_K 0.70 0.35 0.09
91_A 211_D 0.70 0.35 0.09
32_A 143_N 0.70 0.35 0.09
152_V 169_I 0.70 0.35 0.09
152_V 125_D 0.70 0.35 0.09
51_T 179_T 0.69 0.34 0.09
76_D 49_I 0.69 0.34 0.09
127_Y 75_I 0.69 0.33 0.08
151_F 110_R 0.68 0.33 0.08
68_L 191_S 0.68 0.32 0.08
224_R 293_L 0.68 0.32 0.08
195_R 117_P 0.68 0.32 0.08
69_M 166_A 0.67 0.32 0.08
204_K 251_R 0.67 0.32 0.08
158_F 207_A 0.67 0.31 0.08
205_D 141_D 0.67 0.31 0.08
116_L 217_K 0.67 0.31 0.08
215_Y 287_Y 0.67 0.31 0.08
171_I 126_L 0.67 0.31 0.08
24_A 300_L 0.67 0.31 0.08
158_F 205_A 0.66 0.31 0.07
220_P 134_I 0.66 0.30 0.07
21_T 85_L 0.66 0.30 0.07
143_A 174_S 0.65 0.30 0.07
150_V 144_V 0.65 0.30 0.07
250_K 109_Q 0.65 0.29 0.07
89_I 208_A 0.65 0.29 0.07
68_L 209_A 0.64 0.28 0.07
154_L 158_F 0.64 0.28 0.07
226_S 75_I 0.64 0.28 0.07
187_V 193_L 0.64 0.28 0.07
259_E 64_R 0.63 0.27 0.07
66_D 299_R 0.63 0.27 0.06
158_F 226_V 0.63 0.27 0.06
196_N 168_T 0.63 0.27 0.06
27_L 141_D 0.63 0.27 0.06
156_C 202_H 0.63 0.27 0.06
197_S 81_L 0.62 0.26 0.06
37_R 231_A 0.62 0.26 0.06
246_Q 174_S 0.62 0.26 0.06
238_Y 151_Y 0.62 0.26 0.06
143_A 290_L 0.62 0.26 0.06
47_G 189_V 0.62 0.26 0.06
159_F 174_S 0.62 0.26 0.06
78_A 275_D 0.62 0.26 0.06
187_V 155_M 0.62 0.26 0.06
173_R 23_S 0.62 0.26 0.06
251_L 130_E 0.62 0.26 0.06
129_L 76_R 0.62 0.26 0.06
67_V 98_I 0.62 0.26 0.06
152_V 46_E 0.62 0.26 0.06
139_L 27_G 0.61 0.25 0.06
133_P 147_E 0.61 0.25 0.06
8_V 132_G 0.61 0.25 0.06
96_S 78_K 0.61 0.25 0.06
158_F 27_G 0.61 0.25 0.06
113_R 51_I 0.61 0.25 0.06
92_D 137_V 0.61 0.25 0.06
188_V 200_A 0.61 0.25 0.06
242_C 130_E 0.61 0.25 0.06
196_N 260_L 0.61 0.25 0.06
169_R 133_I 0.61 0.25 0.06
242_C 28_E 0.61 0.25 0.06
196_N 162_Q 0.61 0.25 0.06
159_F 298_N 0.61 0.25 0.06
71_E 211_D 0.60 0.24 0.06
194_R 97_Q 0.60 0.24 0.06
184_I 75_I 0.60 0.24 0.06
173_R 26_L 0.60 0.24 0.06
69_M 274_I 0.60 0.24 0.06
47_G 192_Y 0.60 0.24 0.06
49_C 166_A 0.60 0.24 0.06
184_I 67_D 0.60 0.24 0.05
147_A 225_S 0.60 0.24 0.05
247_A 175_H 0.60 0.24 0.05
207_R 294_D 0.60 0.24 0.05
247_A 172_S 0.60 0.24 0.05
165_T 27_G 0.60 0.24 0.05
231_F 171_K 0.60 0.24 0.05
187_V 296_L 0.60 0.23 0.05
235_V 184_A 0.59 0.23 0.05
51_T 134_I 0.59 0.23 0.05
238_Y 287_Y 0.59 0.23 0.05
12_A 254_D 0.59 0.23 0.05
28_G 290_L 0.59 0.23 0.05
166_Q 85_L 0.59 0.23 0.05
164_L 276_H 0.59 0.23 0.05
120_R 45_R 0.59 0.23 0.05
218_V 261_E 0.59 0.23 0.05
151_F 67_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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