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OPENSEQ.org
1EFP_A_B
Genes: A B A+B
Length: 307 252 555
Sequences: 3025 2626 2366
Seq/Len: 9.85 10.42 4.26
MirrorTree (Pazo et al. 2001) 0.90
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 4.20
2 0.01 0.01 4.23
5 0.01 0.01 4.24
10 0.01 0.01 4.23
20 0.02 0.02 4.23
100 0.03 0.03 4.26
∞ 0.09 0.08 4.30
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
175_S 171_A 4.19 1.00 1.00
104_L 137_A 3.34 1.00 1.00
100_R 137_A 2.95 1.00 1.00
136_K 220_E 2.71 1.00 1.00
306_K 240_D 2.15 1.00 0.99
106_D 103_K 1.98 1.00 0.99
274_V 242_L 1.92 1.00 0.98
109_V 130_A 1.81 1.00 0.97
179_D 168_Q 1.70 0.99 0.96
134_V 223_S 1.70 0.99 0.96
123_E 225_R 1.70 0.99 0.96
100_R 143_Q 1.67 0.99 0.96
103_A 134_M 1.66 0.99 0.96
178_A 169_T 1.55 0.98 0.93
173_L 140_G 1.50 0.98 0.92
306_K 243_V 1.42 0.97 0.90
69_A 143_Q 1.33 0.95 0.85
173_L 142_A 1.30 0.94 0.84
290_Y 242_L 1.30 0.94 0.84
177_V 169_T 1.28 0.93 0.82
177_V 171_A 1.23 0.91 0.79
103_A 138_I 1.18 0.89 0.75
108_M 97_E 1.10 0.84 0.68
174_S 170_I 1.07 0.81 0.65
131_A 224_V 1.00 0.75 0.56
292_L 239_V 0.99 0.74 0.55
96_N 143_Q 0.99 0.74 0.55
74_A 140_G 0.98 0.73 0.54
136_K 222_V 0.96 0.71 0.52
104_L 140_G 0.95 0.69 0.50
131_A 19_V 0.94 0.69 0.50
99_P 129_N 0.93 0.67 0.48
111_S 130_A 0.92 0.66 0.47
111_S 128_M 0.92 0.66 0.47
106_D 138_I 0.90 0.63 0.44
272_V 249_A 0.89 0.62 0.43
294_G 116_L 0.89 0.62 0.43
303_L 243_V 0.88 0.60 0.41
138_K 220_E 0.86 0.58 0.39
127_Y 25_G 0.86 0.58 0.39
194_R 211_Y 0.84 0.55 0.36
211_I 17_A 0.83 0.54 0.35
96_N 145_T 0.82 0.52 0.34
177_V 158_K 0.81 0.51 0.33
99_P 36_N 0.80 0.50 0.31
201_G 58_I 0.79 0.49 0.31
180_E 169_T 0.78 0.47 0.29
173_L 173_S 0.78 0.47 0.29
271_K 249_A 0.77 0.46 0.28
175_S 173_S 0.77 0.46 0.28
132_I 225_R 0.76 0.45 0.27
292_L 236_V 0.76 0.45 0.27
121_T 222_V 0.76 0.44 0.27
69_A 170_I 0.75 0.43 0.26
145_T 24_S 0.75 0.43 0.26
99_P 144_A 0.73 0.41 0.24
109_V 128_M 0.73 0.41 0.24
225_S 195_I 0.73 0.40 0.24
291_G 198_A 0.73 0.40 0.24
147_R 36_N 0.72 0.39 0.23
243_T 180_A 0.71 0.38 0.22
170_D 142_A 0.71 0.38 0.22
73_A 137_A 0.71 0.38 0.22
195_V 131_T 0.71 0.38 0.22
229_V 127_D 0.71 0.38 0.22
279_D 199_K 0.71 0.37 0.21
152_D 251_V 0.70 0.37 0.21
93_D 170_I 0.70 0.36 0.20
274_V 160_T 0.69 0.35 0.20
273_I 230_R 0.68 0.34 0.19
233_Y 6_P 0.68 0.34 0.19
134_V 222_V 0.67 0.33 0.18
307_L 247_K 0.67 0.33 0.18
264_L 77_A 0.67 0.33 0.18
300_V 105_L 0.67 0.32 0.18
271_K 202_P 0.67 0.32 0.18
230_D 188_R 0.66 0.32 0.17
195_V 244_G 0.66 0.32 0.17
133_Q 221_V 0.65 0.31 0.17
195_V 118_I 0.65 0.31 0.17
108_M 219_L 0.65 0.30 0.16
125_P 127_D 0.65 0.30 0.16
106_D 99_L 0.64 0.30 0.16
124_R 127_D 0.64 0.29 0.15
94_A 42_A 0.64 0.29 0.15
69_A 137_A 0.63 0.29 0.15
243_T 14_N 0.63 0.28 0.15
95_K 146_F 0.63 0.28 0.15
278_K 199_K 0.62 0.28 0.14
133_Q 224_V 0.62 0.28 0.14
113_V 101_V 0.62 0.27 0.14
180_E 158_K 0.62 0.27 0.14
108_M 218_R 0.62 0.27 0.14
280_E 168_Q 0.62 0.27 0.14
280_E 118_I 0.61 0.27 0.14
240_V 182_L 0.61 0.26 0.13
255_V 192_L 0.61 0.26 0.13
299_V 157_A 0.60 0.26 0.13
18_T 47_I 0.60 0.26 0.13
21_A 88_A 0.60 0.26 0.13
99_P 130_A 0.60 0.25 0.13
134_V 225_R 0.60 0.25 0.13
146_I 6_P 0.59 0.24 0.12
38_A 86_V 0.59 0.24 0.12
90_A 127_D 0.59 0.24 0.12
236_N 135_L 0.59 0.24 0.12
242_Q 124_I 0.58 0.24 0.12
276_I 61_V 0.58 0.23 0.12
274_V 245_K 0.58 0.23 0.11
151_F 162_E 0.58 0.23 0.11
62_A 247_K 0.58 0.23 0.11
305_G 178_V 0.58 0.23 0.11
286_Q 190_A 0.58 0.23 0.11
149_A 224_V 0.58 0.23 0.11
144_F 4_L 0.58 0.23 0.11
7_E 166_G 0.58 0.23 0.11
172_G 140_G 0.58 0.23 0.11
134_V 145_T 0.57 0.23 0.11
145_T 130_A 0.57 0.23 0.11
270_S 49_L 0.57 0.22 0.11
276_I 222_V 0.57 0.22 0.11
90_A 28_L 0.57 0.22 0.11
180_E 163_V 0.57 0.22 0.11
307_L 171_A 0.57 0.22 0.11
226_R 44_E 0.57 0.22 0.11
223_G 109_A 0.57 0.22 0.10
128_A 26_V 0.57 0.22 0.10
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
7247 4.26 1EFP_A_B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
3656 4.54 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
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