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OPENSEQ.org
3rlf_E_G
Genes: A B A+B
Length: 380 296 644
Sequences: 15263 21436 1624
Seq/Len: 40.17 72.42 2.52
MirrorTree (Pazo et al. 2001) 0.71
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 0.44 0.23
2 0.02 0.44 2.31
5 0.04 0.45 2.38
10 0.07 0.46 2.39
20 0.10 0.47 2.40
100 0.18 0.49 2.44
∞ 0.25 0.51 2.49
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
46_K 238_R 1.14 0.74 0.03
266_I 93_G 1.01 0.60 0.02
45_E 91_V 0.98 0.57 0.02
57_P 278_F 0.97 0.56 0.02
30_D 194_L 0.96 0.55 0.02
228_G 278_F 0.96 0.54 0.02
122_L 264_A 0.95 0.54 0.01
100_N 286_V 0.94 0.52 0.01
186_A 163_I 0.88 0.45 0.01
55_D 145_D 0.88 0.45 0.01
106_Y 230_V 0.85 0.42 0.01
312_A 205_L 0.84 0.40 0.01
5_G 283_R 0.82 0.39 0.01
50_V 238_R 0.81 0.37 0.01
137_K 276_I 0.78 0.34 0.01
361_L 130_M 0.77 0.33 0.01
166_G 108_Y 0.77 0.33 0.01
187_G 188_L 0.77 0.33 0.01
35_V 60_K 0.77 0.33 0.01
140_K 59_W 0.76 0.32 0.01
55_D 141_Y 0.76 0.31 0.01
197_D 91_V 0.75 0.31 0.01
156_F 289_L 0.75 0.30 0.01
364_A 98_G 0.74 0.30 0.01
163_A 114_R 0.74 0.29 0.01
27_F 138_V 0.74 0.29 0.01
106_Y 218_V 0.73 0.29 0.01
125_P 232_V 0.73 0.29 0.01
274_E 206_V 0.73 0.29 0.01
244_V 285_L 0.72 0.28 0.01
197_D 19_L 0.72 0.28 0.01
236_D 219_F 0.72 0.28 0.01
52_A 139_A 0.72 0.28 0.01
162_A 131_F 0.71 0.27 0.01
278_E 187_S 0.71 0.27 0.01
54_G 296_G 0.71 0.27 0.01
76_L 163_I 0.71 0.27 0.01
188_A 289_L 0.71 0.27 0.01
187_G 158_T 0.70 0.26 0.01
105_A 230_V 0.70 0.26 0.01
230_W 248_G 0.70 0.26 0.01
366_T 125_M 0.69 0.25 0.01
191_G 91_V 0.69 0.25 0.01
230_W 278_F 0.69 0.25 0.01
168_A 263_F 0.69 0.25 0.01
143_G 204_R 0.69 0.25 0.01
68_G 194_L 0.69 0.25 0.01
129_W 104_T 0.68 0.24 0.01
49_Q 138_V 0.68 0.24 0.01
202_K 283_R 0.68 0.24 0.01
233_S 116_P 0.68 0.24 0.01
354_R 194_L 0.68 0.24 0.01
161_I 22_L 0.67 0.24 0.01
186_A 164_F 0.67 0.23 0.01
129_W 107_A 0.67 0.23 0.01
362_K 101_A 0.67 0.23 0.01
288_E 249_M 0.67 0.23 0.01
230_W 203_F 0.67 0.23 0.01
303_A 276_I 0.66 0.23 0.01
82_D 158_T 0.66 0.23 0.01
85_F 206_V 0.66 0.23 0.01
118_N 289_L 0.66 0.23 0.01
92_F 222_S 0.66 0.23 0.01
298_P 158_T 0.66 0.22 0.01
186_A 187_S 0.66 0.22 0.01
124_N 15_I 0.66 0.22 0.01
151_L 293_G 0.66 0.22 0.01
80_T 283_R 0.66 0.22 0.01
24_G 248_G 0.65 0.22 0.01
235_I 109_A 0.65 0.22 0.01
96_A 269_M 0.65 0.22 0.01
119_K 60_K 0.65 0.22 0.01
53_T 39_L 0.65 0.22 0.01
33_I 88_S 0.65 0.21 0.01
193_T 194_L 0.64 0.21 0.01
191_G 37_I 0.64 0.21 0.01
341_Y 267_A 0.64 0.21 0.01
337_S 191_A 0.64 0.21 0.01
322_E 101_A 0.64 0.21 0.01
241_N 93_G 0.64 0.21 0.01
233_S 24_I 0.64 0.21 0.01
163_A 277_V 0.64 0.21 0.01
187_G 277_V 0.64 0.21 0.01
268_A 57_D 0.64 0.21 0.01
156_F 285_L 0.64 0.21 0.01
325_Q 82_L 0.64 0.21 0.01
55_D 157_N 0.64 0.21 0.01
119_K 25_A 0.64 0.21 0.01
51_A 234_S 0.64 0.21 0.01
135_L 272_L 0.64 0.21 0.01
276_A 223_F 0.64 0.20 0.01
89_L 164_F 0.64 0.20 0.01
100_N 119_A 0.64 0.20 0.01
128_T 176_T 0.63 0.20 0.01
36_T 241_N 0.63 0.20 0.01
100_N 53_Q 0.63 0.20 0.01
246_V 282_Q 0.63 0.20 0.01
301_A 259_L 0.63 0.20 0.01
49_Q 39_L 0.63 0.20 0.01
77_A 200_W 0.63 0.20 0.01
278_E 110_F 0.63 0.20 0.01
106_Y 145_D 0.63 0.20 0.01
261_V 130_M 0.63 0.20 0.01
313_K 276_I 0.63 0.20 0.01
266_I 86_W 0.62 0.20 0.01
26_K 206_V 0.62 0.20 0.01
45_E 215_L 0.62 0.20 0.01
231_A 249_M 0.62 0.20 0.01
37_V 107_A 0.62 0.19 0.01
356_T 147_L 0.62 0.19 0.01
130_E 60_K 0.62 0.19 0.01
83_K 276_I 0.62 0.19 0.01
226_I 233_A 0.62 0.19 0.01
25_K 198_T 0.62 0.19 0.01
53_T 137_L 0.62 0.19 0.01
29_K 57_D 0.61 0.19 0.01
276_A 110_F 0.61 0.19 0.01
54_G 18_L 0.61 0.19 0.01
195_L 145_D 0.61 0.19 0.01
345_T 141_Y 0.61 0.19 0.01
366_T 241_N 0.61 0.19 0.01
15_K 210_L 0.61 0.19 0.01
53_T 142_A 0.61 0.19 0.01
53_T 286_V 0.61 0.18 0.01
338_A 200_W 0.61 0.18 0.01
246_V 91_V 0.61 0.18 0.01
138_E 235_L 0.61 0.18 0.01
34_K 102_L 0.61 0.18 0.01
62_W 207_L 0.61 0.18 0.01
241_N 164_F 0.61 0.18 0.01
246_V 213_P 0.61 0.18 0.01
246_V 103_S 0.61 0.18 0.01
58_D 295_K 0.60 0.18 0.01
257_P 208_L 0.60 0.18 0.01
18_N 276_I 0.60 0.18 0.01
71_A 113_M 0.60 0.18 0.01
36_T 167_L 0.60 0.18 0.01
222_T 88_S 0.60 0.18 0.01
210_Y 161_G 0.60 0.18 0.01
126_P 97_I 0.60 0.18 0.01
28_E 59_W 0.60 0.18 0.01
361_L 161_G 0.60 0.18 0.01
221_E 62_A 0.60 0.18 0.01
97_V 206_V 0.60 0.18 0.01
132_I 232_V 0.60 0.18 0.01
30_D 93_G 0.60 0.18 0.01
146_A 128_F 0.60 0.18 0.01
73_S 55_S 0.60 0.18 0.01
89_L 158_T 0.59 0.17 0.01
7_L 205_L 0.59 0.17 0.01
266_I 190_E 0.59 0.17 0.01
221_E 124_G 0.59 0.17 0.01
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.47 > 0.4) of paralogs.
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