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OPENSEQ.org
3PNLA
Genes: A B A+B
Length: 357 211 542
Sequences: 1718 2044 1656
Seq/Len: 4.81 9.69 3.06
MirrorTree (Pazo et al. 2001) 0.76
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 2.85
2 0.07 0.05 2.89
5 0.09 0.05 2.91
10 0.10 0.05 2.92
20 0.10 0.05 2.92
100 0.11 0.06 2.92
∞ 0.14 0.09 2.93
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
120_L 90_I 1.20 0.84 0.11
108_T 182_Y 1.12 0.78 0.09
115_E 121_R 1.06 0.72 0.07
49_L 43_M 1.00 0.65 0.06
147_G 182_Y 0.98 0.63 0.06
85_D 75_S 0.95 0.59 0.05
119_E 121_R 0.95 0.59 0.05
119_E 91_R 0.94 0.58 0.05
123_D 90_I 0.94 0.57 0.05
123_D 94_Q 0.90 0.53 0.04
187_S 96_T 0.85 0.47 0.04
80_T 45_R 0.85 0.47 0.04
152_A 37_A 0.84 0.46 0.03
105_K 81_S 0.84 0.46 0.03
120_L 71_M 0.80 0.41 0.03
154_T 81_S 0.78 0.39 0.03
212_M 43_M 0.78 0.38 0.03
80_T 42_N 0.77 0.37 0.03
120_L 75_S 0.77 0.37 0.03
301_L 15_R 0.77 0.37 0.03
127_K 165_S 0.76 0.36 0.03
36_V 132_C 0.75 0.35 0.02
194_A 32_R 0.74 0.34 0.02
77_E 73_L 0.74 0.34 0.02
70_L 182_Y 0.73 0.33 0.02
147_G 181_S 0.73 0.33 0.02
115_E 123_K 0.72 0.32 0.02
58_E 79_G 0.71 0.31 0.02
8_D 109_Q 0.71 0.30 0.02
236_V 207_L 0.70 0.30 0.02
61_H 182_Y 0.70 0.29 0.02
80_T 73_L 0.70 0.29 0.02
133_I 81_S 0.69 0.28 0.02
307_Q 105_E 0.69 0.28 0.02
132_V 84_L 0.68 0.28 0.02
153_N 37_A 0.68 0.27 0.02
204_S 32_R 0.68 0.27 0.02
108_T 39_H 0.68 0.27 0.02
324_L 111_F 0.67 0.27 0.02
115_E 80_A 0.67 0.27 0.02
61_H 81_S 0.67 0.27 0.02
19_G 78_G 0.67 0.27 0.02
138_A 193_P 0.66 0.26 0.02
84_P 39_H 0.66 0.26 0.02
187_S 206_A 0.66 0.25 0.02
17_L 124_A 0.66 0.25 0.02
306_Q 140_E 0.66 0.25 0.02
226_R 62_I 0.66 0.25 0.02
22_K 18_D 0.65 0.25 0.02
50_L 108_Y 0.65 0.24 0.02
84_P 197_S 0.65 0.24 0.02
27_L 158_A 0.65 0.24 0.02
111_I 45_R 0.64 0.24 0.02
342_A 22_T 0.64 0.23 0.01
131_V 157_E 0.64 0.23 0.01
35_Y 13_L 0.63 0.23 0.01
352_A 79_G 0.63 0.23 0.01
245_V 153_P 0.63 0.23 0.01
187_S 177_K 0.62 0.22 0.01
241_D 105_E 0.62 0.22 0.01
172_D 15_R 0.62 0.22 0.01
74_C 37_A 0.62 0.21 0.01
50_L 157_E 0.61 0.21 0.01
348_V 32_R 0.61 0.21 0.01
172_D 157_E 0.61 0.21 0.01
49_L 22_T 0.61 0.21 0.01
245_V 18_D 0.61 0.21 0.01
179_R 56_A 0.61 0.21 0.01
204_S 135_W 0.61 0.21 0.01
111_I 197_S 0.60 0.20 0.01
105_K 182_Y 0.60 0.20 0.01
154_T 182_Y 0.60 0.20 0.01
116_T 43_M 0.60 0.20 0.01
58_E 78_G 0.59 0.20 0.01
272_P 19_I 0.59 0.20 0.01
182_N 44_N 0.59 0.19 0.01
214_F 25_E 0.58 0.19 0.01
202_K 29_G 0.58 0.19 0.01
104_I 182_Y 0.58 0.19 0.01
84_P 83_P 0.58 0.19 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)
ID Seq/Len Name Options I_Prob Status
7278 1.5 3PNLA Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.03 Done - Shared
7269 3.06 3PNLA Δgene:(0, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.11 Done - Shared
7244 1.6 3PNLA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.07 Done - Shared
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