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OPENSEQ.org
2Y69_BC
Genes: A B A+B
Length: 227 259 483
Sequences: 4332 2510 1464
Seq/Len: 19.08 9.69 3.03
MirrorTree (Pazo et al. 2001) 0.84
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 0.28
2 0.01 0.01 0.49
5 0.01 0.01 2.75
10 0.01 0.01 2.94
20 0.01 0.01 3.01
100 0.02 0.01 3.05
∞ 0.07 0.01 3.10
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
4_P 226_T 1.37 0.92 0.46
36_S 148_S 1.13 0.78 0.26
169_G 139_G 0.98 0.62 0.16
65_W 146_H 0.95 0.59 0.14
155_S 90_L 0.94 0.58 0.14
156_S 35_F 0.94 0.57 0.14
144_L 125_L 0.93 0.57 0.14
202_S 196_F 0.93 0.57 0.14
18_E 248_L 0.93 0.57 0.14
27_T 32_W 0.91 0.54 0.13
39_L 89_V 0.89 0.51 0.12
206_F 191_Y 0.88 0.51 0.11
194_G 88_E 0.88 0.50 0.11
23_F 196_F 0.87 0.49 0.11
191_L 189_G 0.86 0.49 0.10
99_T 28_G 0.85 0.47 0.10
74_I 19_A 0.85 0.47 0.10
99_T 215_V 0.85 0.46 0.10
211_L 259_S 0.84 0.46 0.10
98_K 73_V 0.84 0.45 0.09
15_P 248_L 0.84 0.45 0.09
182_T 24_L 0.83 0.45 0.09
165_V 98_A 0.83 0.44 0.09
160_L 4_H 0.83 0.44 0.09
61_V 245_V 0.82 0.43 0.09
118_F 145_A 0.82 0.43 0.09
85_Y 9_V 0.81 0.42 0.09
55_T 101_H 0.81 0.42 0.09
182_T 23_L 0.81 0.42 0.08
143_V 90_L 0.81 0.42 0.08
25_D 14_W 0.81 0.41 0.08
24_H 224_H 0.80 0.40 0.08
223_S 208_I 0.80 0.40 0.08
65_W 238_W 0.80 0.40 0.08
203_N 61_R 0.79 0.40 0.08
154_V 34_H 0.79 0.40 0.08
57_D 90_L 0.79 0.39 0.08
215_P 163_I 0.78 0.39 0.07
70_A 77_L 0.78 0.38 0.07
85_Y 57_R 0.78 0.38 0.07
80_S 97_W 0.78 0.38 0.07
155_S 44_G 0.78 0.38 0.07
19_E 127_V 0.78 0.38 0.07
74_I 207_I 0.77 0.37 0.07
16_I 237_A 0.77 0.37 0.07
6_Q 3_T 0.76 0.36 0.07
43_S 169_V 0.76 0.36 0.07
211_L 157_M 0.76 0.36 0.07
184_L 11_P 0.76 0.36 0.07
76_I 4_H 0.76 0.36 0.07
99_T 130_L 0.76 0.35 0.07
130_P 166_T 0.76 0.35 0.07
182_T 49_M 0.76 0.35 0.07
211_L 54_Q 0.76 0.35 0.07
150_I 24_L 0.75 0.35 0.07
223_S 36_N 0.75 0.35 0.07
226_M 13_P 0.75 0.34 0.06
170_L 53_Y 0.75 0.34 0.06
98_K 248_L 0.75 0.34 0.06
71_I 121_P 0.74 0.34 0.06
129_K 21_S 0.74 0.34 0.06
154_V 173_L 0.74 0.33 0.06
182_T 44_G 0.74 0.33 0.06
109_E 134_V 0.73 0.33 0.06
6_Q 148_S 0.73 0.33 0.06
150_I 222_K 0.73 0.33 0.06
1_M 168_G 0.73 0.33 0.06
73_L 129_L 0.73 0.33 0.06
110_Y 141_S 0.73 0.33 0.06
99_T 120_H 0.73 0.32 0.06
170_L 180_Y 0.72 0.32 0.06
140_N 21_S 0.72 0.32 0.06
153_L 47_T 0.72 0.31 0.06
16_I 248_L 0.72 0.31 0.06
152_M 169_V 0.72 0.31 0.06
157_E 100_Y 0.72 0.31 0.06
210_V 196_F 0.72 0.31 0.06
38_V 232_G 0.72 0.31 0.06
67_I 214_I 0.72 0.31 0.06
165_V 130_L 0.71 0.31 0.06
55_T 8_M 0.71 0.31 0.06
141_R 93_T 0.71 0.31 0.06
100_M 6_Y 0.71 0.31 0.06
74_I 144_W 0.71 0.31 0.06
39_L 74_Q 0.71 0.30 0.05
160_L 197_V 0.70 0.30 0.05
180_N 9_V 0.70 0.30 0.05
152_M 222_K 0.70 0.29 0.05
60_E 160_A 0.70 0.29 0.05
71_I 93_T 0.70 0.29 0.05
168_L 211_T 0.70 0.29 0.05
17_M 204_L 0.70 0.29 0.05
31_V 19_A 0.70 0.29 0.05
66_T 146_H 0.69 0.28 0.05
143_V 118_G 0.69 0.28 0.05
65_W 115_P 0.69 0.28 0.05
187_S 110_L 0.69 0.28 0.05
109_E 58_D 0.69 0.28 0.05
61_V 127_V 0.69 0.28 0.05
100_M 26_T 0.69 0.28 0.05
89_E 101_H 0.69 0.28 0.05
9_F 191_Y 0.69 0.28 0.05
100_M 107_T 0.68 0.27 0.05
175_I 144_W 0.68 0.27 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
12327 0.87 2y69 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done
10438 3.03 2Y69_BC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.46 Done - Shared
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