OPENSEQ.org
C E

Genes: A B A+B
Length: 250 254 484
Sequences: 282 256 237
Seq/Len: 1.13 1.01 0.49
MirrorTree (Pazo et al. 2001) 0.76
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.

Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.00 0.01
2 0.06 0.00 0.47
5 0.06 0.00 0.47
10 0.06 0.00 0.47
20 0.06 0.00 0.47
100 0.06 0.00 0.47
0.06 0.00 0.47
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
90_D 212_L 1.32 0.42 0.00
175_E 35_M 1.32 0.42 0.00
154_Q 40_L 1.31 0.41 0.00
211_A 181_N 1.26 0.37 0.00
93_A 170_S 1.24 0.36 0.00
157_N 76_A 1.22 0.35 0.00
96_T 219_V 1.22 0.35 0.00
127_N 56_F 1.21 0.34 0.00
163_A 74_V 1.20 0.33 0.00
137_N 151_A 1.18 0.32 0.00
95_I 211_V 1.15 0.30 0.00
160_I 12_W 1.14 0.29 0.00
14_L 35_M 1.12 0.28 0.00
6_A 128_A 1.12 0.28 0.00
69_S 126_V 1.10 0.27 0.00
15_A 13_L 1.09 0.27 0.00
212_S 169_E 1.09 0.26 0.00
77_L 35_M 1.08 0.26 0.00
174_T 143_V 1.07 0.25 0.00
168_V 205_N 1.06 0.25 0.00
90_D 42_E 1.04 0.24 0.00
41_A 14_T 1.04 0.23 0.00
201_N 177_V 1.04 0.23 0.00
50_S 138_N 1.03 0.23 0.00
185_N 87_P 1.03 0.23 0.00
150_Q 211_V 1.02 0.23 0.00
139_S 48_V 1.02 0.22 0.00
85_S 46_R 1.02 0.22 0.00
89_Q 40_L 1.01 0.22 0.00
51_K 201_I 1.01 0.22 0.00
224_G 206_V 1.01 0.22 0.00
99_A 103_R 1.01 0.22 0.00
49_V 41_A 1.01 0.22 0.00
14_L 210_T 1.00 0.21 0.00
69_S 173_G 1.00 0.21 0.00
88_Q 76_A 0.99 0.21 0.00
40_V 151_A 0.99 0.21 0.00
204_L 201_I 0.99 0.21 0.00
157_N 119_G 0.98 0.20 0.00
172_S 177_V 0.98 0.20 0.00
57_D 194_Q 0.97 0.20 0.00
70_L 65_T 0.97 0.20 0.00
69_S 43_L 0.97 0.20 0.00
128_N 92_Q 0.97 0.20 0.00
18_M 67_A 0.97 0.20 0.00
142_V 254_Y 0.96 0.19 0.00
232_T 212_L 0.95 0.19 0.00
210_N 23_P 0.95 0.19 0.00
144_V 144_S 0.94 0.18 0.00
90_D 184_V 0.94 0.18 0.00
57_D 87_P 0.94 0.18 0.00
14_L 92_Q 0.94 0.18 0.00
172_S 203_G 0.92 0.17 0.00
172_S 188_I 0.92 0.17 0.00
213_G 182_G 0.91 0.17 0.00
138_S 193_N 0.91 0.17 0.00
169_A 41_A 0.91 0.17 0.00
11_V 88_Q 0.90 0.17 0.00
148_A 42_E 0.90 0.17 0.00
195_P 58_I 0.90 0.17 0.00
211_A 78_M 0.90 0.16 0.00
124_G 241_C 0.89 0.16 0.00
134_S 22_M 0.89 0.16 0.00
205_L 14_T 0.89 0.16 0.00
162_T 145_E 0.89 0.16 0.00
97_S 15_A 0.88 0.16 0.00
62_N 39_E 0.88 0.16 0.00
137_N 178_S 0.88 0.16 0.00
44_V 9_T 0.88 0.16 0.00
57_D 116_L 0.87 0.15 0.00
23_Q 17_C 0.87 0.15 0.00
81_I 31_K 0.87 0.15 0.00
209_N 41_A 0.87 0.15 0.00
62_N 87_P 0.87 0.15 0.00
82_A 40_L 0.87 0.15 0.00
132_N 227_V 0.87 0.15 0.00
70_L 211_V 0.87 0.15 0.00
103_A 174_R 0.87 0.15 0.00
124_G 81_D 0.86 0.15 0.00
162_T 181_N 0.86 0.15 0.00
204_L 206_V 0.86 0.15 0.00
148_A 72_S 0.86 0.15 0.00
147_A 28_S 0.86 0.15 0.00
199_V 99_N 0.86 0.15 0.00
147_A 162_A 0.86 0.15 0.00
148_A 107_T 0.86 0.15 0.00
60_T 43_L 0.85 0.15 0.00
180_D 47_F 0.85 0.15 0.00
159_A 141_I 0.85 0.15 0.00
202_A 125_T 0.85 0.14 0.00
181_N 202_G 0.84 0.14 0.00
19_A 59_V 0.84 0.14 0.00
111_I 223_T 0.84 0.14 0.00
119_K 18_L 0.84 0.14 0.00
36_P 80_I 0.84 0.14 0.00
182_H 143_V 0.84 0.14 0.00
56_D 151_A 0.84 0.14 0.00
19_A 156_S 0.84 0.14 0.00
107_A 58_I 0.84 0.14 0.00
139_S 184_V 0.83 0.14 0.00
9_P 223_T 0.83 0.14 0.00
63_N 14_T 0.83 0.14 0.00
117_D 218_F 0.83 0.14 0.00
218_N 182_G 0.83 0.14 0.00
22_A 29_A 0.83 0.14 0.00
162_T 182_G 0.83 0.14 0.00
60_T 173_G 0.83 0.14 0.00
160_I 118_S 0.83 0.14 0.00
17_L 219_V 0.83 0.14 0.00
19_A 27_A 0.83 0.14 0.00
134_S 24_A 0.82 0.14 0.00
40_V 141_I 0.82 0.14 0.00
65_G 128_A 0.82 0.14 0.00
189_S 201_I 0.82 0.14 0.00
201_N 82_S 0.82 0.14 0.00
147_A 107_T 0.82 0.14 0.00
12_F 91_V 0.82 0.13 0.00
173_N 205_N 0.82 0.13 0.00
9_P 205_N 0.82 0.13 0.00
202_A 184_V 0.82 0.13 0.00
60_T 86_T 0.81 0.13 0.00
4_T 231_N 0.81 0.13 0.00
9_P 139_V 0.81 0.13 0.00
63_N 99_N 0.81 0.13 0.00
59_K 141_I 0.81 0.13 0.00
104_T 251_T 0.81 0.13 0.00
115_S 67_A 0.81 0.13 0.00
67_N 100_G 0.81 0.13 0.00
54_K 77_N 0.81 0.13 0.00
5_M 88_Q 0.81 0.13 0.00
135_A 127_R 0.80 0.13 0.00
168_V 181_N 0.80 0.13 0.00
21_A 135_A 0.80 0.13 0.00
98_S 103_R 0.80 0.13 0.00
207_S 41_A 0.80 0.13 0.00
139_S 190_A 0.80 0.13 0.00
44_V 146_N 0.80 0.13 0.00
81_I 23_P 0.80 0.13 0.00
98_S 47_F 0.79 0.13 0.00
57_D 39_E 0.79 0.13 0.00
96_T 125_T 0.79 0.12 0.00
160_I 254_Y 0.79 0.12 0.00
64_A 75_S 0.79 0.12 0.00
150_Q 125_T 0.79 0.12 0.00
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
7917 0.49 C E Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7909 0.1 C E Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared

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