May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
N32_P_SrBDH1
Genes: A B A+B
Length: 280 290 477
Sequences: 48631 34977 91
Seq/Len: 173.68 120.61 0.19
MirrorTree (Pazo et al. 2001) 0.23
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 0.04 0.03 0.02
2 0.05 0.04 0.05
5 0.07 0.06 0.08
10 0.11 0.08 0.11
20 0.14 0.11 0.16
100 0.23 0.19 0.34
∞ 0.29 0.26 0.48
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
191_E 35_V 1.49 0.30 0.00
164_A 111_M 1.28 0.21 0.00
204_P 142_G 1.27 0.21 0.00
91_V 193_S 1.25 0.20 0.00
133_N 139_N 1.22 0.18 0.00
43_V 71_Q 1.19 0.18 0.00
80_D 87_D 1.16 0.17 0.00
118_I 88_V 1.14 0.16 0.00
47_W 169_C 1.13 0.16 0.00
177_S 88_V 1.11 0.15 0.00
133_N 249_A 1.10 0.15 0.00
101_L 165_T 1.10 0.15 0.00
176_A 98_V 1.10 0.15 0.00
38_I 137_G 1.09 0.15 0.00
31_I 156_P 1.07 0.14 0.00
71_G 61_V 1.05 0.13 0.00
29_A 162_I 1.05 0.13 0.00
246_A 162_I 1.04 0.13 0.00
108_A 184_K 1.04 0.13 0.00
243_V 61_V 1.03 0.13 0.00
137_G 137_G 1.02 0.13 0.00
90_L 194_L 1.02 0.13 0.00
174_Y 167_S 1.02 0.12 0.00
71_G 92_D 1.01 0.12 0.00
121_T 187_I 1.01 0.12 0.00
29_A 183_S 0.99 0.12 0.00
46_F 199_G 0.99 0.12 0.00
131_G 108_V 0.99 0.12 0.00
29_A 99_D 0.99 0.12 0.00
38_I 107_G 0.99 0.12 0.00
156_I 66_Q 0.99 0.12 0.00
177_S 37_I 0.99 0.12 0.00
104_M 63_A 0.98 0.11 0.00
181_I 142_G 0.98 0.11 0.00
61_D 193_S 0.97 0.11 0.00
44_R 193_S 0.97 0.11 0.00
54_V 144_F 0.96 0.11 0.00
34_G 151_A 0.96 0.11 0.00
58_I 243_L 0.95 0.11 0.00
201_C 192_K 0.95 0.11 0.00
123_K 60_V 0.95 0.11 0.00
157_L 163_I 0.95 0.11 0.00
173_A 108_V 0.95 0.11 0.00
159_T 206_N 0.94 0.11 0.00
25_E 146_A 0.94 0.11 0.00
173_A 101_A 0.94 0.11 0.00
181_I 37_I 0.94 0.10 0.00
154_G 201_H 0.94 0.10 0.00
187_N 147_A 0.93 0.10 0.00
226_M 195_A 0.93 0.10 0.00
132_V 97_L 0.93 0.10 0.00
34_G 166_A 0.92 0.10 0.00
53_V 198_L 0.92 0.10 0.00
198_R 36_A 0.92 0.10 0.00
141_A 254_Y 0.92 0.10 0.00
94_T 208_V 0.91 0.10 0.00
134_L 42_A 0.91 0.10 0.00
196_G 101_A 0.91 0.10 0.00
55_I 104_K 0.91 0.10 0.00
105_F 58_A 0.91 0.10 0.00
197_I 163_I 0.91 0.10 0.00
146_R 195_A 0.90 0.10 0.00
131_G 101_A 0.90 0.10 0.00
64_Q 185_Y 0.90 0.10 0.00
39_G 167_S 0.89 0.10 0.00
90_L 91_E 0.89 0.10 0.00
48_E 147_A 0.89 0.09 0.00
103_I 216_G 0.89 0.09 0.00
205_Y 164_F 0.88 0.09 0.00
45_L 150_A 0.88 0.09 0.00
109_G 35_V 0.88 0.09 0.00
191_E 144_F 0.88 0.09 0.00
181_I 138_I 0.88 0.09 0.00
60_D 203_I 0.87 0.09 0.00
27_K 154_M 0.87 0.09 0.00
173_A 53_F 0.87 0.09 0.00
174_Y 180_Y 0.87 0.09 0.00
190_A 251_T 0.87 0.09 0.00
184_L 96_A 0.87 0.09 0.00
178_K 40_G 0.87 0.09 0.00
90_L 45_I 0.86 0.09 0.00
202_V 208_V 0.86 0.09 0.00
144_A 108_V 0.86 0.09 0.00
178_K 46_G 0.86 0.09 0.00
187_N 195_A 0.86 0.09 0.00
89_N 81_I 0.86 0.09 0.00
191_E 166_A 0.85 0.09 0.00
30_I 71_Q 0.85 0.09 0.00
227_L 163_I 0.85 0.09 0.00
178_K 39_T 0.85 0.09 0.00
105_F 200_S 0.85 0.09 0.00
41_S 42_A 0.85 0.09 0.00
131_G 35_V 0.84 0.09 0.00
108_A 115_A 0.84 0.09 0.00
92_D 205_A 0.84 0.09 0.00
145_A 195_A 0.84 0.09 0.00
157_L 61_V 0.84 0.09 0.00
162_A 192_K 0.84 0.09 0.00
29_A 45_I 0.84 0.09 0.00
47_W 147_A 0.84 0.09 0.00
191_E 198_L 0.84 0.09 0.00
207_V 254_Y 0.84 0.09 0.00
39_G 249_A 0.84 0.09 0.00
181_I 159_K 0.84 0.09 0.00
105_F 93_Q 0.84 0.08 0.00
258_V 178_H 0.83 0.08 0.00
164_A 181_T 0.83 0.08 0.00
181_I 161_C 0.83 0.08 0.00
242_D 254_Y 0.83 0.08 0.00
81_V 122_N 0.82 0.08 0.00
28_V 178_H 0.82 0.08 0.00
74_V 142_G 0.82 0.08 0.00
188_L 94_V 0.82 0.08 0.00
66_I 193_S 0.82 0.08 0.00
131_G 165_T 0.82 0.08 0.00
41_S 132_L 0.82 0.08 0.00
175_T 35_V 0.82 0.08 0.00
150_P 242_I 0.81 0.08 0.00
178_K 184_K 0.81 0.08 0.00
164_A 161_C 0.81 0.08 0.00
248_L 156_P 0.81 0.08 0.00
144_A 226_L 0.80 0.08 0.00
177_S 169_C 0.80 0.08 0.00
159_T 190_L 0.80 0.08 0.00
120_D 130_D 0.80 0.08 0.00
197_I 45_I 0.80 0.08 0.00
196_G 163_I 0.80 0.08 0.00
48_E 94_V 0.80 0.08 0.00
135_V 198_L 0.80 0.08 0.00
36_S 150_A 0.79 0.08 0.00
103_I 201_H 0.79 0.08 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)
WARNING: The input alignment may be corrupted!
  • Sequence A is very similar to Sequence B (HHΔ = 0.192), these maybe paralogs! HHΔ is a measure (0 to 1) of how different two alignments are (the larger the value the more different they are).
Page generated in 0.1245 seconds.