May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
K-B
Genes: A B A+B
Length: 291 343 593
Sequences: 2129 1352 972
Seq/Len: 7.32 3.94 1.64
MirrorTree (Pazo et al. 2001) 0.74
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 0.00 0.00 0.70
2 0.00 0.00 1.16
5 0.00 0.00 1.48
10 0.01 0.01 1.52
20 0.01 0.01 1.53
100 0.02 0.01 1.66
∞ 0.14 0.12 1.84
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_S 224_V 1.09 0.56 0.00
87_E 246_P 0.94 0.41 0.00
86_Q 59_T 0.92 0.38 0.00
96_S 247_Y 0.90 0.36 0.00
45_A 247_Y 0.88 0.35 0.00
87_E 161_P 0.88 0.34 0.00
184_E 206_K 0.87 0.33 0.00
225_V 269_I 0.86 0.33 0.00
33_V 196_A 0.86 0.32 0.00
46_S 186_D 0.85 0.32 0.00
93_H 193_L 0.84 0.31 0.00
46_S 196_A 0.84 0.30 0.00
283_F 216_C 0.83 0.30 0.00
78_T 230_F 0.83 0.30 0.00
247_L 33_V 0.82 0.28 0.00
85_V 247_Y 0.81 0.28 0.00
157_I 154_L 0.81 0.28 0.00
125_S 83_G 0.81 0.28 0.00
87_E 43_D 0.80 0.27 0.00
152_V 154_L 0.80 0.27 0.00
232_L 228_L 0.79 0.26 0.00
242_E 210_D 0.79 0.26 0.00
51_M 247_Y 0.78 0.26 0.00
96_S 245_E 0.78 0.25 0.00
132_S 299_S 0.78 0.25 0.00
86_Q 186_D 0.78 0.25 0.00
46_S 207_N 0.78 0.25 0.00
226_I 198_G 0.77 0.25 0.00
200_I 209_R 0.77 0.25 0.00
158_S 80_F 0.77 0.24 0.00
272_L 220_M 0.76 0.24 0.00
272_L 70_L 0.75 0.23 0.00
179_E 53_L 0.75 0.23 0.00
153_T 300_C 0.75 0.23 0.00
273_E 178_G 0.75 0.23 0.00
251_L 12_I 0.74 0.23 0.00
62_Y 279_S 0.74 0.23 0.00
261_V 247_Y 0.74 0.23 0.00
46_S 185_I 0.73 0.22 0.00
93_H 107_L 0.73 0.22 0.00
187_C 103_K 0.73 0.22 0.00
117_W 72_E 0.72 0.21 0.00
170_Y 7_P 0.72 0.21 0.00
39_R 272_S 0.72 0.21 0.00
86_Q 13_A 0.72 0.21 0.00
163_Q 127_R 0.72 0.21 0.00
35_L 271_F 0.72 0.21 0.00
247_L 188_S 0.72 0.21 0.00
46_S 18_Q 0.71 0.20 0.00
97_F 55_L 0.71 0.20 0.00
97_F 255_M 0.71 0.20 0.00
61_S 32_E 0.71 0.20 0.00
96_S 193_L 0.71 0.20 0.00
86_Q 224_V 0.71 0.20 0.00
152_V 287_R 0.71 0.20 0.00
45_A 295_Q 0.70 0.20 0.00
232_L 161_P 0.70 0.20 0.00
124_C 151_V 0.70 0.20 0.00
110_R 11_V 0.70 0.20 0.00
101_E 179_F 0.70 0.20 0.00
43_L 271_F 0.70 0.20 0.00
201_L 300_C 0.70 0.19 0.00
228_C 81_G 0.70 0.19 0.00
227_F 250_S 0.70 0.19 0.00
132_S 326_E 0.69 0.19 0.00
119_L 293_W 0.69 0.19 0.00
39_R 186_D 0.69 0.19 0.00
93_H 161_P 0.69 0.19 0.00
153_T 295_Q 0.69 0.19 0.00
130_P 221_V 0.69 0.19 0.00
87_E 171_L 0.69 0.19 0.00
264_V 66_L 0.68 0.18 0.00
123_G 13_A 0.68 0.18 0.00
39_R 251_I 0.68 0.18 0.00
66_V 230_F 0.68 0.18 0.00
154_G 174_G 0.68 0.18 0.00
240_R 59_T 0.68 0.18 0.00
257_L 313_G 0.68 0.18 0.00
132_S 220_M 0.67 0.18 0.00
115_R 179_F 0.67 0.18 0.00
82_R 307_D 0.67 0.18 0.00
97_F 17_L 0.67 0.18 0.00
119_L 240_Q 0.67 0.18 0.00
157_I 167_F 0.67 0.18 0.00
119_L 138_A 0.67 0.17 0.00
157_I 181_Y 0.67 0.17 0.00
39_R 224_V 0.67 0.17 0.00
256_L 269_I 0.67 0.17 0.00
200_I 228_L 0.67 0.17 0.00
57_G 179_F 0.67 0.17 0.00
33_V 59_T 0.67 0.17 0.00
203_E 58_L 0.66 0.17 0.00
46_S 190_E 0.66 0.17 0.00
191_A 326_E 0.66 0.17 0.00
252_A 26_L 0.66 0.17 0.00
97_F 246_P 0.66 0.17 0.00
50_R 71_L 0.66 0.17 0.00
102_R 7_P 0.65 0.17 0.00
258_V 220_M 0.65 0.17 0.00
159_L 80_F 0.65 0.17 0.00
100_L 205_V 0.65 0.17 0.00
56_I 299_S 0.65 0.17 0.00
86_Q 196_A 0.65 0.17 0.00
247_L 269_I 0.65 0.17 0.00
117_W 27_L 0.65 0.17 0.00
121_S 148_A 0.65 0.17 0.00
69_G 328_L 0.65 0.16 0.00
78_T 11_V 0.65 0.16 0.00
85_V 59_T 0.65 0.16 0.00
273_E 28_G 0.65 0.16 0.00
272_L 80_F 0.65 0.16 0.00
87_E 17_L 0.65 0.16 0.00
164_R 164_V 0.64 0.16 0.00
201_L 78_V 0.64 0.16 0.00
83_L 156_A 0.64 0.16 0.00
232_L 68_D 0.64 0.16 0.00
88_T 289_G 0.64 0.16 0.00
85_V 162_A 0.64 0.16 0.00
96_S 295_Q 0.64 0.16 0.00
117_W 100_L 0.64 0.16 0.00
259_I 303_S 0.64 0.16 0.00
76_W 11_V 0.64 0.16 0.00
267_W 106_R 0.64 0.16 0.00
247_L 17_L 0.64 0.16 0.00
39_R 58_L 0.64 0.16 0.00
64_R 318_N 0.64 0.16 0.00
259_I 94_P 0.64 0.16 0.00
123_G 267_G 0.63 0.15 0.00
166_R 167_F 0.63 0.15 0.00
209_R 156_A 0.63 0.15 0.00
110_R 317_F 0.63 0.15 0.00
97_F 290_G 0.63 0.15 0.00
281_L 58_L 0.63 0.15 0.00
104_L 220_M 0.62 0.15 0.00
256_L 79_L 0.62 0.15 0.00
256_L 300_C 0.62 0.15 0.00
197_V 298_D 0.62 0.15 0.00
135_M 245_E 0.62 0.15 0.00
183_V 70_L 0.62 0.15 0.00
128_E 71_L 0.62 0.15 0.00
242_E 320_S 0.62 0.15 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)
Page generated in 0.1072 seconds.