May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
DNAN_DPO3B_SALTY-UMUC_SALTY
Genes: A B A+B
Length: 366 422 762
Sequences: 7006 15934 77
Seq/Len: 19.14 37.76 0.1
MirrorTree (Pazo et al. 2001) 0.17
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 0.00 0.00 0.00
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.01 0.03
20 0.00 0.01 0.10
100 0.00 0.02 0.55
∞ 0.01 0.07 3.68
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
44_L 68_V 1.41 0.18 0.00
326_D 270_Y 1.38 0.17 0.00
256_L 322_I 1.36 0.16 0.00
147_A 176_L 1.32 0.15 0.00
108_L 74_Y 1.31 0.15 0.00
10_L 200_I 1.26 0.14 0.00
93_E 84_V 1.23 0.13 0.00
285_V 247_I 1.20 0.12 0.00
99_V 200_I 1.19 0.12 0.00
53_M 84_V 1.19 0.12 0.00
333_C 49_I 1.18 0.12 0.00
269_R 145_L 1.18 0.12 0.00
135_M 340_Y 1.17 0.12 0.00
58_T 125_A 1.15 0.11 0.00
46_G 55_Y 1.15 0.11 0.00
259_G 200_I 1.15 0.11 0.00
75_F 60_E 1.12 0.11 0.00
263_L 25_R 1.11 0.10 0.00
349_I 200_I 1.10 0.10 0.00
211_E 11_Y 1.10 0.10 0.00
241_F 352_S 1.09 0.10 0.00
37_V 68_V 1.09 0.10 0.00
79_C 290_T 1.08 0.10 0.00
213_P 288_I 1.08 0.10 0.00
336_V 87_T 1.08 0.10 0.00
272_I 61_R 1.06 0.10 0.00
155_L 218_F 1.06 0.10 0.00
323_Y 212_W 1.06 0.10 0.00
121_D 253_F 1.06 0.10 0.00
294_A 292_V 1.05 0.09 0.00
340_L 309_A 1.05 0.09 0.00
209_G 181_V 1.05 0.09 0.00
270_A 69_C 1.04 0.09 0.00
39_D 272_A 1.04 0.09 0.00
192_S 19_R 1.04 0.09 0.00
267_F 129_K 1.04 0.09 0.00
324_V 267_V 1.03 0.09 0.00
214_L 133_L 1.03 0.09 0.00
160_F 192_S 1.03 0.09 0.00
108_L 27_V 1.02 0.09 0.00
132_Q 384_D 1.01 0.09 0.00
292_I 321_D 1.01 0.09 0.00
172_T 11_Y 1.01 0.09 0.00
326_D 23_C 1.01 0.09 0.00
42_L 86_T 1.01 0.09 0.00
77_D 295_S 1.00 0.09 0.00
3_F 187_V 0.99 0.09 0.00
67_A 100_I 0.99 0.09 0.00
294_A 343_A 0.99 0.08 0.00
216_V 292_V 0.99 0.08 0.00
88_I 354_G 0.99 0.08 0.00
220_S 272_A 0.99 0.08 0.00
349_I 357_Q 0.98 0.08 0.00
116_F 256_R 0.98 0.08 0.00
364_M 252_S 0.98 0.08 0.00
130_L 348_G 0.98 0.08 0.00
114_A 389_L 0.98 0.08 0.00
190_S 127_V 0.98 0.08 0.00
67_A 54_P 0.97 0.08 0.00
42_L 163_V 0.97 0.08 0.00
139_I 232_E 0.97 0.08 0.00
145_S 73_N 0.96 0.08 0.00
228_G 380_L 0.96 0.08 0.00
162_T 357_Q 0.95 0.08 0.00
228_G 131_T 0.95 0.08 0.00
82_L 380_L 0.95 0.08 0.00
145_S 292_V 0.95 0.08 0.00
300_E 113_C 0.95 0.08 0.00
336_V 41_S 0.95 0.08 0.00
113_A 322_I 0.95 0.08 0.00
341_T 133_L 0.94 0.08 0.00
267_F 13_S 0.94 0.08 0.00
173_D 231_G 0.94 0.08 0.00
17_V 104_F 0.94 0.08 0.00
344_V 11_Y 0.94 0.08 0.00
98_L 11_Y 0.94 0.08 0.00
110_T 60_E 0.94 0.08 0.00
25_P 236_E 0.93 0.08 0.00
362_M 36_C 0.93 0.08 0.00
67_A 194_K 0.93 0.07 0.00
112_P 181_V 0.92 0.07 0.00
146_M 346_M 0.92 0.07 0.00
349_I 267_V 0.92 0.07 0.00
151_V 248_V 0.92 0.07 0.00
178_A 181_V 0.92 0.07 0.00
71_P 176_L 0.92 0.07 0.00
99_V 209_Q 0.92 0.07 0.00
147_A 112_N 0.92 0.07 0.00
263_L 267_V 0.92 0.07 0.00
328_L 87_T 0.92 0.07 0.00
271_A 187_V 0.92 0.07 0.00
203_L 201_K 0.91 0.07 0.00
262_I 178_L 0.91 0.07 0.00
115_D 236_E 0.91 0.07 0.00
227_V 205_D 0.91 0.07 0.00
142_T 105_C 0.91 0.07 0.00
36_Q 206_L 0.91 0.07 0.00
12_K 67_V 0.91 0.07 0.00
242_P 48_G 0.91 0.07 0.00
336_V 68_V 0.91 0.07 0.00
32_N 67_V 0.91 0.07 0.00
53_M 322_I 0.91 0.07 0.00
182_M 87_T 0.90 0.07 0.00
281_V 358_L 0.90 0.07 0.00
80_R 10_F 0.90 0.07 0.00
301_E 330_L 0.90 0.07 0.00
269_R 48_G 0.90 0.07 0.00
139_I 88_L 0.90 0.07 0.00
323_Y 146_A 0.90 0.07 0.00
10_L 93_P 0.90 0.07 0.00
5_V 343_A 0.90 0.07 0.00
146_M 296_P 0.90 0.07 0.00
145_S 345_V 0.90 0.07 0.00
323_Y 33_N 0.90 0.07 0.00
147_A 347_L 0.89 0.07 0.00
79_C 133_L 0.89 0.07 0.00
339_M 230_R 0.89 0.07 0.00
14_L 378_D 0.89 0.07 0.00
253_D 292_V 0.89 0.07 0.00
261_D 123_I 0.89 0.07 0.00
326_D 97_I 0.89 0.07 0.00
139_I 373_L 0.89 0.07 0.00
130_L 389_L 0.89 0.07 0.00
183_P 278_L 0.89 0.07 0.00
283_L 103_A 0.88 0.07 0.00
90_V 312_L 0.88 0.07 0.00
364_M 2_F 0.88 0.07 0.00
49_L 22_L 0.88 0.07 0.00
294_A 29_V 0.88 0.07 0.00
334_E 47_L 0.88 0.07 0.00
72_A 22_L 0.88 0.07 0.00
168_R 389_L 0.87 0.07 0.00
229_D 166_L 0.87 0.07 0.00
348_Q 184_V 0.87 0.07 0.00
271_A 292_V 0.87 0.07 0.00
281_V 262_E 0.87 0.07 0.00
216_V 236_E 0.87 0.07 0.00
216_V 91_M 0.87 0.07 0.00
175_H 199_G 0.87 0.07 0.00
256_L 115_D 0.87 0.07 0.00
48_D 67_V 0.87 0.07 0.00
195_V 389_L 0.87 0.07 0.00
13_P 388_T 0.86 0.07 0.00
159_L 170_D 0.86 0.07 0.00
138_L 359_N 0.86 0.07 0.00
326_D 207_S 0.86 0.07 0.00
245_R 322_I 0.86 0.07 0.00
259_G 384_D 0.86 0.07 0.00
283_L 97_I 0.86 0.07 0.00
3_F 137_V 0.85 0.07 0.00
63_H 248_V 0.85 0.07 0.00
161_E 312_L 0.85 0.07 0.00
315_M 108_T 0.85 0.07 0.00
48_D 8_N 0.85 0.07 0.00
195_V 32_N 0.85 0.07 0.00
48_D 132_H 0.84 0.06 0.00
3_F 281_E 0.84 0.06 0.00
224_R 108_T 0.84 0.06 0.00
58_T 27_V 0.84 0.06 0.00
147_A 258_T 0.84 0.06 0.00
145_S 170_D 0.84 0.06 0.00
173_D 360_L 0.84 0.06 0.00
115_D 126_T 0.84 0.06 0.00
222_N 190_R 0.84 0.06 0.00
362_M 148_L 0.84 0.06 0.00
248_L 292_V 0.84 0.06 0.00
340_L 200_I 0.84 0.06 0.00
142_T 70_F 0.84 0.06 0.00
245_R 218_F 0.84 0.06 0.00
196_P 322_I 0.84 0.06 0.00
268_A 187_V 0.84 0.06 0.00
258_A 163_V 0.84 0.06 0.00
205_R 192_S 0.84 0.06 0.00
233_T 124_R 0.84 0.06 0.00
144_F 199_G 0.84 0.06 0.00
190_S 288_I 0.83 0.06 0.00
29_I 231_G 0.83 0.06 0.00
97_M 200_I 0.83 0.06 0.00
130_L 60_E 0.83 0.06 0.00
38_A 105_C 0.83 0.06 0.00
256_L 345_V 0.83 0.06 0.00
61_Q 345_V 0.83 0.06 0.00
218_I 123_I 0.83 0.06 0.00
75_F 345_V 0.83 0.06 0.00
258_A 26_P 0.83 0.06 0.00
232_F 83_R 0.83 0.06 0.00
169_T 345_V 0.83 0.06 0.00
98_L 322_I 0.83 0.06 0.00
199_G 345_V 0.83 0.06 0.00
301_E 133_L 0.83 0.06 0.00
9_H 140_A 0.82 0.06 0.00
241_F 325_A 0.82 0.06 0.00
67_A 124_R 0.82 0.06 0.00
213_P 47_L 0.82 0.06 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
7080 3.81 DNAN_DPO3B_SALTY-UMUC_SALTY HHBlits Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6932 0.03 DNAN_DPO3B_SALTY-UMUC_SALTY HHBlits Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6891 0.1 DNAN_DPO3B_SALTY-UMUC_SALTY Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
Page generated in 1.6096 seconds.