May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cyt1_2_cIV_A_2_human
Genes: A B A+B
Length: 325 513 766
Sequences: 747 5961 201
Seq/Len: 2.3 11.62 0.26
MirrorTree (Pazo et al. 2001) 0.02
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 0.02 0.00 0.00
2 0.02 0.00 0.00
5 0.02 0.01 0.00
10 0.02 0.01 0.01
20 0.02 0.01 0.01
100 0.02 0.02 0.05
∞ 0.02 0.04 0.24
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
267_A 511_M 1.67 0.49 0.00
123_S 35_L 1.50 0.38 0.00
282_H 342_L 1.30 0.27 0.00
271_C 190_I 1.24 0.24 0.00
245_A 258_V 1.19 0.21 0.00
179_Y 374_V 1.16 0.20 0.00
308_R 392_G 1.12 0.19 0.00
310_K 357_V 1.11 0.18 0.00
71_G 466_M 1.09 0.17 0.00
300_V 466_M 1.06 0.17 0.00
278_S 462_L 1.01 0.15 0.00
221_P 453_L 1.00 0.14 0.00
264_S 511_M 1.00 0.14 0.00
312_S 100_M 0.99 0.14 0.00
213_S 477_A 0.98 0.14 0.00
213_S 25_W 0.97 0.13 0.00
154_V 28_V 0.95 0.13 0.00
237_F 250_G 0.94 0.13 0.00
271_C 426_F 0.93 0.12 0.00
237_F 54_Y 0.92 0.12 0.00
130_V 23_G 0.92 0.12 0.00
251_D 267_P 0.92 0.12 0.00
212_F 49_G 0.91 0.12 0.00
154_V 463_T 0.90 0.12 0.00
74_L 283_L 0.90 0.12 0.00
250_T 253_M 0.90 0.11 0.00
122_A 419_I 0.89 0.11 0.00
212_F 25_W 0.89 0.11 0.00
282_H 9_S 0.89 0.11 0.00
218_Y 360_N 0.88 0.11 0.00
302_L 120_A 0.88 0.11 0.00
267_A 400_F 0.88 0.11 0.00
267_A 215_L 0.88 0.11 0.00
221_P 392_G 0.88 0.11 0.00
213_S 85_L 0.88 0.11 0.00
154_V 25_W 0.88 0.11 0.00
227_L 359_A 0.88 0.11 0.00
211_V 299_V 0.87 0.11 0.00
278_S 146_T 0.87 0.11 0.00
127_M 54_Y 0.86 0.10 0.00
211_V 7_L 0.86 0.10 0.00
298_L 220_F 0.85 0.10 0.00
295_M 110_L 0.84 0.10 0.00
229_E 398_P 0.84 0.10 0.00
134_H 118_V 0.83 0.10 0.00
292_M 511_M 0.83 0.10 0.00
215_L 100_M 0.83 0.10 0.00
277_A 130_P 0.83 0.10 0.00
102_L 253_M 0.83 0.10 0.00
300_V 153_A 0.83 0.10 0.00
306_I 152_L 0.82 0.10 0.00
312_S 230_L 0.82 0.10 0.00
78_L 359_A 0.82 0.10 0.00
99_R 37_I 0.82 0.09 0.00
253_L 357_V 0.81 0.09 0.00
305_T 114_A 0.81 0.09 0.00
101_L 331_N 0.81 0.09 0.00
79_H 57_I 0.81 0.09 0.00
242_I 258_V 0.81 0.09 0.00
209_D 311_I 0.81 0.09 0.00
166_M 258_V 0.81 0.09 0.00
70_G 473_W 0.81 0.09 0.00
312_S 464_A 0.81 0.09 0.00
159_N 392_G 0.80 0.09 0.00
299_L 423_L 0.80 0.09 0.00
283_D 48_L 0.80 0.09 0.00
212_F 392_G 0.79 0.09 0.00
248_I 101_S 0.79 0.09 0.00
172_F 117_M 0.79 0.09 0.00
283_D 198_S 0.79 0.09 0.00
308_R 403_Y 0.79 0.09 0.00
267_A 446_A 0.79 0.09 0.00
110_I 308_A 0.79 0.09 0.00
218_Y 470_F 0.78 0.09 0.00
245_A 406_D 0.78 0.09 0.00
267_A 39_A 0.78 0.09 0.00
69_A 393_F 0.78 0.09 0.00
145_A 203_A 0.78 0.09 0.00
109_S 398_P 0.78 0.09 0.00
252_V 28_V 0.78 0.09 0.00
122_A 57_I 0.78 0.09 0.00
242_I 318_V 0.78 0.09 0.00
281_E 481_K 0.78 0.09 0.00
170_K 480_R 0.77 0.09 0.00
172_F 59_T 0.77 0.09 0.00
70_G 168_I 0.77 0.08 0.00
97_S 363_L 0.77 0.08 0.00
75_A 145_L 0.77 0.08 0.00
200_I 393_F 0.77 0.08 0.00
293_L 25_W 0.77 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)
ID Seq/Len Name Options I_Prob Status
5465 0.26 cyt1_2_cIV_A_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5451 0 cyt1_2_cIV_A_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
5441 0 cyt1_40_cIV_A_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.0604 seconds.