May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
3vs2_02
Genes: A B A+B
Length: 147 527 655
Sequences: 1424 586 67
Seq/Len: 9.69 1.11 0.1
MirrorTree (Pazo et al. 2001) 0.16
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 0.01 0.00
2 0.03 0.01 0.00
5 0.04 0.01 0.00
10 0.04 0.01 0.00
20 0.04 0.01 0.01
100 0.05 0.01 0.01
∞ 0.07 0.02 0.10
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
69_V 187_I 1.30 0.15 0.00
97_K 364_V 1.18 0.12 0.00
33_A 140_R 1.17 0.12 0.00
25_D 24_E 1.16 0.11 0.00
73_M 508_S 1.15 0.11 0.00
32_E 204_V 1.14 0.11 0.00
48_A 480_I 1.11 0.10 0.00
30_S 362_V 1.06 0.10 0.00
22_A 100_N 1.05 0.09 0.00
81_F 374_S 1.04 0.09 0.00
96_Q 289_F 1.04 0.09 0.00
132_E 446_L 1.03 0.09 0.00
123_R 380_P 1.02 0.09 0.00
48_A 137_L 1.01 0.09 0.00
18_I 210_K 0.99 0.08 0.00
126_D 318_C 0.98 0.08 0.00
121_K 279_E 0.97 0.08 0.00
13_A 95_P 0.97 0.08 0.00
48_A 24_E 0.96 0.08 0.00
108_K 445_I 0.96 0.08 0.00
99_K 445_I 0.95 0.08 0.00
96_Q 129_M 0.95 0.08 0.00
128_D 465_Y 0.95 0.08 0.00
69_V 412_I 0.94 0.08 0.00
33_A 197_L 0.94 0.08 0.00
79_Q 235_F 0.94 0.08 0.00
67_S 349_I 0.93 0.07 0.00
60_K 201_T 0.92 0.07 0.00
37_I 252_R 0.91 0.07 0.00
77_E 230_F 0.91 0.07 0.00
13_A 318_C 0.89 0.07 0.00
118_E 332_K 0.89 0.07 0.00
101_E 207_D 0.88 0.07 0.00
45_V 26_I 0.88 0.07 0.00
123_R 24_E 0.88 0.07 0.00
99_K 88_I 0.88 0.07 0.00
41_A 250_T 0.88 0.07 0.00
29_I 497_I 0.88 0.07 0.00
44_F 441_F 0.87 0.07 0.00
7_D 255_Y 0.87 0.07 0.00
125_E 204_V 0.86 0.07 0.00
103_S 188_T 0.86 0.07 0.00
44_F 365_P 0.85 0.07 0.00
117_E 348_I 0.85 0.07 0.00
123_R 318_C 0.85 0.07 0.00
82_V 362_V 0.85 0.07 0.00
104_E 62_I 0.85 0.07 0.00
72_A 197_L 0.85 0.07 0.00
138_E 260_F 0.85 0.07 0.00
136_E 424_C 0.85 0.07 0.00
6_E 516_N 0.85 0.07 0.00
33_A 519_V 0.85 0.06 0.00
48_A 115_P 0.84 0.06 0.00
109_D 400_T 0.84 0.06 0.00
108_K 418_D 0.84 0.06 0.00
122_S 221_A 0.84 0.06 0.00
117_E 240_F 0.84 0.06 0.00
44_F 235_F 0.84 0.06 0.00
69_V 338_L 0.84 0.06 0.00
71_S 396_S 0.84 0.06 0.00
40_A 163_F 0.84 0.06 0.00
58_K 134_Y 0.84 0.06 0.00
115_D 88_I 0.84 0.06 0.00
11_P 204_V 0.83 0.06 0.00
122_S 450_H 0.83 0.06 0.00
120_D 137_L 0.83 0.06 0.00
33_A 510_K 0.83 0.06 0.00
106_K 301_L 0.83 0.06 0.00
28_N 372_F 0.83 0.06 0.00
25_D 396_S 0.83 0.06 0.00
74_E 494_C 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
4179 0.04 3vs2_02_hh Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
4177 0.1 3vs2_02 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
Page generated in 0.6445 seconds.