May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIV_D_2_cI_J_2_Pdenitr
Genes: A B A+B
Length: 43 200 236
Sequences: 221 6585 98
Seq/Len: 5.14 32.92 0.42
MirrorTree (Pazo et al. 2001) 0.05
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 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.00
100 0.00 0.03 0.06
∞ 0.01 0.06 0.40
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
29_I 116_Q 1.65 0.62 0.00
36_V 146_M 1.38 0.42 0.00
13_Q 39_S 1.35 0.40 0.00
9_D 104_L 1.25 0.33 0.00
26_W 192_K 1.12 0.25 0.00
18_A 83_K 1.08 0.23 0.00
21_I 102_A 1.03 0.21 0.00
13_Q 5_A 1.01 0.20 0.00
30_L 192_K 1.01 0.20 0.00
22_K 149_L 0.97 0.18 0.00
39_A 23_G 0.97 0.18 0.00
29_I 55_L 0.96 0.17 0.00
14_Q 188_T 0.96 0.17 0.00
21_I 114_S 0.94 0.17 0.00
38_L 44_F 0.93 0.16 0.00
35_L 20_V 0.92 0.16 0.00
10_I 39_S 0.92 0.16 0.00
33_A 21_V 0.91 0.16 0.00
30_L 100_L 0.90 0.15 0.00
40_L 128_A 0.90 0.15 0.00
6_G 58_V 0.90 0.15 0.00
17_F 39_S 0.89 0.15 0.00
30_L 132_T 0.88 0.14 0.00
19_G 176_N 0.88 0.14 0.00
21_I 110_G 0.88 0.14 0.00
35_L 188_T 0.87 0.14 0.00
27_V 107_A 0.86 0.14 0.00
27_V 17_G 0.86 0.14 0.00
26_W 127_A 0.86 0.14 0.00
13_Q 193_D 0.86 0.14 0.00
8_M 69_L 0.84 0.13 0.00
41_A 68_F 0.84 0.13 0.00
34_V 14_C 0.84 0.13 0.00
32_I 67_L 0.84 0.13 0.00
13_Q 191_L 0.83 0.13 0.00
13_Q 94_L 0.83 0.13 0.00
5_H 124_P 0.82 0.12 0.00
11_R 142_R 0.82 0.12 0.00
24_A 80_A 0.82 0.12 0.00
23_G 90_L 0.82 0.12 0.00
29_I 38_L 0.81 0.12 0.00
32_I 51_F 0.81 0.12 0.00
21_I 178_L 0.81 0.12 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
3214 0.42 cIV_D_2_cI_J_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3213 0.41 cIV_D_2_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
Page generated in 1.597 seconds.