May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
7-24sc-cjckhmmr
Genes: A B A+B
Length: 240 224 455
Sequences: 1723 1233 337
Seq/Len: 7.18 5.5 0.74
MirrorTree (Pazo et al. 2001) 0.24
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 0.05 0.05 0.01
2 0.05 0.05 0.01
5 0.05 0.05 0.06
10 0.05 0.05 0.08
20 0.05 0.05 0.10
100 0.06 0.12 0.31
∞ 0.10 0.16 0.73
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
95_E 33_K 1.39 0.60 0.00
169_M 69_Y 1.32 0.53 0.00
151_L 82_R 1.15 0.39 0.00
151_L 149_M 1.07 0.33 0.00
147_I 4_I 1.06 0.33 0.00
132_E 176_N 1.06 0.32 0.00
164_D 27_N 1.04 0.31 0.00
146_A 82_R 1.04 0.31 0.00
44_I 50_K 1.04 0.31 0.00
146_A 51_K 0.98 0.27 0.00
97_A 121_L 0.98 0.26 0.00
124_D 221_A 0.98 0.26 0.00
197_V 147_D 0.96 0.25 0.00
184_N 69_Y 0.94 0.24 0.00
164_D 64_Y 0.93 0.23 0.00
124_D 195_E 0.93 0.23 0.00
145_D 146_D 0.93 0.23 0.00
68_K 194_E 0.92 0.23 0.00
88_E 33_K 0.90 0.21 0.00
89_Q 124_L 0.90 0.21 0.00
18_S 189_E 0.88 0.20 0.00
115_K 151_S 0.87 0.20 0.00
209_Q 123_Q 0.87 0.20 0.00
132_E 51_K 0.87 0.20 0.00
202_V 192_A 0.86 0.19 0.00
45_T 56_N 0.86 0.19 0.00
40_L 147_D 0.85 0.19 0.00
168_D 191_A 0.85 0.19 0.00
9_T 54_K 0.84 0.18 0.00
207_I 149_M 0.84 0.18 0.00
67_L 121_L 0.84 0.18 0.00
191_P 193_N 0.84 0.18 0.00
74_E 82_R 0.82 0.17 0.00
168_D 106_A 0.82 0.17 0.00
171_A 147_D 0.82 0.17 0.00
103_T 83_A 0.82 0.17 0.00
152_I 184_Q 0.82 0.17 0.00
88_E 19_R 0.82 0.17 0.00
141_D 56_N 0.81 0.17 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
9419 0.02 7-24sc-d Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed - Shared
9418 0.74 7-24sc-cjckhmmr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9417 0.2 7-24sc-c Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9415 0.02 7-24sc Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed
8464 0.11 jckhmmr Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed
8463 0.01 Snf7 Vps24 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed
8462 0.01 Snf7 Vps24 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
Page generated in 0.0961 seconds.