May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
YDCT - YDCV
Genes: A B A+B
Length: 337 264 573
Sequences: 8908 12685 5009
Seq/Len: 26.43 48.05 8.74
MirrorTree (Pazo et al. 2001) 0.45
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.52 4.71
2 0.05 0.52 6.38
5 0.06 0.56 7.51
10 0.08 0.58 7.87
20 0.14 0.61 8.33
100 0.36 0.71 10.16
∞ 0.85 0.90 13.34
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. Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on HHsearch results which uses the overall probability and per-site alignment confidence. Inter-chain contacts in the pdb are in shades of red. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
48_R 165_E 2.85 1.00 1.00
99_Y 180_Y 2.44 1.00 1.00
99_Y 167_S 2.27 1.00 0.99
102_M 180_Y 2.13 1.00 0.99
88_F 170_L 1.50 1.00 0.93
84_D 162_S 1.42 0.99 0.91
74_W 168_M 1.27 0.98 0.84
100_G 170_L 1.23 0.98 0.81
53_F 169_D 1.19 0.97 0.78
78_V 169_D 1.04 0.93 0.66
103_V 180_Y 1.03 0.92 0.64
103_V 176_Q 1.01 0.91 0.61
80_T 169_D 0.95 0.87 0.54
140_R 162_S 0.91 0.84 0.49
103_V 172_A 0.88 0.81 0.46
79_N 169_D 0.87 0.80 0.45
84_D 160_S 0.83 0.76 0.39
99_Y 172_A 0.82 0.74 0.38
74_W 174_G 0.75 0.64 0.29
90_H 185_N 0.73 0.61 0.27
75_E 173_N 0.71 0.59 0.25
91_M 180_Y 0.70 0.56 0.23
54_E 165_E 0.65 0.47 0.18
74_W 173_N 0.63 0.46 0.17
91_M 181_V 0.62 0.44 0.16
151_N 170_L 0.61 0.42 0.15
82_F 166_A 0.60 0.41 0.15
103_V 171_G 0.58 0.38 0.13
151_N 169_D 0.56 0.34 0.11
256_F 252_G 0.56 0.33 0.11
53_F 165_E 0.53 0.29 0.10
164_A 203_D 0.53 0.29 0.09
86_A 166_A 0.53 0.29 0.09
91_M 172_A 0.51 0.27 0.09
188_F 169_D 0.50 0.26 0.08
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.61 > 0.4) of paralogs.
HHsearch results
3rlfAB:G:FContact Map
3d31AB:CDContact Map
2onkABGF:CHDIContact Map
3tuiCHDG:AEBFContact Map
ID Seq/Len Name Options I_Prob Status
0009 2.92 YDCT - YDCV Δgene:(1, 100) A:(1E-20, 8) B:(1E-60, 8) (2013_03) 1.00 Done - Shared
0008 8.74 YDCT - YDCV Δgene:(1, 20) A:(1E-20, 8) B:(1E-40, 8) (2013_03) 1.00 Done - Shared
0007 2.54 YDCT - YDCV Δgene:(1, 20) A:(1E-20, 8) B:(1E-60, 8) (2013_03) 1.00 Done - Shared
0006 11.45 YDCT - YDCV Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 1.00 Done - Shared
Page generated in 0.2283 seconds.