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OPENSEQ.org
YDCT - YDCV
Genes: A B A+B
Length: 337 264 573
Sequences: 8908 23316 6561
Seq/Len: 26.43 88.32 11.45
MirrorTree (Pazo et al. 2001) 0.33
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 0.65 7.33
2 0.05 0.66 8.97
5 0.06 0.68 9.90
10 0.08 0.70 10.34
20 0.14 0.73 10.92
100 0.36 0.83 13.14
∞ 0.85 0.95 16.62
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 2.96 1.00 1.00
99_Y 180_Y 2.78 1.00 1.00
99_Y 167_S 2.05 1.00 0.99
102_M 180_Y 1.98 1.00 0.99
74_W 168_M 1.74 1.00 0.97
53_F 169_D 1.73 1.00 0.97
88_F 170_L 1.61 1.00 0.95
84_D 162_S 1.54 1.00 0.94
100_G 170_L 1.29 0.99 0.85
103_V 180_Y 1.08 0.96 0.70
90_H 185_N 1.04 0.94 0.65
103_V 176_Q 1.03 0.94 0.64
78_V 169_D 0.98 0.91 0.58
99_Y 172_A 0.96 0.90 0.55
80_T 169_D 0.96 0.90 0.55
140_R 162_S 0.94 0.89 0.53
103_V 172_A 0.93 0.88 0.52
91_M 180_Y 0.90 0.86 0.49
79_N 169_D 0.82 0.78 0.38
84_D 160_S 0.81 0.77 0.37
82_F 166_A 0.79 0.75 0.35
54_E 165_E 0.79 0.74 0.34
151_N 170_L 0.74 0.67 0.28
74_W 174_G 0.74 0.67 0.28
75_E 173_N 0.69 0.59 0.23
74_W 173_N 0.67 0.56 0.21
104_K 171_G 0.66 0.54 0.20
103_V 171_G 0.60 0.43 0.14
151_N 169_D 0.56 0.38 0.12
189_I 122_T 0.54 0.34 0.11
102_M 179_R 0.51 0.29 0.09
73_P 168_M 0.49 0.27 0.08
89_P 163_L 0.48 0.25 0.07
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 (0.73 > 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
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