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: 337 264 579
Sequences: 8908 1638 1689
Seq/Len: 26.43 6.2 2.92
MirrorTree (Pazo et al. 2001) 0.43
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 0.00 0.47
2 0.05 0.00 1.84
5 0.06 0.00 2.29
10 0.08 0.01 2.35
20 0.14 0.01 2.45
100 0.36 0.05 2.81
∞ 0.85 0.45 3.80
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
99_Y 167_S 2.78 1.00 1.00
99_Y 180_Y 2.25 1.00 0.99
102_M 180_Y 2.03 1.00 0.98
48_R 165_E 1.84 0.99 0.97
74_W 168_M 1.53 0.96 0.91
53_F 169_D 1.47 0.95 0.88
79_N 169_D 1.20 0.83 0.70
80_T 169_D 1.16 0.80 0.67
91_M 181_V 1.11 0.76 0.62
74_W 174_G 1.07 0.72 0.57
103_V 180_Y 0.94 0.57 0.41
151_N 169_D 0.92 0.54 0.39
100_G 170_L 0.85 0.46 0.30
74_W 173_N 0.84 0.44 0.29
314_T 244_L 0.81 0.41 0.26
85_Y 203_D 0.79 0.38 0.24
140_R 162_S 0.79 0.38 0.24
5_V 190_L 0.74 0.33 0.20
84_D 160_S 0.74 0.32 0.19
91_M 172_A 0.72 0.31 0.18
5_V 116_T 0.72 0.31 0.18
97_V 83_G 0.72 0.30 0.17
91_M 180_Y 0.68 0.26 0.14
228_T 111_L 0.67 0.26 0.14
256_F 167_S 0.66 0.25 0.13
188_F 169_D 0.66 0.24 0.13
243_G 242_V 0.65 0.24 0.13
189_I 18_V 0.65 0.23 0.12
8_D 16_G 0.65 0.23 0.12
7_F 247_T 0.64 0.23 0.12
97_V 138_V 0.64 0.23 0.12
189_I 26_L 0.63 0.22 0.11
103_V 176_Q 0.63 0.22 0.11
41_S 204_E 0.62 0.21 0.11
44_T 55_A 0.62 0.21 0.10
202_S 118_L 0.61 0.20 0.10
291_L 19_V 0.60 0.20 0.10
81_V 48_T 0.60 0.20 0.10
63_I 165_E 0.60 0.20 0.10
103_V 167_S 0.60 0.20 0.09
126_F 190_L 0.60 0.19 0.09
120_E 101_I 0.59 0.19 0.09
41_S 150_N 0.59 0.19 0.09
80_T 107_L 0.59 0.19 0.09
176_E 72_A 0.59 0.19 0.09
130_R 119_A 0.59 0.19 0.09
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)
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 0.0406 seconds.