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OPENSEQ.org
YDCT - YDCV
Genes: A B A+B
Length: 337 264 580
Sequences: 8908 1638 1473
Seq/Len: 26.43 6.2 2.54
MirrorTree (Pazo et al. 2001) 0.61
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 3.43 1.00 1.00
99_Y 180_Y 2.65 1.00 1.00
102_M 180_Y 2.46 1.00 0.99
48_R 165_E 2.27 1.00 0.99
74_W 168_M 1.95 0.99 0.97
53_F 169_D 1.73 0.98 0.95
79_N 169_D 1.56 0.95 0.90
80_T 169_D 1.44 0.92 0.85
91_M 181_V 1.43 0.92 0.84
74_W 174_G 1.27 0.84 0.74
103_V 180_Y 1.18 0.77 0.65
151_N 169_D 1.12 0.72 0.59
100_G 170_L 1.10 0.70 0.56
188_F 169_D 1.00 0.60 0.45
85_Y 203_D 0.97 0.56 0.41
5_V 116_T 0.95 0.54 0.39
74_W 173_N 0.92 0.50 0.35
140_R 162_S 0.89 0.47 0.32
84_D 160_S 0.88 0.45 0.30
75_E 173_N 0.87 0.44 0.29
5_V 190_L 0.86 0.43 0.28
243_G 242_V 0.81 0.37 0.23
314_T 244_L 0.80 0.36 0.22
97_V 83_G 0.78 0.34 0.21
91_M 172_A 0.78 0.34 0.21
177_L 143_F 0.78 0.34 0.20
103_V 176_Q 0.77 0.33 0.20
222_L 250_I 0.77 0.33 0.20
41_S 204_E 0.76 0.32 0.19
176_E 72_A 0.75 0.31 0.18
7_F 247_T 0.75 0.31 0.18
91_M 180_Y 0.74 0.30 0.17
80_T 107_L 0.73 0.29 0.17
88_F 170_L 0.73 0.29 0.16
11_S 126_T 0.73 0.29 0.16
48_R 220_L 0.73 0.29 0.16
44_T 55_A 0.73 0.28 0.16
90_H 185_N 0.72 0.28 0.16
202_S 118_L 0.72 0.28 0.15
79_N 31_Y 0.72 0.28 0.15
53_F 88_A 0.71 0.27 0.15
150_V 195_M 0.71 0.27 0.15
163_G 183_L 0.71 0.27 0.15
189_I 26_L 0.71 0.27 0.15
122_V 118_L 0.71 0.27 0.15
41_S 150_N 0.71 0.27 0.15
201_M 253_A 0.70 0.27 0.14
120_E 101_I 0.70 0.26 0.14
97_V 138_V 0.70 0.26 0.14
240_V 199_A 0.69 0.26 0.14
79_N 155_R 0.69 0.25 0.14
130_R 203_D 0.69 0.25 0.14
103_V 167_S 0.69 0.25 0.13
41_S 225_Q 0.69 0.25 0.13
81_V 48_T 0.69 0.25 0.13
158_L 170_L 0.68 0.25 0.13
256_F 167_S 0.68 0.24 0.13
189_I 23_F 0.68 0.24 0.12
11_S 28_I 0.68 0.24 0.12
41_S 121_L 0.67 0.23 0.12
106_V 71_V 0.67 0.23 0.12
189_I 18_V 0.66 0.23 0.12
228_T 111_L 0.66 0.23 0.12
84_D 162_S 0.66 0.23 0.12
135_L 127_I 0.66 0.23 0.11
263_I 96_F 0.66 0.22 0.11
29_D 104_L 0.66 0.22 0.11
265_L 186_L 0.66 0.22 0.11
208_F 239_A 0.65 0.22 0.11
63_I 240_L 0.65 0.22 0.11
230_F 172_A 0.65 0.22 0.11
100_G 61_I 0.65 0.22 0.11
81_V 244_L 0.65 0.22 0.11
145_I 223_L 0.65 0.22 0.11
320_Q 19_V 0.65 0.22 0.11
151_N 170_L 0.65 0.21 0.11
323_V 147_V 0.65 0.21 0.11
93_I 101_I 0.65 0.21 0.11
151_N 61_I 0.65 0.21 0.11
180_L 202_F 0.64 0.21 0.10
53_F 129_L 0.64 0.21 0.10
65_G 94_D 0.63 0.20 0.10
208_F 65_V 0.63 0.20 0.10
320_Q 81_V 0.63 0.20 0.10
275_G 130_E 0.63 0.20 0.10
61_I 85_L 0.62 0.20 0.09
263_I 127_I 0.62 0.20 0.09
323_V 74_L 0.62 0.20 0.09
173_M 206_I 0.62 0.20 0.09
199_L 109_I 0.62 0.19 0.09
130_R 119_A 0.62 0.19 0.09
46_C 22_H 0.62 0.19 0.09
95_D 176_Q 0.62 0.19 0.09
68_A 14_A 0.61 0.19 0.09
164_A 225_Q 0.61 0.19 0.09
207_V 133_F 0.61 0.19 0.09
109_K 63_D 0.61 0.19 0.09
265_L 241_L 0.61 0.19 0.09
188_F 150_N 0.61 0.19 0.09
182_Q 89_A 0.61 0.19 0.09
164_A 228_R 0.61 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
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