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OPENSEQ.org
YIAM - YIAN
Genes: A B A+B
Length: 157 425 567
Sequences: 5631 6044 4516
Seq/Len: 35.87 14.22 7.96
MirrorTree (Pazo et al. 2001) 0.69
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 0.00 0.00 7.68
2 0.00 0.01 7.74
5 0.02 0.03 7.76
10 0.04 0.05 7.75
20 0.06 0.08 7.76
100 0.12 0.15 7.80
∞ 0.20 0.22 7.81
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
21_F 246_F 4.19 1.00 1.00
91_I 25_L 3.56 1.00 1.00
42_R 52_D 2.11 1.00 0.99
28_Y 234_L 2.06 1.00 0.99
59_D 273_K 1.95 1.00 0.99
14_A 268_L 1.92 1.00 0.98
87_L 26_L 1.57 1.00 0.95
17_S 245_A 1.56 1.00 0.95
24_I 243_V 1.52 1.00 0.94
84_T 18_L 1.48 0.99 0.93
13_L 271_A 1.45 0.99 0.92
10_A 268_L 1.39 0.99 0.90
52_G 276_S 1.34 0.99 0.88
53_A 280_F 1.34 0.99 0.88
61_A 273_K 1.33 0.98 0.87
9_L 272_A 1.29 0.98 0.85
56_A 277_V 1.20 0.97 0.80
52_G 272_A 1.19 0.97 0.79
64_Q 17_G 1.17 0.96 0.77
91_I 26_L 1.15 0.95 0.76
46_V 52_D 1.14 0.95 0.74
43_Y 48_V 1.13 0.95 0.74
10_A 269_I 1.09 0.94 0.70
27_R 239_E 1.08 0.93 0.70
46_V 51_A 1.07 0.93 0.69
41_S 57_L 1.07 0.93 0.68
56_A 276_S 1.07 0.93 0.68
95_L 47_L 1.04 0.91 0.65
10_A 265_W 1.04 0.91 0.65
49_T 275_T 1.02 0.90 0.63
50_F 47_L 1.02 0.90 0.63
20_V 54_F 1.02 0.90 0.63
6_E 269_I 1.01 0.90 0.62
17_S 246_F 1.01 0.90 0.61
50_F 51_A 1.01 0.90 0.61
21_F 242_A 1.00 0.89 0.61
45_F 279_M 1.00 0.89 0.60
88_I 22_W 0.93 0.83 0.52
13_L 272_A 0.92 0.82 0.50
83_V 16_I 0.87 0.78 0.44
25_I 246_F 0.85 0.76 0.42
68_L 15_A 0.85 0.76 0.42
72_L 16_I 0.84 0.75 0.41
16_L 57_L 0.84 0.74 0.40
56_A 273_K 0.82 0.71 0.37
69_V 17_G 0.81 0.70 0.37
14_A 264_L 0.81 0.70 0.36
17_S 64_L 0.79 0.67 0.34
20_V 242_A 0.77 0.65 0.32
63_V 281_L 0.74 0.60 0.28
121_M 48_V 0.73 0.59 0.27
66_T 390_D 0.72 0.57 0.26
63_V 382_S 0.72 0.57 0.26
49_T 279_M 0.71 0.56 0.25
18_C 249_L 0.71 0.56 0.25
80_V 16_I 0.71 0.56 0.25
49_T 51_A 0.71 0.55 0.25
43_Y 52_D 0.70 0.54 0.24
21_F 243_V 0.70 0.53 0.23
30_F 234_L 0.69 0.53 0.23
132_I 22_W 0.68 0.50 0.21
62_H 277_V 0.66 0.47 0.19
14_A 265_W 0.66 0.46 0.19
88_I 18_L 0.65 0.46 0.19
16_L 61_F 0.65 0.46 0.19
14_A 64_L 0.65 0.46 0.19
63_V 277_V 0.65 0.46 0.19
92_C 22_W 0.63 0.43 0.17
17_S 61_F 0.63 0.42 0.17
53_A 21_A 0.62 0.41 0.17
128_T 280_F 0.62 0.41 0.16
50_F 283_A 0.62 0.40 0.16
65_V 14_I 0.61 0.40 0.15
113_I 367_I 0.61 0.40 0.15
94_A 29_A 0.60 0.39 0.15
55_V 269_I 0.60 0.38 0.14
29_G 234_L 0.59 0.37 0.14
63_V 20_I 0.59 0.36 0.14
119_G 331_D 0.59 0.36 0.14
48_L 275_T 0.58 0.35 0.13
67_F 149_I 0.57 0.33 0.12
135_F 112_V 0.57 0.33 0.12
11_I 321_V 0.57 0.33 0.12
83_V 18_L 0.56 0.33 0.12
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
7874 7.88 YIAM - YIAN Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
7873 16.22 YIAM YIAN Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done
7872 7.96 YIAM - YIAN Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
1487 5.56 YIAM_YIAN Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done
1371 4.51 YIAM_YIAN Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 1.00 Done
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