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OPENSEQ.org
YIAM - YIAN
Genes: A B A+B
Length: 157 425 567
Sequences: 5631 6044 4469
Seq/Len: 35.87 14.22 7.88
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 7.75
5 0.02 0.03 7.77
10 0.04 0.05 7.77
20 0.06 0.08 7.76
100 0.12 0.15 7.80
∞ 0.20 0.22 7.84
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 4.29 1.00 1.00
91_I 25_L 3.53 1.00 1.00
42_R 52_D 2.18 1.00 0.99
28_Y 234_L 2.07 1.00 0.99
59_D 273_K 1.96 1.00 0.99
14_A 268_L 1.85 1.00 0.98
17_S 245_A 1.59 1.00 0.95
87_L 26_L 1.53 1.00 0.94
24_I 243_V 1.51 0.99 0.94
84_T 18_L 1.47 0.99 0.92
13_L 271_A 1.42 0.99 0.91
52_G 276_S 1.41 0.99 0.91
10_A 268_L 1.39 0.99 0.90
53_A 280_F 1.35 0.99 0.88
9_L 272_A 1.30 0.98 0.86
52_G 272_A 1.26 0.98 0.84
61_A 273_K 1.22 0.97 0.81
56_A 277_V 1.22 0.97 0.81
43_Y 48_V 1.20 0.97 0.79
64_Q 17_G 1.19 0.96 0.79
56_A 276_S 1.14 0.95 0.74
46_V 52_D 1.12 0.95 0.73
91_I 26_L 1.12 0.94 0.73
27_R 239_E 1.09 0.93 0.70
20_V 54_F 1.07 0.92 0.68
46_V 51_A 1.06 0.92 0.68
10_A 269_I 1.06 0.92 0.67
41_S 57_L 1.06 0.92 0.67
10_A 265_W 1.04 0.91 0.65
21_F 242_A 1.03 0.91 0.64
49_T 275_T 1.01 0.89 0.62
95_L 47_L 1.00 0.89 0.61
6_E 269_I 1.00 0.89 0.60
17_S 246_F 0.99 0.88 0.60
50_F 47_L 0.99 0.88 0.59
45_F 279_M 0.99 0.88 0.59
50_F 51_A 0.98 0.88 0.58
25_I 246_F 0.93 0.84 0.52
72_L 16_I 0.93 0.83 0.52
83_V 16_I 0.91 0.81 0.49
88_I 22_W 0.91 0.81 0.49
68_L 15_A 0.90 0.81 0.48
13_L 272_A 0.89 0.79 0.46
56_A 273_K 0.85 0.76 0.42
69_V 17_G 0.83 0.72 0.39
18_C 249_L 0.83 0.72 0.39
16_L 57_L 0.82 0.72 0.38
14_A 264_L 0.79 0.67 0.34
17_S 64_L 0.79 0.67 0.34
20_V 242_A 0.79 0.66 0.34
63_V 281_L 0.76 0.62 0.30
66_T 390_D 0.75 0.62 0.30
30_F 234_L 0.73 0.58 0.27
21_F 243_V 0.72 0.57 0.26
49_T 51_A 0.71 0.55 0.25
80_V 16_I 0.70 0.54 0.24
63_V 382_S 0.70 0.54 0.24
132_I 22_W 0.70 0.53 0.23
43_Y 52_D 0.69 0.52 0.23
49_T 279_M 0.69 0.51 0.22
121_M 48_V 0.69 0.51 0.22
62_H 277_V 0.68 0.49 0.21
55_V 269_I 0.68 0.49 0.21
63_V 277_V 0.66 0.47 0.20
94_A 29_A 0.66 0.47 0.20
88_I 18_L 0.65 0.45 0.19
65_V 14_I 0.65 0.45 0.19
16_L 61_F 0.65 0.45 0.18
83_V 18_L 0.63 0.43 0.17
92_C 22_W 0.63 0.42 0.17
29_G 234_L 0.63 0.42 0.17
128_T 280_F 0.63 0.42 0.17
14_A 64_L 0.62 0.40 0.16
119_G 331_D 0.61 0.39 0.15
50_F 283_A 0.61 0.39 0.15
113_I 367_I 0.61 0.39 0.15
48_L 275_T 0.61 0.39 0.15
14_A 265_W 0.60 0.38 0.15
53_A 21_A 0.60 0.37 0.14
87_L 18_L 0.60 0.37 0.14
17_S 61_F 0.59 0.36 0.14
67_F 149_I 0.58 0.35 0.13
98_G 44_A 0.58 0.34 0.13
17_S 68_I 0.57 0.33 0.12
135_F 112_V 0.57 0.33 0.12
17_S 241_G 0.56 0.32 0.12
20_V 57_L 0.56 0.32 0.12
27_R 236_T 0.56 0.31 0.11
81_A 17_G 0.55 0.31 0.11
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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