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OPENSEQ.org
YIAM_YIAN
Genes: A B A+B
Length: 157 425 574
Sequences: 3964 5875 3192
Seq/Len: 25.25 13.82 5.56
MirrorTree (Pazo et al. 2001) 0.72
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.03 5.48
2 0.01 0.03 5.52
5 0.02 0.04 5.53
10 0.03 0.06 5.54
20 0.04 0.07 5.54
100 0.06 0.10 5.57
∞ 0.11 0.15 5.60
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 3.76 1.00 1.00
91_I 25_L 3.39 1.00 1.00
42_R 52_D 2.44 1.00 1.00
14_A 268_L 1.95 1.00 0.99
28_Y 234_L 1.65 0.99 0.96
59_D 273_K 1.56 0.99 0.94
87_L 26_L 1.55 0.99 0.94
17_S 245_A 1.51 0.99 0.93
9_L 272_A 1.51 0.99 0.93
43_Y 48_V 1.49 0.99 0.93
24_I 243_V 1.34 0.97 0.87
10_A 269_I 1.33 0.97 0.86
17_S 246_F 1.29 0.96 0.85
46_V 51_A 1.29 0.96 0.84
56_A 277_V 1.26 0.95 0.83
10_A 265_W 1.23 0.94 0.81
53_A 280_F 1.22 0.94 0.80
46_V 52_D 1.20 0.94 0.79
52_G 276_S 1.19 0.93 0.78
84_T 18_L 1.16 0.92 0.76
50_F 47_L 1.16 0.92 0.76
66_T 390_D 1.15 0.92 0.75
61_A 273_K 1.13 0.91 0.73
13_L 271_A 1.13 0.90 0.73
41_S 57_L 1.12 0.90 0.72
45_F 279_M 1.09 0.88 0.69
16_L 57_L 1.07 0.87 0.67
50_F 51_A 1.06 0.86 0.66
43_Y 52_D 1.04 0.85 0.64
64_Q 17_G 1.02 0.83 0.62
88_I 22_W 1.01 0.82 0.60
6_E 269_I 1.00 0.81 0.59
95_L 47_L 0.97 0.79 0.56
56_A 276_S 0.97 0.79 0.56
21_F 242_A 0.95 0.77 0.53
49_T 275_T 0.94 0.75 0.51
68_L 15_A 0.90 0.71 0.47
98_G 40_V 0.88 0.69 0.45
83_V 16_I 0.87 0.68 0.43
91_I 26_L 0.86 0.67 0.42
49_T 51_A 0.85 0.65 0.40
20_V 54_F 0.85 0.65 0.40
18_C 249_L 0.84 0.64 0.39
50_F 283_A 0.83 0.63 0.38
63_V 281_L 0.81 0.60 0.36
10_A 268_L 0.79 0.56 0.33
16_L 61_F 0.78 0.55 0.31
125_C 48_V 0.77 0.54 0.31
87_L 18_L 0.76 0.53 0.30
20_V 242_A 0.75 0.51 0.29
29_G 234_L 0.75 0.50 0.28
49_T 279_M 0.73 0.47 0.26
71_K 390_D 0.72 0.47 0.25
63_V 382_S 0.69 0.42 0.22
83_V 405_S 0.69 0.42 0.22
70_E 388_K 0.69 0.42 0.21
75_A 257_R 0.66 0.38 0.19
94_A 29_A 0.66 0.38 0.19
5_L 112_V 0.66 0.38 0.19
52_G 272_A 0.66 0.38 0.19
72_L 16_I 0.65 0.37 0.18
56_A 273_K 0.65 0.37 0.18
135_F 112_V 0.65 0.36 0.18
96_A 163_S 0.64 0.35 0.17
94_A 40_V 0.63 0.34 0.17
14_A 265_W 0.63 0.33 0.16
114_L 220_L 0.63 0.33 0.16
135_F 377_V 0.63 0.33 0.16
13_L 272_A 0.63 0.33 0.16
132_I 181_M 0.62 0.32 0.15
65_V 23_A 0.62 0.32 0.15
84_T 17_G 0.61 0.31 0.15
65_V 14_I 0.61 0.31 0.14
38_D 96_V 0.60 0.30 0.14
17_S 64_L 0.60 0.30 0.14
57_F 22_W 0.59 0.29 0.13
36_S 104_M 0.59 0.29 0.13
9_L 269_I 0.59 0.28 0.13
63_V 322_A 0.59 0.28 0.13
134_F 207_Q 0.58 0.28 0.13
53_A 276_S 0.57 0.27 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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