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OPENSEQ.org
YIAM YIAN
Genes: A B A+B
Length: 157 425 563
Sequences: 12088 16662 9131
Seq/Len: 76.99 39.2 16.22
MirrorTree (Pazo et al. 2001) 0.84
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 0.00 0.00 15.69
2 0.00 0.00 15.81
5 0.01 0.01 15.84
10 0.01 0.03 15.86
20 0.02 0.04 15.89
100 0.05 0.08 15.92
∞ 0.10 0.13 16.04
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 3.69 1.00 1.00
91_I 25_L 3.12 1.00 1.00
14_A 268_L 2.05 1.00 0.99
42_R 52_D 2.04 1.00 0.99
9_L 272_A 1.96 1.00 0.99
59_D 273_K 1.86 1.00 0.98
28_Y 234_L 1.83 1.00 0.98
87_L 26_L 1.73 1.00 0.97
17_S 246_F 1.53 1.00 0.94
52_G 276_S 1.49 1.00 0.93
84_T 18_L 1.48 1.00 0.93
17_S 245_A 1.46 1.00 0.92
10_A 269_I 1.39 0.99 0.90
61_A 273_K 1.39 0.99 0.90
53_A 280_F 1.28 0.99 0.85
10_A 265_W 1.23 0.98 0.82
88_I 22_W 1.20 0.98 0.80
13_L 271_A 1.17 0.97 0.78
41_S 57_L 1.13 0.97 0.74
6_E 269_I 1.12 0.96 0.73
46_V 52_D 1.12 0.96 0.73
10_A 268_L 1.11 0.96 0.72
21_F 242_A 1.07 0.95 0.68
43_Y 48_V 1.05 0.95 0.67
64_Q 17_G 1.05 0.94 0.66
50_F 51_A 1.04 0.94 0.66
56_A 277_V 1.02 0.93 0.63
45_F 279_M 1.02 0.93 0.63
125_C 48_V 1.01 0.93 0.61
24_I 243_V 1.00 0.92 0.60
91_I 26_L 0.96 0.90 0.56
66_T 390_D 0.95 0.90 0.55
20_V 54_F 0.95 0.90 0.55
20_V 242_A 0.95 0.90 0.55
50_F 47_L 0.94 0.89 0.53
46_V 51_A 0.93 0.89 0.53
49_T 51_A 0.93 0.88 0.52
70_E 388_K 0.92 0.87 0.51
87_L 18_L 0.92 0.87 0.50
17_S 64_L 0.84 0.81 0.41
95_L 47_L 0.82 0.78 0.38
56_A 276_S 0.82 0.78 0.38
94_A 29_A 0.81 0.77 0.37
49_T 279_M 0.81 0.76 0.36
7_A 265_W 0.80 0.75 0.35
84_T 17_G 0.78 0.73 0.33
98_G 40_V 0.78 0.72 0.33
71_K 390_D 0.78 0.72 0.33
16_L 57_L 0.77 0.71 0.32
52_G 272_A 0.77 0.71 0.32
69_V 17_G 0.76 0.70 0.30
13_L 272_A 0.75 0.68 0.29
92_C 22_W 0.74 0.67 0.28
121_M 48_V 0.74 0.66 0.28
63_V 281_L 0.73 0.65 0.27
17_S 61_F 0.72 0.64 0.26
132_I 22_W 0.72 0.64 0.26
18_C 249_L 0.71 0.62 0.25
55_V 269_I 0.69 0.60 0.23
94_A 40_V 0.69 0.59 0.23
14_A 265_W 0.69 0.59 0.23
70_E 390_D 0.68 0.57 0.21
25_I 246_F 0.67 0.56 0.21
48_L 272_A 0.67 0.56 0.21
98_G 44_A 0.66 0.55 0.20
53_A 21_A 0.66 0.54 0.20
48_L 275_T 0.66 0.53 0.19
83_V 16_I 0.65 0.52 0.19
68_L 15_A 0.63 0.48 0.17
57_F 22_W 0.62 0.46 0.16
80_V 16_I 0.61 0.46 0.16
55_V 273_K 0.61 0.45 0.15
20_V 61_F 0.61 0.45 0.15
61_A 386_K 0.60 0.43 0.14
13_L 268_L 0.59 0.41 0.14
53_A 276_S 0.58 0.40 0.13
14_A 249_L 0.57 0.39 0.13
16_L 61_F 0.57 0.38 0.12
49_T 275_T 0.56 0.37 0.12
50_F 283_A 0.56 0.36 0.11
43_Y 52_D 0.55 0.36 0.11
91_I 284_S 0.55 0.36 0.11
62_H 277_V 0.55 0.35 0.11
45_F 57_L 0.54 0.34 0.11
67_F 390_D 0.54 0.33 0.10
88_I 18_L 0.54 0.33 0.10
90_F 26_L 0.53 0.33 0.10
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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