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OPENSEQ.org
YIAM_YIAN
Genes: A B A+B
Length: 157 425 574
Sequences: 3164 4549 2587
Seq/Len: 20.15 10.7 4.51
MirrorTree (Pazo et al. 2001) 0.70
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 4.40
2 0.00 0.00 4.43
5 0.01 0.01 4.44
10 0.01 0.03 4.44
20 0.02 0.05 4.45
100 0.05 0.08 4.45
∞ 0.11 0.14 4.51
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 3.73 1.00 1.00
91_I 25_L 3.46 1.00 1.00
42_R 52_D 2.49 1.00 1.00
14_A 268_L 1.92 1.00 0.98
28_Y 234_L 1.91 1.00 0.98
59_D 273_K 1.70 0.99 0.96
87_L 26_L 1.57 0.99 0.94
43_Y 48_V 1.50 0.98 0.92
9_L 272_A 1.47 0.98 0.91
17_S 245_A 1.39 0.97 0.89
66_T 390_D 1.31 0.95 0.84
24_I 243_V 1.29 0.94 0.83
10_A 265_W 1.25 0.93 0.81
41_S 57_L 1.22 0.92 0.79
61_A 273_K 1.22 0.92 0.79
53_A 280_F 1.18 0.90 0.76
10_A 269_I 1.18 0.90 0.76
45_F 279_M 1.14 0.88 0.72
56_A 277_V 1.11 0.86 0.70
17_S 246_F 1.11 0.86 0.70
46_V 51_A 1.11 0.86 0.69
46_V 52_D 1.09 0.84 0.68
84_T 18_L 1.09 0.84 0.67
13_L 271_A 1.07 0.83 0.66
56_A 276_S 1.05 0.81 0.63
64_Q 17_G 1.05 0.81 0.63
88_I 22_W 1.02 0.79 0.60
50_F 47_L 0.98 0.74 0.55
68_L 15_A 0.97 0.73 0.54
10_A 268_L 0.96 0.72 0.53
6_E 269_I 0.95 0.71 0.51
50_F 51_A 0.94 0.70 0.50
52_G 276_S 0.93 0.68 0.48
91_I 26_L 0.88 0.63 0.43
16_L 57_L 0.86 0.60 0.40
56_A 273_K 0.86 0.59 0.39
72_L 16_I 0.83 0.56 0.36
98_G 40_V 0.82 0.55 0.35
20_V 54_F 0.82 0.55 0.35
83_V 16_I 0.82 0.54 0.34
49_T 51_A 0.81 0.53 0.34
21_F 242_A 0.79 0.51 0.31
134_F 207_Q 0.79 0.50 0.31
48_L 275_T 0.77 0.47 0.29
95_L 47_L 0.77 0.47 0.28
63_V 281_L 0.77 0.47 0.28
65_V 14_I 0.76 0.46 0.28
43_Y 52_D 0.75 0.45 0.27
33_S 43_M 0.74 0.44 0.26
87_L 18_L 0.74 0.44 0.26
50_F 283_A 0.74 0.43 0.26
49_T 275_T 0.74 0.43 0.25
17_S 61_F 0.73 0.43 0.25
70_E 388_K 0.73 0.42 0.24
144_I 179_M 0.72 0.41 0.24
90_F 26_L 0.71 0.40 0.23
20_V 242_A 0.71 0.40 0.23
8_I 419_L 0.71 0.39 0.22
63_V 382_S 0.71 0.39 0.22
53_A 276_S 0.71 0.39 0.22
71_K 390_D 0.70 0.39 0.22
63_V 18_L 0.69 0.37 0.21
52_G 272_A 0.69 0.37 0.21
132_I 181_M 0.67 0.34 0.18
104_I 14_I 0.67 0.34 0.18
14_A 250_F 0.67 0.34 0.18
72_L 18_L 0.66 0.33 0.18
125_C 48_V 0.66 0.33 0.17
50_F 63_V 0.64 0.30 0.16
135_F 377_V 0.64 0.30 0.16
16_L 61_F 0.64 0.30 0.16
83_V 405_S 0.63 0.30 0.15
94_A 40_V 0.63 0.30 0.15
11_I 210_W 0.63 0.29 0.15
13_L 272_A 0.63 0.29 0.15
57_F 22_W 0.62 0.28 0.14
26_L 160_G 0.62 0.28 0.14
135_F 112_V 0.62 0.28 0.14
49_T 279_M 0.62 0.28 0.14
14_A 264_L 0.61 0.27 0.14
36_S 104_M 0.61 0.27 0.14
141_Y 4_L 0.61 0.27 0.14
38_D 279_M 0.61 0.27 0.13
55_V 401_L 0.60 0.26 0.13
5_L 112_V 0.60 0.26 0.13
4_I 354_P 0.60 0.26 0.13
8_I 416_L 0.60 0.26 0.13
31_Q 240_A 0.59 0.25 0.12
38_D 96_V 0.58 0.24 0.12
86_S 409_V 0.58 0.24 0.12
17_S 64_L 0.58 0.24 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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