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OPENSEQ.org
YEFM - YOEB
Genes: A B A+B
Length: 83 84 167
Sequences: 491 562 265
Seq/Len: 5.92 6.69 1.59
MirrorTree (Pazo et al. 2001) 0.62
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 1.55
2 0.00 0.00 1.56
5 0.00 0.00 1.56
10 0.01 0.00 1.57
20 0.01 0.01 1.59
100 0.01 0.02 1.63
∞ 0.08 0.10 2.23
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
72_K 69_A 2.41 1.00 0.99
66_D 8_E 2.21 0.99 0.97
57_S 82_Y 2.14 0.99 0.97
67_S 6_S 1.91 0.97 0.93
56_R 82_Y 1.85 0.97 0.92
63_R 79_A 1.61 0.92 0.83
70_S 6_S 1.60 0.91 0.82
79_K 5_W 1.58 0.91 0.81
70_S 7_E 1.56 0.90 0.80
71_L 78_A 1.56 0.90 0.80
76_G 6_S 1.45 0.85 0.72
53_Y 61_T 1.41 0.82 0.68
60_N 82_Y 1.35 0.79 0.64
71_L 76_L 1.30 0.75 0.58
72_K 55_F 1.21 0.67 0.49
68_I 55_F 1.21 0.67 0.48
78_E 2_K 1.16 0.62 0.43
63_R 12_D 1.15 0.61 0.42
80_D 5_W 1.13 0.59 0.40
70_S 8_E 1.13 0.59 0.40
66_D 49_K 1.12 0.58 0.39
5_S 5_W 1.07 0.53 0.34
48_L 50_H 1.05 0.51 0.31
74_G 60_I 1.04 0.49 0.30
7_S 8_E 1.00 0.46 0.27
62_R 6_S 0.99 0.45 0.26
7_S 71_T 0.98 0.44 0.25
65_M 49_K 0.97 0.43 0.24
65_M 51_N 0.95 0.41 0.23
54_L 81_R 0.95 0.40 0.22
41_S 14_L 0.94 0.40 0.22
44_E 63_E 0.94 0.39 0.21
55_L 52_L 0.92 0.38 0.20
31_R 80_C 0.92 0.38 0.20
41_S 21_K 0.92 0.38 0.20
54_L 67_V 0.92 0.37 0.20
11_Q 26_K 0.91 0.37 0.19
81_I 26_K 0.91 0.37 0.19
71_L 55_F 0.91 0.37 0.19
9_A 38_P 0.91 0.36 0.19
69_D 64_H 0.91 0.36 0.19
58_P 67_V 0.90 0.36 0.18
55_L 38_P 0.90 0.36 0.18
67_S 69_A 0.90 0.35 0.18
83_E 64_H 0.90 0.35 0.18
64_L 55_F 0.89 0.35 0.17
13_L 39_F 0.89 0.35 0.17
48_L 40_E 0.88 0.33 0.16
60_N 12_D 0.87 0.33 0.16
31_R 56_W 0.87 0.32 0.16
69_D 31_I 0.86 0.32 0.15
55_L 10_W 0.85 0.31 0.15
23_D 56_W 0.85 0.31 0.15
38_V 54_G 0.85 0.31 0.14
44_E 64_H 0.84 0.30 0.14
76_G 78_A 0.83 0.29 0.14
2_R 66_L 0.83 0.29 0.13
54_L 82_Y 0.83 0.29 0.13
20_A 82_Y 0.83 0.29 0.13
36_A 75_L 0.82 0.28 0.13
63_R 11_D 0.82 0.28 0.12
79_K 10_W 0.82 0.28 0.12
83_E 32_K 0.81 0.27 0.12
43_E 79_A 0.81 0.27 0.12
29_I 20_D 0.81 0.27 0.12
51_T 38_P 0.80 0.27 0.12
53_Y 21_K 0.80 0.27 0.12
74_G 1_M 0.79 0.26 0.11
2_R 9_S 0.79 0.26 0.11
47_S 26_K 0.79 0.26 0.11
33_N 34_T 0.79 0.26 0.11
36_A 66_L 0.79 0.25 0.11
69_D 66_L 0.78 0.25 0.11
64_L 78_A 0.78 0.25 0.10
43_E 73_D 0.78 0.25 0.10
48_L 73_D 0.77 0.24 0.10
70_S 31_I 0.77 0.24 0.10
23_D 54_G 0.77 0.24 0.10
57_S 47_P 0.76 0.24 0.10
18_M 61_T 0.76 0.24 0.10
20_A 29_E 0.76 0.24 0.10
58_P 64_H 0.76 0.23 0.10
41_S 13_Y 0.76 0.23 0.09
17_M 82_Y 0.75 0.23 0.09
63_R 1_M 0.75 0.22 0.09
26_P 33_D 0.74 0.22 0.09
16_T 26_K 0.74 0.22 0.09
64_L 28_N 0.74 0.22 0.09
12_N 73_D 0.74 0.22 0.08
13_L 38_P 0.74 0.22 0.08
60_N 81_R 0.73 0.22 0.08
80_D 9_S 0.73 0.22 0.08
6_Y 70_V 0.73 0.21 0.08
54_L 12_D 0.73 0.21 0.08
71_L 6_S 0.73 0.21 0.08
41_S 10_W 0.72 0.21 0.08
72_K 29_E 0.71 0.20 0.07
29_I 76_L 0.71 0.20 0.07
73_S 7_E 0.71 0.20 0.07
67_S 78_A 0.71 0.20 0.07
76_G 4_I 0.71 0.20 0.07
64_L 24_V 0.71 0.20 0.07
32_Q 31_I 0.71 0.20 0.07
44_E 33_D 0.70 0.20 0.07
44_E 62_E 0.70 0.20 0.07
32_Q 80_C 0.70 0.19 0.07
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
4755 4.57 TA_seven Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
0722 3.69 2A6Q_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done
0720 5.44 2A6Q Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 1.00 Done - Shared
0068 2.23 YEFM - YOEB Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.99 Done
0010 5.05 YEFM - YOEB Δgene:(0, 20) A:(1E-04, 8) B:(1E-04, 8) (2013_03) 0.99 Done - Shared
0005 1.59 YEFM - YOEB Δgene:(0, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.99 Done - Shared
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