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OPENSEQ.org
TA_seven
Genes: A B A+B
Length: 83 84 167
Sequences: 2284 3230 764
Seq/Len: 27.52 38.45 4.57
MirrorTree (Pazo et al. 2001) 0.76
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 0.01 4.57
2 0.01 0.02 4.63
5 0.02 0.03 4.75
10 0.03 0.04 4.76
20 0.03 0.05 4.87
100 0.05 0.07 5.19
∞ 0.10 0.12 6.29
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
66_D 8_E 2.99 1.00 1.00
67_S 6_S 2.65 1.00 1.00
70_S 6_S 2.17 1.00 0.99
70_S 7_E 2.16 1.00 0.99
57_S 82_Y 2.14 1.00 0.99
72_K 69_A 2.07 1.00 0.99
68_I 55_F 1.97 1.00 0.99
78_E 2_K 1.91 1.00 0.98
63_R 79_A 1.70 0.99 0.96
65_M 51_N 1.59 0.99 0.95
76_G 6_S 1.59 0.99 0.94
63_R 11_D 1.56 0.99 0.94
79_K 5_W 1.47 0.98 0.91
56_R 82_Y 1.43 0.97 0.90
68_I 78_A 1.30 0.95 0.84
71_L 76_L 1.30 0.94 0.84
60_N 82_Y 1.28 0.94 0.83
71_L 78_A 1.24 0.93 0.80
72_K 55_F 1.22 0.92 0.79
71_L 6_S 1.22 0.92 0.79
54_L 67_V 1.05 0.81 0.63
65_M 52_L 1.02 0.79 0.60
70_S 8_E 0.94 0.70 0.50
76_G 4_I 0.91 0.67 0.46
52_A 50_H 0.91 0.66 0.46
39_L 29_E 0.85 0.58 0.38
71_L 55_F 0.84 0.57 0.37
80_D 5_W 0.83 0.57 0.36
64_L 55_F 0.82 0.55 0.35
76_G 76_L 0.81 0.54 0.34
63_R 12_D 0.80 0.52 0.33
67_S 55_F 0.80 0.52 0.32
55_L 52_L 0.79 0.51 0.32
68_I 69_A 0.78 0.49 0.30
83_E 32_K 0.77 0.48 0.29
20_A 29_E 0.77 0.48 0.29
20_A 82_Y 0.77 0.48 0.29
56_R 31_I 0.76 0.47 0.28
44_E 62_E 0.76 0.46 0.28
38_V 54_G 0.74 0.44 0.26
55_L 10_W 0.74 0.44 0.25
56_R 50_H 0.71 0.39 0.22
54_L 81_R 0.69 0.37 0.21
72_K 18_E 0.68 0.36 0.20
13_L 52_L 0.67 0.34 0.18
69_D 75_L 0.65 0.33 0.17
3_T 33_D 0.65 0.32 0.17
61_A 51_N 0.65 0.32 0.17
31_R 80_C 0.65 0.32 0.17
44_E 63_E 0.64 0.31 0.16
57_S 45_P 0.64 0.31 0.16
77_T 7_E 0.63 0.30 0.15
16_T 50_H 0.63 0.30 0.15
53_Y 61_T 0.62 0.29 0.15
79_K 7_E 0.62 0.29 0.15
43_E 73_D 0.62 0.28 0.14
21_V 26_K 0.62 0.28 0.14
28_L 19_T 0.61 0.28 0.14
44_E 64_H 0.61 0.28 0.14
38_V 52_L 0.61 0.28 0.14
57_S 43_G 0.61 0.28 0.14
59_A 20_D 0.61 0.27 0.14
45_Y 9_S 0.60 0.27 0.13
76_G 78_A 0.60 0.26 0.13
67_S 78_A 0.60 0.26 0.13
56_R 49_K 0.60 0.26 0.13
54_L 82_Y 0.59 0.26 0.12
18_M 80_C 0.59 0.25 0.12
45_Y 33_D 0.58 0.25 0.12
53_Y 30_L 0.58 0.25 0.12
32_Q 22_R 0.58 0.24 0.12
75_K 71_T 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
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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