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OPENSEQ.org
2A6Q_Jackhmmer
Genes: A B A+B
Length: 83 84 167
Sequences: 1727 2567 616
Seq/Len: 20.81 30.56 3.69
MirrorTree (Pazo et al. 2001) 0.77
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 3.69
2 0.00 0.01 3.73
5 0.01 0.01 3.82
10 0.01 0.02 3.86
20 0.01 0.02 3.95
100 0.08 0.06 4.26
∞ 0.13 0.11 5.14
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
67_S 6_S 2.65 1.00 1.00
66_D 8_E 2.57 1.00 1.00
70_S 6_S 2.21 1.00 0.99
57_S 82_Y 1.93 1.00 0.98
63_R 79_A 1.86 0.99 0.98
72_K 69_A 1.85 0.99 0.97
78_E 2_K 1.82 0.99 0.97
68_I 55_F 1.81 0.99 0.97
56_R 82_Y 1.74 0.99 0.96
70_S 7_E 1.70 0.99 0.96
76_G 6_S 1.60 0.98 0.94
60_N 82_Y 1.39 0.95 0.87
71_L 76_L 1.37 0.94 0.86
71_L 6_S 1.34 0.94 0.84
63_R 11_D 1.33 0.93 0.84
65_M 51_N 1.19 0.87 0.73
71_L 78_A 1.16 0.85 0.71
79_K 5_W 1.11 0.81 0.67
83_E 32_K 1.05 0.76 0.60
68_I 78_A 1.04 0.75 0.58
54_L 67_V 1.02 0.73 0.56
70_S 8_E 1.00 0.71 0.54
80_D 5_W 0.94 0.64 0.47
72_K 55_F 0.93 0.63 0.45
55_L 52_L 0.92 0.61 0.44
65_M 52_L 0.92 0.61 0.43
63_R 12_D 0.91 0.60 0.42
76_G 4_I 0.90 0.59 0.41
69_D 75_L 0.87 0.55 0.38
76_G 76_L 0.87 0.55 0.37
20_A 29_E 0.85 0.52 0.35
16_T 26_K 0.84 0.51 0.34
44_E 62_E 0.82 0.49 0.32
64_L 55_F 0.82 0.49 0.32
56_R 50_H 0.82 0.49 0.32
52_A 50_H 0.81 0.48 0.31
56_R 31_I 0.81 0.47 0.30
68_I 69_A 0.79 0.45 0.28
61_A 51_N 0.79 0.44 0.28
67_S 55_F 0.78 0.44 0.28
47_S 40_E 0.77 0.42 0.26
57_S 45_P 0.76 0.41 0.25
39_L 29_E 0.73 0.37 0.22
44_E 63_E 0.72 0.36 0.21
76_G 78_A 0.72 0.36 0.21
9_A 38_P 0.72 0.35 0.21
4_I 47_P 0.69 0.33 0.19
60_N 81_R 0.68 0.31 0.17
71_L 55_F 0.68 0.31 0.17
38_V 52_L 0.68 0.31 0.17
44_E 64_H 0.67 0.30 0.17
7_S 4_I 0.67 0.30 0.17
48_L 50_H 0.67 0.30 0.16
6_Y 16_W 0.66 0.29 0.16
57_S 43_G 0.66 0.29 0.16
3_T 34_T 0.66 0.29 0.16
54_L 81_R 0.65 0.28 0.15
55_L 10_W 0.65 0.28 0.15
19_K 14_L 0.65 0.28 0.15
45_Y 23_I 0.65 0.28 0.15
67_S 78_A 0.65 0.28 0.15
65_M 78_A 0.65 0.27 0.15
57_S 41_G 0.64 0.27 0.14
79_K 18_E 0.64 0.26 0.14
70_S 16_W 0.63 0.26 0.14
44_E 50_H 0.63 0.26 0.13
4_I 51_N 0.63 0.25 0.13
32_Q 22_R 0.62 0.25 0.13
20_A 82_Y 0.62 0.24 0.12
55_L 54_G 0.61 0.24 0.12
73_S 72_D 0.61 0.24 0.12
23_D 41_G 0.61 0.24 0.12
73_S 7_E 0.61 0.23 0.12
7_S 81_R 0.60 0.23 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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