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OPENSEQ.org
binding2
Genes: A B A+B
Length: 88 236 315
Sequences: 1720 8083 1091
Seq/Len: 19.55 34.25 3.46
MirrorTree (Pazo et al. 2001) 0.30
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 0.05 0.02
2 0.00 0.07 0.10
5 0.00 0.09 0.54
10 0.00 0.10 0.75
20 0.01 0.11 1.17
100 0.01 0.15 2.27
∞ 0.03 0.21 3.37
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
81_K 175_T 2.03 1.00 0.98
76_D 183_S 1.77 0.99 0.96
63_L 201_L 1.60 0.98 0.93
55_D 208_K 1.53 0.97 0.91
72_Y 194_Q 1.35 0.93 0.82
77_E 179_K 1.24 0.89 0.75
54_K 27_T 1.16 0.83 0.67
76_D 182_V 1.15 0.82 0.66
56_L 44_S 1.14 0.82 0.65
56_L 202_P 1.09 0.78 0.60
79_V 194_Q 1.08 0.78 0.59
63_L 227_R 1.07 0.76 0.58
23_T 120_K 1.07 0.76 0.58
44_Q 218_S 1.04 0.73 0.54
56_L 28_N 1.02 0.71 0.52
49_N 23_K 0.98 0.67 0.47
66_K 44_S 0.94 0.62 0.43
65_E 107_E 0.94 0.61 0.42
68_E 211_E 0.90 0.57 0.37
73_E 208_K 0.90 0.57 0.37
59_K 201_L 0.88 0.54 0.35
67_I 41_D 0.87 0.54 0.34
18_E 57_L 0.87 0.53 0.34
46_L 52_K 0.85 0.51 0.32
79_V 182_V 0.85 0.50 0.31
25_Q 192_V 0.84 0.50 0.31
84_I 5_Y 0.84 0.49 0.30
40_S 229_R 0.83 0.48 0.29
81_K 68_Y 0.83 0.47 0.29
45_E 145_E 0.81 0.46 0.28
58_K 181_A 0.81 0.45 0.27
72_Y 61_N 0.80 0.44 0.26
60_V 212_T 0.80 0.43 0.26
25_Q 116_E 0.78 0.42 0.24
84_I 211_E 0.78 0.41 0.24
59_K 105_L 0.77 0.40 0.23
64_K 128_E 0.77 0.40 0.23
54_K 23_K 0.77 0.40 0.23
73_E 194_Q 0.77 0.40 0.23
53_E 188_R 0.76 0.39 0.23
62_E 104_K 0.76 0.39 0.22
81_K 179_K 0.76 0.39 0.22
31_N 157_E 0.76 0.39 0.22
54_K 229_R 0.75 0.38 0.21
71_E 118_V 0.75 0.38 0.21
63_L 124_I 0.75 0.37 0.21
72_Y 58_S 0.74 0.37 0.21
26_K 102_V 0.74 0.37 0.21
68_E 55_D 0.74 0.37 0.20
56_L 76_A 0.74 0.37 0.20
78_K 43_I 0.74 0.36 0.20
25_Q 168_E 0.74 0.36 0.20
84_I 108_K 0.73 0.36 0.20
22_N 152_A 0.73 0.35 0.19
54_K 221_K 0.73 0.35 0.19
59_K 111_R 0.72 0.34 0.18
82_G 67_A 0.71 0.33 0.18
71_E 126_T 0.70 0.32 0.17
78_K 157_E 0.70 0.32 0.17
67_I 9_I 0.70 0.32 0.17
55_D 203_A 0.70 0.32 0.17
60_V 128_E 0.70 0.32 0.17
79_V 4_P 0.70 0.32 0.17
28_S 127_E 0.70 0.32 0.17
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
7801 3.43 DI1200004_1SC5 Δgene:(1, ∞) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (r132) 0.98 Done - Shared
5232 3.46 binding2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06) 0.98 Done
5231 1.23 biding Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06) 0.95 Done
4635 2.27 flgm-flia_str Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
4634 0.02 flgm-flia_str Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) Killed - Shared
2161 0 flgm-sigma factor Δgene:(0, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
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