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OPENSEQ.org
biding
Genes: A B A+B
Length: 88 236 308
Sequences: 1720 8083 380
Seq/Len: 19.55 34.25 1.23
MirrorTree (Pazo et al. 2001) 0.65
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
63_L 201_L 2.22 0.99 0.95
56_L 44_S 1.80 0.94 0.83
81_K 175_T 1.50 0.82 0.62
55_D 208_K 1.49 0.81 0.61
79_V 194_Q 1.48 0.81 0.60
72_Y 194_Q 1.42 0.77 0.55
56_L 202_P 1.41 0.76 0.54
72_Y 199_E 1.35 0.72 0.48
56_L 28_N 1.35 0.71 0.47
59_K 73_I 1.34 0.71 0.47
64_K 128_E 1.32 0.69 0.44
79_V 182_V 1.31 0.69 0.44
54_K 27_T 1.28 0.66 0.41
75_S 28_N 1.25 0.63 0.37
59_K 201_L 1.24 0.62 0.36
54_K 23_K 1.15 0.53 0.28
85_E 114_T 1.10 0.49 0.24
64_K 52_K 1.10 0.48 0.23
76_D 213_S 1.09 0.48 0.23
83_L 125_S 1.09 0.48 0.23
72_Y 220_L 1.08 0.46 0.22
57_E 229_R 1.08 0.46 0.22
44_Q 218_S 1.07 0.46 0.22
37_V 217_V 1.07 0.46 0.22
66_K 46_G 1.07 0.45 0.21
72_Y 51_I 1.07 0.45 0.21
76_D 182_V 1.05 0.43 0.20
85_E 48_I 1.04 0.43 0.19
60_V 208_K 1.03 0.42 0.19
66_K 24_A 1.02 0.41 0.18
56_L 198_Y 1.00 0.39 0.17
25_Q 161_S 1.00 0.39 0.16
73_E 194_Q 1.00 0.39 0.16
56_L 24_A 0.98 0.37 0.15
68_E 211_E 0.97 0.37 0.15
72_Y 191_L 0.97 0.36 0.15
79_V 193_I 0.96 0.36 0.14
67_I 103_E 0.96 0.35 0.14
40_S 42_L 0.96 0.35 0.14
36_K 62_P 0.95 0.34 0.13
73_E 198_Y 0.95 0.34 0.13
79_V 224_A 0.95 0.34 0.13
55_D 228_L 0.93 0.33 0.12
50_D 218_S 0.93 0.33 0.12
60_V 182_V 0.93 0.33 0.12
78_K 118_V 0.93 0.32 0.12
76_D 218_S 0.92 0.32 0.12
43_A 26_A 0.92 0.32 0.12
77_E 179_K 0.92 0.32 0.12
23_T 108_K 0.92 0.31 0.12
84_I 25_I 0.91 0.31 0.11
19_K 104_K 0.90 0.30 0.11
82_G 215_S 0.90 0.30 0.10
40_S 213_S 0.89 0.29 0.10
72_Y 15_I 0.89 0.29 0.10
56_L 203_A 0.88 0.29 0.10
54_K 221_K 0.88 0.28 0.10
33_I 123_G 0.88 0.28 0.10
26_K 162_S 0.87 0.28 0.10
67_I 21_L 0.87 0.28 0.10
63_L 77_I 0.87 0.28 0.10
47_S 144_L 0.87 0.28 0.10
36_K 57_L 0.87 0.28 0.09
79_V 23_K 0.86 0.27 0.09
63_L 227_R 0.86 0.27 0.09
47_S 192_V 0.86 0.27 0.09
65_E 174_L 0.85 0.26 0.09
67_I 201_L 0.85 0.26 0.08
63_L 16_L 0.84 0.26 0.08
74_V 194_Q 0.84 0.26 0.08
33_I 162_S 0.84 0.25 0.08
55_D 30_K 0.84 0.25 0.08
67_I 208_K 0.84 0.25 0.08
37_V 229_R 0.83 0.25 0.08
64_K 190_K 0.83 0.25 0.08
84_I 73_I 0.83 0.24 0.08
23_T 172_R 0.82 0.24 0.08
28_S 121_E 0.82 0.24 0.08
79_V 107_E 0.82 0.24 0.07
39_L 58_S 0.82 0.24 0.07
55_D 153_R 0.82 0.24 0.07
44_Q 200_E 0.82 0.24 0.07
24_E 115_D 0.81 0.23 0.07
20_R 160_P 0.81 0.23 0.07
25_Q 108_K 0.81 0.23 0.07
81_K 228_L 0.81 0.23 0.07
75_S 198_Y 0.80 0.23 0.07
86_F 225_L 0.80 0.23 0.07
73_E 107_E 0.80 0.22 0.07
78_K 137_N 0.80 0.22 0.07
54_K 148_F 0.79 0.22 0.07
60_V 178_V 0.79 0.22 0.07
27_E 147_V 0.79 0.22 0.06
53_E 222_A 0.78 0.21 0.06
82_G 139_S 0.78 0.21 0.06
43_A 92_R 0.78 0.21 0.06
66_K 217_V 0.78 0.21 0.06
55_D 44_S 0.78 0.21 0.06
10_L 211_E 0.77 0.21 0.06
80_V 215_S 0.77 0.21 0.06
54_K 18_Y 0.77 0.21 0.06
80_V 182_V 0.77 0.20 0.06
79_V 38_D 0.77 0.20 0.06
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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