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OPENSEQ.org
flgm-flia_str
Genes: A B A+B
Length: 88 236 318
Sequences: 1165 5877 723
Seq/Len: 13.24 24.9 2.27
MirrorTree (Pazo et al. 2001) 0.32
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 0.03 0.00
2 0.00 0.04 0.06
5 0.00 0.05 0.27
10 0.00 0.07 0.40
20 0.00 0.08 0.68
100 0.01 0.11 1.43
∞ 0.02 0.20 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
81_K 175_T 1.95 0.99 0.96
76_D 183_S 1.44 0.91 0.78
63_L 201_L 1.34 0.86 0.70
72_Y 194_Q 1.32 0.85 0.69
55_D 208_K 1.26 0.81 0.63
81_K 68_Y 1.23 0.79 0.60
54_K 27_T 1.22 0.78 0.59
79_V 194_Q 1.21 0.77 0.58
76_D 182_V 1.20 0.76 0.56
79_V 182_V 1.14 0.71 0.50
51_V 38_D 1.14 0.70 0.49
56_L 28_N 1.13 0.70 0.49
69_K 170_I 1.09 0.66 0.44
66_K 44_S 1.09 0.66 0.44
55_D 203_A 1.06 0.63 0.41
18_E 217_V 1.05 0.62 0.40
18_E 122_L 1.03 0.59 0.37
56_L 202_P 1.02 0.58 0.36
59_K 105_L 1.00 0.56 0.35
56_L 44_S 1.00 0.56 0.35
28_S 104_K 1.00 0.56 0.34
39_L 25_I 0.98 0.54 0.32
67_I 41_D 0.98 0.54 0.32
23_T 40_R 0.97 0.53 0.32
59_K 201_L 0.96 0.51 0.30
72_Y 58_S 0.95 0.50 0.29
58_K 181_A 0.93 0.48 0.27
59_K 199_E 0.92 0.47 0.26
54_K 23_K 0.92 0.46 0.26
2_V 211_E 0.89 0.44 0.24
56_L 76_A 0.89 0.44 0.24
66_K 188_R 0.88 0.43 0.23
63_L 194_Q 0.87 0.42 0.22
68_E 55_D 0.87 0.41 0.22
47_S 54_V 0.85 0.39 0.20
59_K 109_L 0.83 0.37 0.18
60_V 175_T 0.83 0.37 0.18
37_V 48_I 0.83 0.36 0.18
23_T 160_P 0.81 0.35 0.17
60_V 73_I 0.81 0.34 0.17
72_Y 61_N 0.81 0.34 0.17
79_V 4_P 0.81 0.34 0.17
49_N 23_K 0.80 0.34 0.17
56_L 193_I 0.80 0.34 0.16
79_V 44_S 0.80 0.33 0.16
51_V 125_S 0.79 0.33 0.16
62_E 104_K 0.79 0.33 0.16
83_L 113_P 0.79 0.33 0.16
74_V 123_G 0.79 0.33 0.15
74_V 162_S 0.79 0.32 0.15
26_K 35_E 0.79 0.32 0.15
56_L 24_A 0.79 0.32 0.15
62_E 122_L 0.78 0.32 0.15
47_S 178_V 0.78 0.32 0.15
79_V 190_K 0.78 0.32 0.15
40_S 68_Y 0.78 0.32 0.15
78_K 157_E 0.78 0.32 0.15
84_I 211_E 0.77 0.31 0.14
83_L 179_K 0.77 0.30 0.14
59_K 111_R 0.76 0.30 0.14
51_V 175_T 0.76 0.30 0.14
60_V 53_A 0.76 0.30 0.14
31_N 15_I 0.76 0.30 0.14
73_E 218_S 0.76 0.29 0.13
72_Y 27_T 0.75 0.29 0.13
63_L 28_N 0.75 0.29 0.13
68_E 15_I 0.75 0.29 0.13
44_Q 218_S 0.75 0.28 0.13
60_V 212_T 0.75 0.28 0.13
68_E 211_E 0.75 0.28 0.13
62_E 61_N 0.74 0.28 0.13
37_V 218_S 0.74 0.28 0.13
75_S 44_S 0.74 0.28 0.12
39_L 103_E 0.74 0.28 0.12
72_Y 198_Y 0.73 0.27 0.12
65_E 29_I 0.73 0.27 0.12
72_Y 83_S 0.73 0.27 0.12
30_T 172_R 0.73 0.27 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
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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