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OPENSEQ.org
DI1200004_1SC5
Genes: A B A+B
Length: 88 236 306
Sequences: 1930 13743 1050
Seq/Len: 21.93 58.23 3.43
MirrorTree (Pazo et al. 2001) 0.26
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 0.01 0.01
2 0.00 0.01 0.11
5 0.00 0.01 0.27
10 0.00 0.04 0.48
20 0.00 0.05 0.77
100 0.00 0.07 1.95
∞ 0.00 0.14 3.24
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 2.01 1.00 0.98
79_V 194_Q 1.64 0.98 0.93
76_D 183_S 1.61 0.98 0.93
59_K 111_R 1.09 0.77 0.59
68_E 211_E 1.08 0.77 0.58
76_D 15_I 1.07 0.76 0.58
64_K 14_L 1.06 0.75 0.56
72_Y 194_Q 1.04 0.73 0.54
75_S 98_I 1.03 0.72 0.53
67_I 210_L 1.00 0.68 0.49
59_K 105_L 0.98 0.67 0.47
63_L 201_L 0.96 0.65 0.45
83_L 220_L 0.96 0.65 0.45
66_K 15_I 0.90 0.56 0.37
60_V 202_P 0.88 0.54 0.35
58_K 161_S 0.88 0.54 0.34
22_N 159_I 0.87 0.53 0.34
24_E 125_S 0.87 0.53 0.34
56_L 28_N 0.87 0.53 0.34
76_D 182_V 0.86 0.52 0.33
40_S 56_N 0.86 0.52 0.32
63_L 147_V 0.86 0.52 0.32
75_S 44_S 0.85 0.51 0.32
28_S 123_G 0.85 0.50 0.31
63_L 28_N 0.84 0.49 0.30
56_L 202_P 0.82 0.47 0.28
23_T 68_Y 0.81 0.45 0.27
18_E 150_D 0.80 0.44 0.26
55_D 208_K 0.80 0.44 0.26
39_L 95_E 0.80 0.44 0.26
84_I 108_K 0.80 0.44 0.26
45_E 18_Y 0.79 0.42 0.25
60_V 138_F 0.78 0.42 0.24
79_V 153_R 0.78 0.42 0.24
63_L 124_I 0.78 0.41 0.24
14_L 218_S 0.78 0.41 0.24
60_V 226_E 0.77 0.40 0.22
60_V 73_I 0.76 0.39 0.22
66_K 44_S 0.76 0.39 0.22
84_I 229_R 0.76 0.38 0.22
63_L 166_E 0.75 0.38 0.21
63_L 139_S 0.75 0.38 0.21
27_E 184_K 0.75 0.38 0.21
58_K 48_I 0.75 0.38 0.21
60_V 48_I 0.74 0.37 0.20
59_K 166_E 0.74 0.37 0.20
24_E 126_T 0.74 0.36 0.20
54_K 27_T 0.73 0.35 0.19
82_G 189_E 0.73 0.35 0.19
32_K 120_K 0.72 0.34 0.19
62_E 163_T 0.72 0.34 0.18
73_E 113_P 0.72 0.34 0.18
67_I 114_T 0.71 0.33 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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