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OPENSEQ.org
EcoliTtd-JAck
Genes: A B A+B
Length: 303 201 476
Sequences: 2888 2927 1510
Seq/Len: 9.53 14.56 3.17
MirrorTree (Pazo et al. 2001) 0.92
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 2.89
2 0.00 0.00 2.96
5 0.00 0.00 2.98
10 0.00 0.00 2.98
20 0.00 0.00 3.00
100 0.03 0.03 3.02
∞ 0.05 0.05 3.12
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
168_S 85_S 2.32 1.00 0.99
66_L 133_T 2.22 1.00 0.99
55_T 124_P 1.70 0.99 0.95
183_S 179_K 1.65 0.98 0.94
68_R 132_A 1.32 0.91 0.81
187_V 166_S 1.23 0.86 0.74
51_I 22_V 1.21 0.85 0.72
55_T 130_L 1.19 0.83 0.70
187_V 104_G 1.18 0.83 0.69
248_L 122_I 1.16 0.82 0.68
47_S 182_F 1.12 0.78 0.63
62_K 129_V 1.10 0.77 0.61
246_Q 124_P 1.05 0.72 0.56
168_S 86_F 1.01 0.68 0.51
56_M 127_C 0.99 0.65 0.48
58_D 134_Q 0.98 0.64 0.47
189_A 81_M 0.96 0.62 0.45
188_N 81_M 0.94 0.59 0.42
69_P 62_I 0.93 0.58 0.41
72_Q 76_G 0.90 0.54 0.37
68_R 65_K 0.89 0.54 0.37
248_L 164_I 0.87 0.51 0.34
62_K 133_T 0.87 0.50 0.33
189_A 104_G 0.86 0.49 0.33
52_I 166_S 0.83 0.46 0.30
183_S 183_A 0.83 0.46 0.29
264_R 167_I 0.83 0.45 0.29
154_G 167_I 0.80 0.42 0.26
66_L 68_D 0.80 0.41 0.26
248_L 124_P 0.79 0.40 0.24
52_I 164_I 0.78 0.40 0.24
58_D 133_T 0.75 0.36 0.21
38_K 18_R 0.75 0.35 0.21
268_T 167_I 0.73 0.34 0.20
210_S 12_E 0.71 0.32 0.18
232_L 12_E 0.71 0.31 0.17
59_N 129_V 0.71 0.31 0.17
93_L 107_P 0.70 0.30 0.17
177_F 59_A 0.70 0.30 0.17
109_P 66_N 0.70 0.30 0.17
68_R 68_D 0.69 0.29 0.16
237_G 180_K 0.68 0.28 0.15
74_T 62_I 0.66 0.26 0.14
95_S 40_L 0.66 0.26 0.14
205_T 135_V 0.66 0.26 0.14
66_L 65_K 0.66 0.26 0.14
267_S 60_G 0.65 0.25 0.13
169_E 85_S 0.64 0.24 0.12
246_Q 59_A 0.64 0.24 0.12
172_E 85_S 0.63 0.23 0.12
74_T 31_T 0.62 0.23 0.11
128_G 149_P 0.61 0.22 0.10
168_S 35_V 0.61 0.21 0.10
191_P 83_M 0.61 0.21 0.10
178_V 45_R 0.60 0.21 0.10
234_L 156_R 0.59 0.20 0.10
49_G 183_A 0.59 0.20 0.09
168_S 160_F 0.58 0.20 0.09
147_I 154_V 0.58 0.19 0.09
154_G 113_C 0.58 0.19 0.09
202_S 175_I 0.57 0.18 0.08
280_H 131_A 0.57 0.18 0.08
246_Q 22_V 0.57 0.18 0.08
229_E 12_E 0.57 0.18 0.08
37_L 42_E 0.57 0.18 0.08
147_I 133_T 0.57 0.18 0.08
55_T 131_A 0.57 0.18 0.08
211_R 125_A 0.57 0.18 0.08
45_T 181_L 0.57 0.18 0.08
12_N 12_E 0.57 0.18 0.08
145_A 114_Q 0.56 0.18 0.08
188_N 175_I 0.56 0.18 0.08
187_V 81_M 0.56 0.18 0.08
95_S 144_T 0.56 0.18 0.08
213_A 176_A 0.56 0.17 0.08
237_G 26_T 0.56 0.17 0.08
46_S 183_A 0.56 0.17 0.08
162_S 68_D 0.56 0.17 0.08
34_V 135_V 0.55 0.17 0.07
212_K 135_V 0.55 0.17 0.07
152_A 120_H 0.55 0.17 0.07
236_E 12_E 0.55 0.17 0.07
72_Q 34_D 0.54 0.16 0.07
269_I 90_F 0.54 0.16 0.07
38_K 16_D 0.54 0.16 0.07
276_G 59_A 0.54 0.16 0.07
232_L 135_V 0.54 0.16 0.07
228_A 107_P 0.53 0.16 0.07
70_A 128_A 0.53 0.16 0.07
282_R 81_M 0.53 0.15 0.06
153_G 33_R 0.53 0.15 0.06
248_L 166_S 0.53 0.15 0.06
43_A 6_T 0.53 0.15 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
7294 3.17 EcoliTtd-JAck Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.99 Done - Shared
7293 1.31 EcoliTtd Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.93 Done
0882 2.07 TTDA_TTDB Δgene:(0, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.94 Done
0881 1.17 TTDA_TTDB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.82 Done
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