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OPENSEQ.org
DT gene 8 -6
Genes: A B A+B
Length: 141 239 369
Sequences: 4093 128 80
Seq/Len: 29.03 0.54 0.22
MirrorTree (Pazo et al. 2001) 0.28
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.10 0.00 0.02
2 0.10 0.00 0.02
5 0.10 0.00 0.02
10 0.10 0.00 0.02
20 0.10 0.00 0.02
100 0.14 0.00 0.02
∞ 0.24 0.00 0.21
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
83_D 33_H 1.28 0.23 0.00
31_L 212_R 1.19 0.19 0.00
91_N 236_T 1.14 0.17 0.00
88_T 211_R 1.10 0.16 0.00
87_I 233_N 1.05 0.14 0.00
81_V 237_E 1.02 0.14 0.00
83_D 146_V 1.00 0.13 0.00
53_T 63_P 0.98 0.12 0.00
125_A 158_R 0.97 0.12 0.00
42_T 39_P 0.96 0.12 0.00
88_T 7_R 0.96 0.12 0.00
31_L 77_P 0.96 0.12 0.00
112_Y 153_P 0.96 0.12 0.00
54_S 212_R 0.94 0.11 0.00
91_N 60_A 0.94 0.11 0.00
76_I 232_I 0.93 0.11 0.00
31_L 73_P 0.93 0.11 0.00
83_D 226_V 0.93 0.11 0.00
29_V 204_R 0.92 0.11 0.00
49_L 204_R 0.92 0.11 0.00
79_D 162_Q 0.91 0.11 0.00
88_T 140_A 0.91 0.11 0.00
53_T 193_I 0.90 0.10 0.00
54_S 47_V 0.89 0.10 0.00
84_E 203_E 0.89 0.10 0.00
104_F 188_V 0.89 0.10 0.00
91_N 235_T 0.89 0.10 0.00
88_T 216_E 0.88 0.10 0.00
122_L 166_R 0.87 0.10 0.00
80_P 169_A 0.87 0.10 0.00
109_T 36_I 0.87 0.10 0.00
56_P 57_P 0.86 0.10 0.00
66_L 235_T 0.86 0.10 0.00
31_L 100_P 0.86 0.10 0.00
33_I 204_R 0.85 0.10 0.00
109_T 90_E 0.85 0.09 0.00
67_S 180_F 0.85 0.09 0.00
42_T 28_L 0.84 0.09 0.00
79_D 182_V 0.84 0.09 0.00
79_D 236_T 0.84 0.09 0.00
115_L 69_V 0.84 0.09 0.00
66_L 239_Q 0.84 0.09 0.00
87_I 168_Q 0.84 0.09 0.00
93_L 143_S 0.83 0.09 0.00
121_T 10_P 0.83 0.09 0.00
88_T 189_D 0.82 0.09 0.00
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
10530 18.75 ExbD-TonB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.10 Done
10528 11.86 ExbD-TonB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done
10526 0.22 ExbD-TonB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
8585 21.61 Dale 6-20 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.60 Done - Shared
8568 19.56 DT gene 8, -6 jack Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.40 Done - Shared
8566 0.22 DT gene 8 -6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8565 0.02 DT -6 Δgene:(1, 20) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
8564 0.02 DT gene 100 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
8563 16.31 DT -10 Jack Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.45 Done - Shared
8562 0.02 DT -10 Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
8561 17.39 Dale Δgene:(1, 20) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.61 Done - Shared
7825 9.5 DT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.18 Done - Shared
7822 0.02 DT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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