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OPENSEQ.org
Fan
Genes: A B A+B
Length: 104 246 345
Sequences: 2038 3957 146
Seq/Len: 19.6 16.09 0.42
MirrorTree (Pazo et al. 2001) 0.44
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 0.12 0.08 0.02
2 0.13 0.09 0.03
5 0.14 0.11 0.04
10 0.15 0.12 0.06
20 0.15 0.13 0.07
100 0.16 0.14 0.14
∞ 0.18 0.19 0.42
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
19_F 89_S 1.46 0.48 0.00
98_L 84_V 1.18 0.29 0.00
79_V 50_L 1.17 0.28 0.00
20_L 204_I 1.12 0.26 0.00
66_G 17_I 1.10 0.24 0.00
4_W 127_F 1.08 0.23 0.00
4_W 39_D 1.08 0.23 0.00
85_F 68_L 1.07 0.23 0.00
82_V 113_R 1.06 0.22 0.00
86_F 133_R 1.04 0.21 0.00
72_R 51_K 1.04 0.21 0.00
17_V 84_V 1.00 0.19 0.00
75_S 64_E 0.97 0.18 0.00
4_W 132_C 0.94 0.17 0.00
102_L 230_Q 0.93 0.16 0.00
88_L 122_G 0.93 0.16 0.00
20_L 185_I 0.93 0.16 0.00
99_A 188_L 0.92 0.16 0.00
28_E 74_K 0.91 0.16 0.00
76_G 231_I 0.91 0.15 0.00
89_I 65_I 0.90 0.15 0.00
76_G 196_A 0.90 0.15 0.00
59_L 108_I 0.89 0.15 0.00
8_V 24_F 0.89 0.15 0.00
4_W 91_G 0.87 0.14 0.00
12_I 67_E 0.87 0.14 0.00
56_W 43_L 0.87 0.14 0.00
81_G 89_S 0.87 0.14 0.00
94_Y 201_F 0.87 0.14 0.00
104_V 128_I 0.86 0.14 0.00
71_P 133_R 0.86 0.14 0.00
82_V 112_F 0.86 0.14 0.00
89_I 63_E 0.85 0.14 0.00
87_T 65_I 0.85 0.14 0.00
51_I 214_T 0.85 0.13 0.00
100_A 208_V 0.84 0.13 0.00
23_R 204_I 0.84 0.13 0.00
20_L 126_L 0.83 0.13 0.00
54_S 195_Y 0.83 0.13 0.00
12_I 46_T 0.83 0.13 0.00
6_C 184_F 0.83 0.13 0.00
100_A 72_V 0.83 0.13 0.00
18_L 188_L 0.82 0.12 0.00
21_V 191_M 0.81 0.12 0.00
98_L 205_L 0.81 0.12 0.00
20_L 232_P 0.81 0.12 0.00
4_W 35_G 0.81 0.12 0.00
82_V 94_G 0.81 0.12 0.00
59_L 15_L 0.81 0.12 0.00
90_I 66_V 0.80 0.12 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
9475 0.07 evolve2 Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
9464 0.07 evolve2 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
9463 0.05 evolve2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
9412 0.42 Fan Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
9411 0.06 Fan Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed
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