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OPENSEQ.org
Ec EZ
Genes: A B A+B
Length: 222 383 534
Sequences: 88685 2098 542
Seq/Len: 399.48 5.48 1.01
MirrorTree (Pazo et al. 2001) 0.06
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 0.09 0.02 0.01
2 0.10 0.02 0.04
5 0.14 0.02 0.15
10 0.19 0.02 0.35
20 0.25 0.02 0.90
100 0.36 0.03 3.39
∞ 0.37 0.05 4.52
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
191_L 116_V 1.09 0.42 0.00
28_G 100_I 1.07 0.41 0.00
2_I 42_V 1.05 0.38 0.00
51_I 122_D 0.96 0.31 0.00
51_I 116_V 0.93 0.29 0.00
136_I 116_V 0.91 0.27 0.00
42_S 262_V 0.90 0.26 0.00
48_I 21_G 0.89 0.26 0.00
25_M 41_A 0.86 0.24 0.00
64_H 60_I 0.84 0.22 0.00
159_L 80_A 0.83 0.21 0.00
138_L 264_I 0.83 0.21 0.00
144_Q 115_V 0.82 0.21 0.00
101_A 41_A 0.82 0.21 0.00
180_F 90_A 0.81 0.20 0.00
28_G 289_N 0.80 0.20 0.00
8_S 92_L 0.79 0.20 0.00
121_A 86_D 0.79 0.19 0.00
120_A 16_I 0.79 0.19 0.00
95_T 206_M 0.78 0.19 0.00
91_L 38_E 0.78 0.18 0.00
48_I 301_D 0.78 0.18 0.00
81_I 241_E 0.77 0.18 0.00
17_A 116_V 0.76 0.18 0.00
168_L 48_A 0.76 0.17 0.00
207_M 216_V 0.75 0.17 0.00
6_H 155_K 0.75 0.17 0.00
54_P 229_V 0.74 0.17 0.00
128_L 42_V 0.74 0.17 0.00
210_L 234_D 0.74 0.16 0.00
59_I 119_V 0.74 0.16 0.00
158_V 144_A 0.73 0.16 0.00
207_M 153_L 0.73 0.16 0.00
96_V 230_A 0.72 0.16 0.00
39_A 94_G 0.72 0.15 0.00
215_L 78_R 0.71 0.15 0.00
45_L 118_E 0.71 0.15 0.00
159_L 306_L 0.71 0.15 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
13125 3.84 ZE Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
12176 5.12 Ec EZ inf Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
12174 1.01 Ec EZ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
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