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OPENSEQ.org
EttA-vs-L5
Genes: A B A+B
Length: 555 179 704
Sequences: 8126 2042 1317
Seq/Len: 14.64 11.41 1.87
MirrorTree (Pazo et al. 2001) 0.29
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 0.01 0.09 0.00
2 0.01 0.09 0.00
5 0.01 0.09 0.00
10 0.01 0.09 0.00
20 0.02 0.09 0.04
100 0.06 0.09 0.37
∞ 0.17 0.09 1.79
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
333_Y 25_V 0.99 0.50 0.00
371_G 132_V 0.96 0.46 0.00
162_N 152_L 0.93 0.42 0.00
330_R 154_I 0.87 0.36 0.00
387_K 154_I 0.84 0.34 0.00
12_G 9_K 0.83 0.32 0.00
517_E 57_L 0.82 0.31 0.00
68_D 31_V 0.81 0.30 0.00
363_S 85_I 0.81 0.30 0.00
328_N 25_V 0.80 0.29 0.00
215_I 120_K 0.79 0.29 0.00
69_I 85_I 0.79 0.29 0.00
328_N 105_T 0.79 0.29 0.00
103_R 9_K 0.77 0.27 0.00
213_V 132_V 0.77 0.27 0.00
327_S 21_N 0.77 0.27 0.00
46_S 35_T 0.76 0.26 0.00
495_M 28_V 0.76 0.26 0.00
203_R 74_V 0.76 0.26 0.00
300_T 117_L 0.76 0.26 0.00
23_K 173_F 0.75 0.25 0.00
213_V 154_I 0.73 0.24 0.00
49_L 85_I 0.73 0.24 0.00
511_I 57_L 0.73 0.23 0.00
333_Y 13_V 0.73 0.23 0.00
154_P 27_Q 0.73 0.23 0.00
92_E 71_R 0.73 0.23 0.00
213_V 64_K 0.72 0.23 0.00
21_I 34_I 0.71 0.22 0.00
259_A 153_D 0.71 0.22 0.00
236_E 159_T 0.71 0.22 0.00
497_I 85_I 0.70 0.22 0.00
459_L 17_M 0.70 0.22 0.00
500_D 152_L 0.70 0.21 0.00
276_V 154_I 0.69 0.21 0.00
63_A 93_G 0.69 0.21 0.00
107_V 21_N 0.69 0.21 0.00
159_K 95_R 0.68 0.20 0.00
466_L 34_I 0.68 0.20 0.00
458_L 56_D 0.68 0.20 0.00
495_M 57_L 0.68 0.20 0.00
62_E 61_S 0.68 0.20 0.00
52_M 106_I 0.67 0.20 0.00
62_E 12_V 0.67 0.19 0.00
161_A 121_S 0.67 0.19 0.00
391_V 142_D 0.67 0.19 0.00
123_A 71_R 0.67 0.19 0.00
58_D 107_A 0.67 0.19 0.00
423_P 162_S 0.66 0.19 0.00
149_D 31_V 0.66 0.19 0.00
324_L 154_I 0.66 0.19 0.00
388_L 100_F 0.66 0.19 0.00
508_A 34_I 0.66 0.19 0.00
329_L 106_I 0.66 0.18 0.00
86_V 95_R 0.66 0.18 0.00
369_I 174_D 0.66 0.18 0.00
498_S 163_D 0.66 0.18 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
5491 1.87 EttA-vs-L5 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done
5466 2.21 EttA-vs-L5 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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