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OPENSEQ.org
CheYFliY
Genes: A B A+B
Length: 120 378 492
Sequences: 45960 2660 927
Seq/Len: 383 7.04 1.88
MirrorTree (Pazo et al. 2001) 0.52
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 0.16 0.13 0.99
2 0.18 0.13 1.17
5 0.18 0.13 1.21
10 0.18 0.13 1.26
20 0.18 0.13 1.36
100 0.21 0.14 1.86
∞ 0.27 0.15 3.28
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
112_L 372_E 1.29 0.79 0.05
115_I 83_F 1.18 0.69 0.04
75_Q 272_P 1.17 0.68 0.03
71_Q 260_P 1.13 0.64 0.03
71_Q 271_A 1.11 0.62 0.03
72_I 247_T 1.10 0.61 0.03
64_T 281_S 1.05 0.56 0.02
78_I 19_G 1.00 0.50 0.02
34_E 134_H 1.00 0.50 0.02
7_I 291_A 0.98 0.49 0.02
71_Q 246_V 0.97 0.48 0.02
64_T 111_A 0.97 0.47 0.02
7_I 274_Q 0.97 0.47 0.02
64_T 292_P 0.96 0.46 0.02
72_I 267_A 0.95 0.45 0.02
34_E 131_G 0.94 0.43 0.02
72_I 243_K 0.92 0.42 0.02
72_I 268_K 0.92 0.42 0.02
116_N 372_E 0.92 0.41 0.02
73_D 289_V 0.91 0.41 0.01
72_I 252_I 0.91 0.41 0.01
35_N 65_D 0.90 0.40 0.01
78_I 288_A 0.90 0.40 0.01
52_T 57_S 0.89 0.39 0.01
37_A 256_Q 0.88 0.38 0.01
79_I 161_I 0.88 0.38 0.01
35_N 345_Q 0.88 0.37 0.01
116_N 248_P 0.88 0.37 0.01
108_A 283_F 0.87 0.37 0.01
78_I 256_Q 0.87 0.36 0.01
3_H 98_F 0.86 0.36 0.01
74_A 291_A 0.86 0.35 0.01
71_Q 266_T 0.85 0.34 0.01
78_I 247_T 0.85 0.34 0.01
30_V 281_S 0.83 0.33 0.01
38_Q 75_P 0.83 0.33 0.01
72_I 253_E 0.83 0.32 0.01
37_A 258_Q 0.82 0.32 0.01
72_I 244_E 0.82 0.32 0.01
35_N 75_P 0.82 0.31 0.01
4_R 243_K 0.82 0.31 0.01
75_Q 259_Q 0.81 0.31 0.01
47_S 251_R 0.81 0.30 0.01
78_I 253_E 0.81 0.30 0.01
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
9390 1.88 CheYFliY Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.05 Done - Shared
9388 0.07 CheYFliY Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
9377 1.75 CheYFliY Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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