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OPENSEQ.org
CheYFliM
Genes: A B A+B
Length: 129 334 447
Sequences: 46004 3269 687
Seq/Len: 356.62 9.79 1.54
MirrorTree (Pazo et al. 2001) 0.44
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 0.19
2 0.18 0.13 0.27
5 0.18 0.14 0.32
10 0.18 0.14 0.44
20 0.18 0.14 0.73
100 0.20 0.15 1.48
∞ 0.25 0.16 3.49
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
97_A 118_F 1.20 0.65 0.00
8_F 217_I 1.09 0.54 0.00
34_E 270_L 1.03 0.48 0.00
33_V 105_I 1.01 0.46 0.00
21_V 104_L 1.00 0.44 0.00
54_I 157_M 0.99 0.43 0.00
51_F 283_V 0.97 0.41 0.00
87_T 127_V 0.96 0.40 0.00
114_A 210_N 0.95 0.40 0.00
8_F 29_I 0.94 0.39 0.00
54_I 22_K 0.93 0.37 0.00
70_K 270_L 0.92 0.37 0.00
63_M 278_L 0.90 0.35 0.00
42_A 12_D 0.90 0.35 0.00
71_T 105_I 0.89 0.34 0.00
21_V 105_I 0.88 0.33 0.00
25_L 153_V 0.88 0.33 0.00
45_K 206_V 0.87 0.32 0.00
38_D 131_F 0.86 0.32 0.00
6_L 170_K 0.85 0.31 0.00
38_D 88_P 0.85 0.30 0.00
93_E 175_L 0.85 0.30 0.00
120_L 119_S 0.83 0.28 0.00
107_V 7_S 0.83 0.28 0.00
44_N 267_D 0.83 0.28 0.00
38_D 161_A 0.82 0.28 0.00
30_F 2_G 0.82 0.28 0.00
7_K 83_A 0.82 0.27 0.00
44_N 261_L 0.80 0.26 0.00
80_A 57_I 0.80 0.26 0.00
25_L 79_I 0.79 0.25 0.00
122_K 153_V 0.79 0.25 0.00
48_A 274_Q 0.79 0.25 0.00
96_I 270_L 0.79 0.25 0.00
124_F 70_F 0.78 0.24 0.00
38_D 203_P 0.78 0.24 0.00
33_V 303_T 0.77 0.24 0.00
45_K 312_Q 0.77 0.23 0.00
51_F 217_I 0.76 0.23 0.00
8_F 24_E 0.76 0.23 0.00
52_G 295_H 0.75 0.22 0.00
76_S 100_T 0.74 0.22 0.00
120_L 25_P 0.74 0.22 0.00
62_N 250_L 0.74 0.22 0.00
38_D 241_H 0.74 0.22 0.00
44_N 175_L 0.74 0.21 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
9391 0.34 CheY-FliM3 Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9389 0.75 CheY-FliM2 Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9375 1.54 CheYFliM Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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