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OPENSEQ.org
yidC-Foc
Genes: A B A+B
Length: 210 79 274
Sequences: 2228 1731 1031
Seq/Len: 10.61 21.91 3.76
MirrorTree (Pazo et al. 2001) 0.35
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 0.00 0.01 0.00
2 0.00 0.01 0.01
5 0.00 0.01 0.04
10 0.00 0.01 0.23
20 0.00 0.01 0.44
100 0.01 0.02 0.93
∞ 0.06 0.06 3.57
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
174_G 62_A 0.81 0.48 0.00
58_R 35_F 0.81 0.47 0.00
133_M 28_I 0.80 0.47 0.00
174_G 38_G 0.80 0.46 0.00
172_P 15_V 0.78 0.43 0.00
28_R 72_L 0.77 0.43 0.00
132_L 55_I 0.76 0.41 0.00
162_V 31_L 0.74 0.39 0.00
154_Q 20_A 0.72 0.36 0.00
166_V 70_L 0.72 0.36 0.00
172_P 40_A 0.71 0.35 0.00
1_P 56_V 0.71 0.35 0.00
142_K 39_A 0.70 0.34 0.00
19_S 48_L 0.69 0.33 0.00
141_Q 25_A 0.69 0.32 0.00
59_L 54_F 0.67 0.30 0.00
63_K 18_G 0.67 0.30 0.00
98_L 22_I 0.66 0.29 0.00
173_S 50_R 0.66 0.29 0.00
5_L 74_V 0.65 0.28 0.00
75_K 12_A 0.65 0.28 0.00
142_K 46_I 0.65 0.28 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
0108 3.76 yidC-Foc Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) (2013_03) 0.00 Done - Shared
0106 2.65 yidC-Foc Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.12 Done - Shared
0104 0.39 yidC-Foc Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) Killed - Shared
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