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OPENSEQ.org
yidC-Foc
Genes: A B A+B
Length: 210 79 277
Sequences: 2085 837 735
Seq/Len: 9.93 10.59 2.65
MirrorTree (Pazo et al. 2001) 0.41
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 0.00 0.00
2 0.00 0.00 0.01
5 0.00 0.00 0.03
10 0.00 0.00 0.20
20 0.00 0.00 0.39
100 0.01 0.00 0.71
∞ 0.06 0.02 2.54
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
171_F 74_V 1.25 0.84 0.12
154_Q 20_A 1.04 0.65 0.07
92_M 38_G 1.01 0.62 0.06
38_Q 63_I 0.99 0.59 0.06
137_M 42_Q 0.98 0.58 0.05
48_L 12_A 0.96 0.56 0.05
91_Q 42_Q 0.90 0.49 0.04
101_M 67_A 0.88 0.47 0.04
20_I 20_A 0.88 0.46 0.04
138_F 72_L 0.85 0.44 0.03
136_T 26_I 0.85 0.43 0.03
1_P 56_V 0.85 0.43 0.03
53_Q 60_V 0.84 0.41 0.03
3_F 62_A 0.82 0.39 0.03
162_V 29_G 0.82 0.39 0.03
47_M 38_G 0.81 0.39 0.03
123_Q 40_A 0.81 0.39 0.03
63_K 18_G 0.81 0.39 0.03
22_I 23_G 0.80 0.38 0.03
83_G 72_L 0.79 0.37 0.03
129_L 49_L 0.78 0.35 0.03
132_L 11_M 0.77 0.34 0.03
58_R 42_Q 0.77 0.34 0.03
82_L 26_I 0.77 0.34 0.02
160_M 19_L 0.76 0.33 0.02
46_R 56_V 0.75 0.32 0.02
90_I 11_M 0.74 0.31 0.02
108_L 36_L 0.74 0.30 0.02
166_V 70_L 0.73 0.30 0.02
143_M 29_G 0.73 0.30 0.02
185_V 74_V 0.73 0.30 0.02
122_A 45_L 0.73 0.30 0.02
142_K 39_A 0.72 0.29 0.02
28_R 26_I 0.71 0.28 0.02
75_K 47_P 0.71 0.28 0.02
19_S 38_G 0.71 0.28 0.02
37_A 39_A 0.71 0.28 0.02
174_G 62_A 0.70 0.27 0.02
117_I 70_L 0.70 0.27 0.02
98_L 23_G 0.70 0.27 0.02
90_I 15_V 0.70 0.26 0.02
94_I 73_Y 0.69 0.26 0.02
144_S 42_Q 0.69 0.26 0.02
16_W 28_I 0.69 0.26 0.02
99_Y 42_Q 0.69 0.26 0.02
181_V 67_A 0.69 0.26 0.02
55_M 77_A 0.69 0.26 0.02
192_L 59_L 0.69 0.25 0.02
23_I 55_I 0.68 0.25 0.02
102_L 67_A 0.68 0.25 0.02
98_L 22_I 0.68 0.25 0.02
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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