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OPENSEQ.org
CoaBC-D
Genes: A B A+B
Length: 414 158 552
Sequences: 2699 3155 1556
Seq/Len: 6.52 19.97 2.82
MirrorTree (Pazo et al. 2001) 0.61
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 0.08 0.00
2 0.00 0.08 0.00
5 0.00 0.08 0.08
10 0.00 0.08 0.23
20 0.00 0.08 0.41
100 0.00 0.08 0.87
∞ 0.00 0.10 2.72
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
330_V 111_V 0.77 0.35 0.00
139_R 75_D 0.68 0.26 0.00
393_S 150_R 0.67 0.25 0.00
52_E 36_L 0.66 0.24 0.00
187_M 18_I 0.66 0.24 0.00
81_L 31_V 0.66 0.24 0.00
55_S 1_M 0.66 0.24 0.00
149_A 47_L 0.63 0.22 0.00
237_G 34_A 0.62 0.21 0.00
9_V 53_M 0.62 0.21 0.00
58_P 46_D 0.61 0.20 0.00
397_M 37_V 0.60 0.19 0.00
203_L 131_K 0.60 0.19 0.00
14_G 104_M 0.59 0.19 0.00
141_R 74_V 0.59 0.18 0.00
192_A 54_I 0.59 0.18 0.00
82_V 54_I 0.59 0.18 0.00
193_L 122_Y 0.58 0.18 0.00
115_V 38_N 0.56 0.16 0.00
56_G 128_S 0.56 0.16 0.00
214_S 153_Q 0.55 0.16 0.00
129_P 86_V 0.54 0.15 0.00
74_R 129_L 0.54 0.15 0.00
208_F 66_V 0.54 0.15 0.00
353_R 113_T 0.54 0.15 0.00
52_E 73_V 0.54 0.15 0.00
70_V 9_S 0.54 0.15 0.00
311_L 117_A 0.54 0.15 0.00
412_Q 55_E 0.53 0.14 0.00
44_R 81_G 0.53 0.14 0.00
92_L 70_Q 0.53 0.14 0.00
237_G 132_E 0.53 0.14 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
8382 0.44 CoaBC-D Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
8029 2.82 CoaBC-D2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8028 2.82 CoaBC-D Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
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