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DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU Jackhammer

Genes: A B A+B
Length: 378 414 761
Sequences: 7006 15947 2898
Seq/Len: 18.53 38.52 3.81
MirrorTree (Pazo et al. 2001) 0.14
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 0.00 0.00 0.00
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.01 0.03
20 0.00 0.01 0.10
100 0.00 0.02 0.54
0.01 0.07 3.66
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
224_I 82_D 0.74 0.39 0.00
33_I 58_V 0.71 0.36 0.00
35_I 255_L 0.70 0.34 0.00
10_L 207_L 0.69 0.32 0.00
106_I 206_E 0.66 0.30 0.00
148_Q 58_V 0.65 0.28 0.00
229_T 58_V 0.64 0.28 0.00
130_E 376_L 0.63 0.26 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
7086 1.88 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU HHBlits Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7082 3.81 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU Jackhammer Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6934 0.03 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU HHBlits Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6894 0.1 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared

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