Tk:Ab hac una re

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Ab hac una re

9 August 2006

Rocha paper on survey of recombination systems in sequenced bacteria. Florum has RecO, RecR, but not RecF in the RecFOR system. RecA present. RecD present. RuvAB present, ruvC not, but replaced with RecU. yqgF gene part of the recomination system. PriA missing. RecBC missing, RecD form is different from the form found in organisms with RecBC also.

Received yeast strains and plasmids from Weiss lab. Confirmed that they cannot PCR through the centromere CDS II region.

Codon usage of the P1014 cassette. CTC codon (Lys) is rare and used 4+ times. CGG is not present in the CDS. Three GATC sequences.

7 August 2006

SMC proteins maintain chromosome condensation. Co-factors scpA and scpB. Me. florum proteins are AAT7589, AAT75908, AAT75907 respectively. B. subtilis homologs: P51834, P35154, P35155. Volkov03. Notarnicola91 reports SMC protein in M. hyorhinis (P115).

Compromise codon usage: multiply codon probabilities for corresponding codons from each organism, then take the square root (geometric mean). Renormalize within each amino acid to establish new relative probabilities.

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