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recA
an evolutionary investigation
Andrew Lloyd
Bacterial Gene Day 2006
Why recA
• Lloyd, A.T. and Sharp, P.M. (1993)
Evolution of the recA gene and the
molecular phylogeny of bacteria. J. Mol.
Evol. 37:399-407.
• It was the most widely sequenced protein
– 23 genes available in 1993
– 62 two years later
recA – protein trees vs RNA trees
recA
SS-rRNA
Eisen 1995 enteric bacteria only: Trees match pretty good
MSA Ecoli vs Bacsu
RECA_ECOLI MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMG
RECA_BACSU ---MSDRQAALDMALKQIEKQFGKGSIMKLGEKTDTRISTVPSGSLALDTALGIGGYPRG
.::* ** ** ************:***. . :.*:.:***:** *** ** * *
RECA_ECOLI RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQP
RECA_BACSU RIIEVYGPESSGKTTVALHAIAEVQQQ-RTSAFIDAEHALDPVYAQKLGVNIEELLLSQP
**:*:**********::*:.** .*:: :*.***********:**:****:*::** ***
RECA_ECOLI DTGEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLA
RECA_BACSU DTGEQALEIAEALVRSGAVDIVVVDSVAALVPKAEIEGDMGDSHVGLQARLMSQALRKLS
*********.:**.******::********.*******::****:** **:****:***:
RECA_ECOLI GNLKQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVG
RECA_BACSU GAINKSKTIAIFINQIREKVGVMFGNPETTPGGRALKFYSSVRLEVRRAEQLKQGNDVMG
* :::*:*: ******* *:**********.**.*****:****::**
:*:*::*:*
RECA_ECOLI SETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIG
RECA_BACSU NKTKIKVVKNKVAPPFRTAEVDIMYGEGISKEGEIIDLGTELDIVQKSGSWYSYEEERLG
.:*::******:*.**: **.:*:*****. **::***.: .:::*:*:****: *::*
RECA_ECOLI QGKANATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF
RECA_BACSU QGRENAKQFLKENKDIMLMIQEQIREHYGLDNNGVVQQQAEETQEELEFEE-**: **. :**:* :
*::::**
: *.. : ..::::
* :*
203 Identities/348 aligned residues 58% identity
One internal gap
Genomic context
E.coli
Blast each neighbour against thye other genome…
B.subtilis
Schematic
Is it in a conserved operon?
In an operon
58% identical
Bsub (1764kb) cinA
recA
pbpX
cinA
(2361kb)
Ecoli (2821kb) ygaD
recA
recX
Two cinA like genes in E.coli only one in B.sub