So far, our in-frame deletion efforts have focused on URFs (reading frames of unknown function) which contain DNA-binding Helix-Turn-Helix (HTH) motifs. There are also a few known genes, conserved URFs, and URFs without motifs on our short list.
**NEW** E. coli knockout and amplification primers
See our related web pages for details on homologous recombination general mutation substitution strategy (pKO3) and multiplex knockout strain pool competition readout methods. See also: Link, A.J., Phillips, D. and Church, G.M. (1997) Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: Application to open reading frame characterization. J. Bacteriol. 179: 6228-6237.
The 33 bp tag oligomers that we and others have used for the in frame deletions are:
5' gtt ata aat ttg gag tgt gaa ggt tat tgc gtg 3' :c22plex tag forward
5' cac gca ata acc ttc aca ctc caa att tat aac 3' :c22plex tag reverse
Constructs using these 33-mers should be compatible with our growth rate quantitation methods and should all make the same (innocuous) peptide.
The yabC nomenclature was setup by Kenn Rudd and Amos Bairoch and is analogous to the zabC type transposon Demerec-like designators where the "a" represents the map-minutes tens place and the b the ones place (a=0, b=1, ... j=9, k=1 ...). The "C" is in rough order within the minute position set by "ab". We intend to include gene name synonyms and sequences in later versions of the table.
Note that the list below is to help coordinate comprehensive knockout projects. It is not intended to inhibit other labs from making similar constructs nor to offer strains (at present).
Another 10 are in early construction phases: sdhA, rpe, talA, sucD, mgs, gpmA, nuoA, cyoA, gcd, mdh.
The p & K indicators below mean that we have putative plasmid and/or
knockout constructs made but not neccessarily proven/characterized. The
absence of K does not imply that the knockout is lethal.
| Gene | Family | plasmid/KO |
| Unknown Function | ||
| yidL_3858583 | araC | p & K |
| yijO | araC | p & K |
| yhiW | araC | p & K |
| yhiX | araC | p & K |
| yjeB | yjeB | p & K |
| yijC | yijC | p & K |
| yiaG | yiaG | p & K |
| yheO | yheO | p |
| yjgS | lacI | p & K |
| glpG | glpG | p & K |
| frvR | frvR | p & K |
| yjhU | sorC | p & K |
| yjbK | fur | p & K |
| yfeC | yfeD | |
| yfeD | yfeD | p |
| yebK | rpiR | p |
| yfhH | rpiR | p & K |
| yehV | merR | |
| yhdM | merR | |
| yiaJ | iclR | p & K |
| yjhI | iclR | |
| ttk | tetR | p & K |
| envR | tetR | p |
| ygaA | ntrC | p |
| ygeV | ntrC | p & K |
| yfhA | ntrC | p |
| yhgB | ntrC | p & K |
| ygbI | deoR | p |
| agaR | deoR | p |
| yihW | deoR | p |
| yjfQ | deoR | p & K |
| yjhJ | deoR | p & K |
| yhjB | luxR | p & K |
| yjjR | luxR | p |
| yjjQ | luxR | p & K |
| evgA | luxR | p & K |
| yhiF | luxR | p & K |
| y64_o6 | luxR | p & K |
| lldR | gntR | p & K |
| yihL | gntR | p |
| yidP | gntR | p & K |
| yhcK | gntR | p & K |
| yhfR | gntR | |
| farR | gntR | p & K |
| phnF | gntR | p & K |
| yjiR | gntR | p |
| pssR | lysR | p & K |
| yoxA | lysR | p & K |
| ydhB | lysR | p & K |
| yfiE | lysR | p & K |
| leuO | lysR | p & K |
| yafC | lysR | p & K |
| ybeF | lysR | p & K |
| yeiE | lysR | p & K |
| yhcS | lysR | p & K |
| yiaU | lysR | p & K |
| yidZ | lysR | |
| yjiE | lysR | p |
| y65_19 | lysR | p & K |
| yhjC | lysR | p & K |
| ygiP | lysR | p & K |
| perR | lysR | |
| cbl | lysR | |
| lrhA | lysR | |
| ybhD | lysR | |
| yhaJ | lysR | |
| Known DNA-binding | ||
| nhaR | lysR | p & K |
| gcvA | lysR | p & K |
| oxyR | lysR | |
| crp | p & K | |
| ihfA | p & K | |
| hupB | p & K | |
| hupA | p & K | |
| iciA | lysR | |
| cynR | lysR | |
| cysB | lysR | |
| ilvy | lysR | |
| lysR | lysR | |
| metR | lysR | |
| xapR | lysR | |
| Conserved URFs | ||
| yjbJ | BCR urf | p & K |
| yaaC | FAD synthase | p |
| yabB | BCR URF | p |
| yabC | SAM-methylase | p |
| yceC | pseudouridylate synthase | p |
| ycfB | GuaA (ATP) | |
| ycfG | thymidylate kinase | |
| ycfH | ACR URF (metals?) | |
| ychF | GTPase | |
| yebC | ACR URF | p |
| yfhD | D-ribulose-5P-3epimerase | p |
| ygfA | 5,10-methenyl-THF synthase | p |
| yggH | SAM-depend | p |
| ygiH | permease | p |
| yhbF-glmM | phosphoglucosamine mutase | p |
| yhbZ | GTPase | p |
| yibDp | glycosyltransferase | |
| yibK | rRNA methylase | p |
| yibO | phosphoglycerate mutase | |
| yidA | hydrolase | |
| yigL | hydrolase | |
| yihA | GTPase | p |
| yjfH | rRNA methylase | p |
| yraL | BCR URF | p |
| E.coli-specific Urfs | ||
| o261_238123 | no family | |
| ybfD | transposonase:ydcC,yhhI | |
| yijP | urfs: yjgX, yhbX, yhjW, yjdB | |
| hdeA | no family | p & K |