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Table 2 Primers used in this work

From: The hyl Efm gene in pHylEfm of Enterococcus faecium is not required in pathogenesis of murine peritonitis

Primer

Sequence (5'-3')

Relevant Characteristics

A

gaagatctgagataggttatgcaagat

Forward, BglII site (underlined), used amplification of aph-2"-ID

B

ccaatgcatgattccggattctaaaaaagg

Reverse, NsiI site (underlined), used amplification of aph-2"-ID

C

cgggatccgtttaaaaccagctggaaaag

Forward, BamHI site (underlined), located 1,251 nucleotides upstream of the start codon of the gene encoding a putative glycosyl hydrolase family 20 (Figure 1.)

D

ccgctcgagcaattcaacattgcaaagac

Reverse, XhoI site (underlined), located 294 nucleotides upstream of the start codon of the gene encoding a putative glycosyl hydrolase family 20 (Figure 1.)

E

cgagggcccgtgaagtattgccagatgt

Forward, ApaI site (underlined); located 592 nucleotides downstream of the down gene (hypothetical, Figure 1.)

F

ccggaattcaaaagcagaattggaaatca

Reverse, EcoRI site, 1,571 nucleotides downstream of the down gene (hypothetical, Figure 1.)

G

gcgagctcgattactttcaaaggaga

Forward, SacI site (underlined), ribosomal binding site of hyl Efm (italics) (Figure 1.)

H

tcccccggg ctaacttttgataatttgctc

Reverse, SmaI site, (underlined) and stop codon of hyl Efm (Figure 1.)

I

tcccccggg ttagcgattgatcgagc

Reverse, SmaI site (underlined), stop codon of down (Figure 1.)

J

cgggatcccaatcaagaagtagcggatt

Forward, BamH site (underlined) 438 nucleotides upstream of the stop codon of carbohydrate ABC transporter gene (Figure 1.)

K

gcggccgctcgagggcccttagtgcgattgtatctgac

Reverse, stop codon of the gene that encodes to transmembrane protein (Figure 1.)

L

gggcccctcgaggcggccgcaaaattaaataaaaaatgg

Forward, ApaI, XhoI, NotI site, stop codon down (Figure 1.)

M

catgcatgaatcaggaactgaaactgc

Reverse, NsiI site, 1,091 nucleotides upstream of stop codon of GMP synthase (opposite orientation) (Figure 1.)

N

ccggaattccagtaaaaggcacagagc

Forward, EcoRI site (underlined), located 2,138 nucleotides down-stream of glycosyl hidrolase family 45-2 start codon (Figure 1.)

O

tcatctattttctcctttgaaagtaatcactatattcc

Reverse, stop codon of glycosyl hydrolase family 45-2 (Figure 1.)

P

tcaaaggagaaaatagatgaatatcttaaaaaataaaaagc

Forward, located 40 nucleotides upstream of down gene start codon (Figure 1.)

Q

ataagaatgcggccgcttagcgattgatcgagcg

Reverse, NotI site (underlined), stop codon of down (Figure 1.)

R

ataagaatgcggccgccagtaaaaggcacagagc

Forward, NotI site (underlined), located 2,138 nucleotides down-stream of glycosyl hydrolase family 45-2 start codon (Figure 1.)

S

tcatctattttctcctttgaaagtaatcactatattcc

Reverse, stop codon of glycosyl hydrolase family 45-2 (Figure 1.)

T

tcaaaggagaaaatagatgacaaaattaaataaaaaatgg

Forward, 1,973 nucleotides upstream of stop codon of GMP synthase (Figure 1.)

U

cggaattcgaatttgtatatgtcttcg

Reverse, EcoRI site (underlined), 994 nucleotides upstream of start codon of GMP synthase (opposite direction) (Figure 1.)

V

aaggaaaaaagcggccgccagaatatgataatcgtcatgg

Forward, NotI site (underlined), 902 nucleotides downstream of hyl Efm start codon (Figure 1.)

W

tttgttctcctttttcttgctttttattttttaag

Reverse, stop codon of of hyl Efm (Figure 1.)

X

gcaagaaaaaggagaacaaacaaaattaaataaaaaatgg

Forward, 1,973 nucleotides upstream of stop codon of GMP synthase (opposite direction) (Figure 1.)

Y

ccggaattcgaatcaggaactgaaactgccc

Reverse, EcoRI site (underlined), 1,094 nucleotides upstream of stop codon of GMP synthase (opposite direction) (Figure 1.)

A1

cgcgtcgtattaaaaatcat

Forward, 143 nucleotides upstream of stop codon of GH20 (Figure 3.)

A2

gatcgataaactggctcgt

Reverse, 139 nucleotides upstream of start codon of GH42 (Figure 3.)

B1

acgcgtcgacagcagctggatatgctga

Forward, SalI site (underlined), 2,316 nucleotides downstream of start codon of GH42 (Figure 3.)

B2

ggaagatctccggtttccagacttctt

Reverse, BglII site (underlined), 159 nucleotides downstream of start codon of hyl Efm (Figure 3.)

C1

gttagaagaagtctggaaaccg

Forward, 138 nucleotides downstream of start codon of hyl Efm (Figure 3.)

C2

tgctaagatattcctctactcg

Reverse, 798 nucleotides upstream of stop codon of hyl Efm (Figure 3.)

D1

acatgcatgcagaattggagccttggtt

Forward, SphI site (underlined), 169 nucleotides upstream of stop codon of hyl Efm (Figure 3.)

D2

cggaattctgcttccgcataagaaa

Reverse, EcoRI site (underlined), 319 nucleotides upstream of stop codon of down gene (Figure 3.)

E1

gcaaggcttcttagaga

Forward, ddl E. faecium [32, 33]

E2

catcgtgtaagctaacttc

Reverse, ddl E. faecium [32, 33]