Table S1. Plasmids, cosmids and shuttle phages used in this study
Plasmids, cosmids
Characteristics
and phages
Plasmids
pCR-BluntII-TOPO
pSM630
pSM631
pSM632
pSM633
pSM634
pSM635
pSM636
pSM637
pSM638
pSM639
pSM640
pSM641
pSM642
pSM643
pSM644
pSM645
pSM646
pSM647
pSM648
Source/reference
Vector for cloning blunt-ended PCR products, Kanr
2.7-kb gyrA fragment in pCR-BluntII-TOPO
0.715-kb Rv0007 fragment in pCR-BluntII-TOPO
2.2-kb gyrB fragment in pCR-BluntII-TOPO
0.83-kb Rv0006 fragment in pCR-BluntII-TOPO
2.7-kb gyrA (T80A) fragment in pCR-BluntII-TOPO
2.7-kb gyrA (A90V) fragment in pCR-BluntII-TOPO
2.7-kb gyrA (D94G) fragment in pCR-BluntII-TOPO
2.7-kb gyrA (G247S) fragment in pCR-BluntII-TOPO
2.7-kb gyrA (A384V) fragment in pCR-BluntII-TOPO
2.2-kb gyrB (M330I)) fragment in pCR-BluntII-TOPO
2.2-kb gyrB (V340L fragment in pCR-BluntII-TOPO
2.2-kb gyrB (D500H) fragment in pCR-BluntII-TOPO
2.2-kb gyrB (D500N) fragment in pCR-BluntII-TOPO
2.2-kb gyrB (N538D) fragment in pCR-BluntII-TOPO
2.2-kb gyrB (N538D + T546M) in pCR-BluntII-TOPO
2.2-kb gyrB (N538T + T546M) in pCR-BluntII-TOPO
2.2-kb gyrB (N538K) fragment in pCR-BluntII-TOPO
2.2-kb gyrB (R485C+T539N) fragment in pCR-BluntII-TOPO
2.2-kb gyrB (T546M) fragment in pCR-BluntII-TOPO
Invitrogen
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Used for cloning allelic exchange substrate; contains λ phage cos site, Hygr
gyrA fragment upstream of Hygr cassette in pYUB854
gyrA and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrB fragment upstream of Hygr cassette in pYUB854
gyrB and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrA (T80A) fragment upstream of Hygr cassette in pYUB854
gyrA (A90V) fragment upstream of Hygr cassette in pYUB854
gyrA (D94G) fragment upstream of Hygr cassette in pYUB854
gyrA (G247S) fragment upstream of Hygr cassette in pYUB854
gyrA (A384V) fragment upstream of Hygr cassette in pYUB854
gyrB (M330I) fragment upstream of Hygr cassette in pYUB854
gyrB (V340L) fragment upstream of Hygr cassette in pYUB854
gyrB (D500H) fragment upstream of Hygr cassette in pYUB854
gyrB (D500N) fragment upstream of Hygr cassette in pYUB854
gyrB (N538D) fragment upstream of Hygr cassette in pYUB854
gyrB (N538D+T546M) fragment upstream of Hygr cassette in pYUB854
gyrB (N538T+T546M) fragment upstream of Hygr cassette in pYUB854
gyrB (N538K) fragment upstream of Hygr cassette in pYUB854
gyrB (R485C+T539N) fragment upstream of Hygr cassette in pYUB854
gyrB (T546M) fragment upstream of Hygr cassette in pYUB854
gyrA (A74S) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (A74S+D94G) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (T80A) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (T80A+A90G) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (A90G) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (A90V) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (D94G) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (G247S) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrA (A384V) and Rv0007 fragment flanking Hygr cassette in pYUB854
gyrB (M330I) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (V340L) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (R485C) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (R485C+T539N) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (D500A) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (D500H) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (D500N) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (D533A) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (N538D) and Rv0006 fragment flanking Hygr cassette in pYUB854
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Cosmids
pYUB854
pCSM649
pCSM650
pCSM651
pCSM652
pCSM653
pCSM654
pCSM655
pCSM656
pCSM657
pCSM658
pCSM659
pCSM660
pCSM661
pCSM662
pCSM663
pCSM664
pCSM665
pCSM666
pCSM667
pCSM668
pCSM669
pCSM670
pCSM671
pCSM672
pCSM673
pCSM674
pCSM675
pCSM676
pCSM677
pCSM678
pCSM679
pCSM680
pCSM681
pCSM682
pCSM683
pCSM684
pCSM685
pCSM686
pCSM687
pCSM688
pCSM689
pCSM690
pCSM691
pCSM692
pCSM693
pCSM694
pCSM695
gyrB (N538D+T546M) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (N538T+T546M) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (N538K) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (T539N) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (T539P) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (E540D) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (E540V) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (A543T) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (A543V) and Rv0006 fragment flanking Hygr cassette in pYUB854
gyrB (T546M) and Rv0006 fragment flanking Hygr cassette in pYUB854
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Temperature sensitive shuttle phasmid derived from the mycobacteriophage TM4
pCSM650 cloned into unique PacI site of phAE159
pCSM652 cloned into unique PacI site of phAE159
pCSM668 cloned into unique PacI site of phAE159
pCSM669 cloned into unique PacI site of phAE159
pCSM670 cloned into unique PacI site of phAE159
pCSM671 cloned into unique PacI site of phAE159
pCSM672 cloned into unique PacI site of phAE159
pCSM673 cloned into unique PacI site of phAE159
pCSM674 cloned into unique PacI site of phAE159
pCSM675 cloned into unique PacI site of phAE159
pCSM676 cloned into unique PacI site of phAE159
pCSM677 cloned into unique PacI site of phAE159
pCSM678 cloned into unique PacI site of phAE159
pCSM679 cloned into unique PacI site of phAE159
pCSM680 cloned into unique PacI site of phAE159
pCSM681 cloned into unique PacI site of phAE159
pCSM682 cloned into unique PacI site of phAE159
pCSM683 cloned into unique PacI site of phAE159
pCSM684 cloned into unique PacI site of phAE159
pCSM685 cloned into unique PacI site of phAE159
pCSM686 cloned into unique PacI site of phAE159
pCSM687 cloned into unique PacI site of phAE159
pCSM688 cloned into unique PacI site of phAE159
pCSM689 cloned into unique PacI site of phAE159
pCSM690 cloned into unique PacI site of phAE159
pCSM691 cloned into unique PacI site of phAE159
pCSM692 cloned into unique PacI site of phAE159
pCSM693 cloned into unique PacI site of phAE159
pCSM694 cloned into unique PacI site of phAE159
pCSM695 cloned into unique PacI site of phAE159
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Phages
phAE159
phSM1000
phSM1001
phSM1002
phSM1003
phSM1004
phSM1005
phSM1006
phSM1007
phSM1008
phSM1009
phSM1010
phSM1011
phSM1012
phSM1013
phSM1014
phSM1015
phSM1016
phSM1017
phSM1018
phSM1019
phSM1020
phSM1021
phSM1022
phSM1023
phSM1024
phSM1025
phSM1026
phSM1027
phSM1028
phSM1029