Mobile element type:
Transposon
Name:
Tn558.1
Synonyms:
Accession:
Tn558.1-AM408573.1
Family:
Tn554
Group:
First isolate:
Yes
Partial:
ND
Evidence of transposition:
Yes
Host Organism:
Staphylococcus warneri
Date of Isolation:
2006
Country:
Denmark
Molecular Source:
plasmid pSCFS6
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tnpA | Tn558.1 | 138-1223 | + | Transposase | |
| tnpB | Tn558.1 | 1220-3139 | + | Transposase | |
| tnpC 5'-end | Tn558.1 | 3141-3410 | + | Accessory Gene | Helper |
| istB | ISSau9 | 3462-4232 | - | Accessory Gene | ATPase Transposition Helper |
| istA | ISSau9 | 4207-5544 | - | Transposase | |
| lsaB (ARO:3003111) | TnSau9 | 6027-7505 | - | Passenger Gene | Antibiotic Resistance |
| cfrA (ARO:3003441) | TnSau9 | 9012-10061 | - | Passenger Gene | Antibiotic Resistance |
| istA | ISSau9.1 | 11349-12686 | - | Transposase | |
| tnpC 3'-end | Tn558.1 | 13005-13106 | + | Accessory Gene | Helper |
| fexA (ARO:3002704) | Tn558.1 | 13983-15410 | - | Passenger Gene | Antibiotic Resistance |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA | TnpA | Tn558.1 | 361 | 138-1223 | + |
|---|
| Class: | Transposase | ||||||||||
| Comment: | tyrosine recombinase XerD||TIGR02225||phage integrase, N-terminal SAM-like domain||DNA breaking-rejoining enzymes C-terminal catalytic domain | ||||||||||
| Protein Sequence: | MKVQKVIVEE KSYPLYIVLD KEFEVIEPVK RFIKYLDNTG KAPNTIKTYC YHLKLFYEFM SQSRIELGDF QFEDLANFVG WLRNPAGHLK VIDIQPKKAK REETSVNSIL NAVTSFLEYL NRTENFKAID MSKEARGRNF KGFLHHISKG RSYKKNILKL RVKKKLVQVL EHGQVKAIIE ACHTKRDKLL IMLMYEGGLR IGEALSLRIE DISTWDNQIN IRPRDHNENG AYIKLKKERT IDVSKELMAL YTDYLVHEYG EDLDHDYIFI NLKDSYFGHP LKYQSVLDLI RRLGKRTGIT FTAHILRHTH ATELIRSGWD AAYVQKRLGH AHVQTTLDTY VHLSDQDMKN EYKKYLQGRE T |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpB | TnpB | Tn558.1 | 639 | 1220-3139 | + |
|---|
| Class: | Transposase | ||||||||||
| Comment: | Phage integrase N-terminal SAM-like domain||Region: Phage_int_SAM_1||cl12235||Phage integrase family|| pfam00589 | ||||||||||
| Protein Sequence: | MTMKFPSVAT NRKLIASTEI NKKIANMTSV LKGYWAADRW DIRICPHPSA IELSKNPSLR NRWVNFDKVE NVWLKTELKY FYYLHLNNGA WNAKSVWIRK GTVISRMMGF LNLKYPNITS ITEVPIKKAL TEYRTYLTEQ KVKTTTTNYK LDVNQQKVTV HANSYYVTHL KQFMEFYEDF YFDGEEWEKD VWNRRKLSLP EDKVNPTSYE YTINFKGFKN NYFKEIVKRY CKLMLNTASF SHVVDIASKL KEFFNFMNKN CEGIQRIHQL TRNEIEQYFN YINLKGLKPS TVTGRISTLD VFFTTIQRYD WKDTPSKILI FQEDYPKVPK ALPRYIDEHI LEQLNGKLDK LEPYIATMVM VLQECGMRIS ELCTLKKGSV ITDKEGDCFL KYYQWKMKKE HIIPISKEIA ALILVQEQRV ADELDDGCVY VFPRKDCSPL KQDTFRVKLN ELAYEEKITD SNGEIFRFHA HAFRHTVGTR MINNGVPQHI VQKFLGHESP EMTARYAHIF DETLKKEFTK FKETLVTNNG SILDLSEENT EADNTDLQWF KKNINAQALP NGYCRLPVIA GPCPHANACL DCTNFCTSKQ FLTEHEEHLE RTKEILNRAK QNQWQRQVET NERVKNRLEQ IIHSLKETN |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpC 5'-end | N/A | Tn558.1 | 90 | 3141-3410 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Helper | ||||||||||
| Sequence Family: | Tn554_family | ||||||||||
| Comment: | tnpC ORF interrupted by insertion of TnSau9 | ||||||||||
| Protein Sequence: | MIRKGNTTAI VQLAKDKSEK TRIRVEKTIS EMALKEEKIN FNSVAQEANV SKSWLYKQKD IRTRVETLRG MQISELTPRK PSKSPRSEDV |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | istB | IstB | ISSau9 | 256 | 3462-4232 | - |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | ATPase Transposition Helper | ||||||||||
| Protein Sequence: | MKECLNMDKK QSVIDLCKEL RLPGIRELVE EDVAFQETTP AIDLLHTVLT KEKNDRWIRS KSTRIRRANF PEKKLLEEID TRALPTDAQQ KLPNLQTLDF IKAGQNVILT GSPGTGKSHL AIGLGVEACL AGYKVYFASV SSLINQLKES RSERTLRSFE LRFEKYDLVI IDELGYISFD KEGAELLFTH LSLRAGRSST IITSNLSFAK WEEVFHDPIL TAALTDRLTH KSHVVNMIGP SYRMRETQKW LENSHS |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | istA | IstA | ISSau9 | 445 | 4207-5544 | - |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MTEEIVERLK GFIQDNEWKR KNNMSKQQMK KIDMYEKLQE EGYDIGYTTV RNFVNSEERR TKEVYIRQRY SAAWEVEFDW GEVKLVIDGK QKSYSLAVFT LAYSNYRFAL LYESETMICI QDAHTKLIDH LGFVPSVFTY DNMRTVVKSF VGTDRKITDG MINLSNYYEF RIRLCEPRKG NQKGHVERSV EVVRRKAFSY DIAFPSLEDA QKRLAQTILS LNKRIHHEKK LAHIELKDQE KVAAAQEALP LPFDVSEVVE CRVDKYSTVT IKQNRYSVPE GHVGAWIRAK VSADSVRLFI EGEFVAEHRR NWGVHQWEMD LYHYIKTFTK KKGALAQSEC LSQAPNQIKK LFENHYIGKE KDFLELLLYV REKNQWDNVM AAVRQIETKG LGDITTEKLI FLSEQTDLVP AVPLHPDETV EQALQNIKAF SAMFNQVDEG VLEHG |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | lsaB (ARO:3003111) | LsaB | TnSau9 | 492 | 6027-7505 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic target protection (ARO:0001003) | ||||||||||
| Sequence Family: | ABC-F ATP-binding cassette ribosomal protection protein (ARO:3004469) | ||||||||||
| Target: | macrolide antibiotic (ARO:0000000)||tetracycline antibiotic (ARO:3000050)||lincosamide antibiotic (ARO:0000017)||pleuromutilin antibiotic (ARO:3000670)||phenicol antibiotic (ARO:3000387)||oxazolidinone antibiotic (ARO:3000079)||streptogramin antibiotic (ARO:0000026) | ||||||||||
| Comment: | ATPase component of ABC transporters with duplicated ATPase domains | ||||||||||
| Protein Sequence: | MSMIHVQNLT FSYPSSFDNI FEDVSFQIDT DWKLGFIGRN GRGKTTLFNL LLDKFEYRGK IISSVDFNYF PYPVEDKSKY THEILEEICP QAEDWEFLRE IAYLNVDAEA MYRPFETLSN GEQTKVLLVA LFLNEGQFLL IDEPTNHLDT EARKTVSNYL RKKKGFILIS HDRNFLDGCV DHILSINRAD IEVQSGNYSS WKLNFDRQQG HEQATNERLQ KDIGRLEQST KRSAGWSNRV EASKNGTTNS GSKLDKGFVG HKAAKMMKRS KNLEARQQKS IEEKSKLLKN IEKTESLQFE PVEYKSKELI QLTDVSVIYD GQVVNKPISF NVEQGDRIVL DGKNGSGKSS ILKLILGDPI QYTGTLNTGS NLITSYVQQD TSHLKGMLAD FIEENEIDES LFKAILRKLD FDRVQFEKDI SHYSGGQKKK LLIAKSLCEK AHLYIWDEPL NFIDIYSRMQ IEELIQTFNP TMVFVEHDQT FQETISTKII KI |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | cfrA (ARO:3003441) | CfrA | TnSau9 | 349 | 9012-10061 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic target alteration (ARO:0001001) | ||||||||||
| Sequence Family: | Cfr 23S ribosomal RNA methyltransferase (ARO:3000202) | ||||||||||
| Target: | phenicol antibiotic (ARO:3000387)||oxazolidinone antibiotic(ARO:3000079)||streptogramin antibiotic (ARO:0000026)||lincosamide antibiotic (ARO:0000017)||pleuromutilin antibiotic (ARO:3000670) | ||||||||||
| Protein Sequence: | MNFNNKTKYG KIQEFLRSNN EPDYRIKQIT NAIFKQRISR FEDMKVLPKL LREDLINNFG ETVLNIKLLA EQNSEQVTKV LFEVSKNERV ETVNMKYKAG WESFCISSQC GCNFGCKFCA TGDIGLKKNL TVDEITDQVL YFHLLGHQID SISFMGMGEA LANRQVFDAL DSFTDPNLFA LSPRRLSIST IGIIPSIKKI TQEYPQVNLT FSLHSPYSEE RSKLMPINDR YPIDEVMNIL DEHIRLTSRK VYIAYIMLPG VNDSLEHANE VVSLLKSRYK SGKLYHVNLI RYNPTISAPE MYGEANEGQV EAFYKVLKSA GIHVTIRSQF GIDIDAACGQ LYGNYQNSQ |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | istA | IstA | ISSau9.1 | 445 | 11349-12686 | - |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | Has two amino acid changes relative to istA (ISSau9) | ||||||||||
| Protein Sequence: | MTEEIVERLK GFIQDNEWKR KNNMSKQQMK KIDMYEKLQE ERYDIGYTTV RNFVNSEERR TKEVYIRQRY SAAWEVEFDW GEVKLVIDGK QKSYSLAVFT LAYSNYRFAL LYESETMICI QDAHTKLIDH LGFVPSVFTY DNMRTVVKSF VGTDRKITDG MINLSNYYEF RIRLCEPRKG NQKGHVERSV EVVRRKAFSY DIAFPSLEDA QKRLAQTILS LNKRIHHEKK LAHIELKDQE KVAAAQGALP LPFDVSEVVE CRVDKYSTVT IKQNRYSVPE GHVGAWIRAK VSADSVRLFI EGEFVAEHRR NWGVHQWEMD LYHYIKTFTK KKGALAQSEC LSQAPNQIKK LFENRYIGKE KDFLELLLYV REKNQWDNVM AAVRQIETKG LGDITTEKLI FLSEQTDLVP AVPLHPDETV EQALQNIKAF SAMFNQVDEG VLEHG |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpC 3'-end | N/A | Tn558.1 | 33 | 13005-13106 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Helper | ||||||||||
| Sequence Family: | Tn554_family | ||||||||||
| Comment: | tnpC ORF interrupted by insertion of TnSau9 | ||||||||||
| Protein Sequence: | DVLIKTLKSR IKALEEENER LKDQVQKLHG KLF |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | fexA (ARO:3002704) | FexA | Tn558.1 | 475 | 13983-15410 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic efflux (ARO:0010000) | ||||||||||
| Sequence Family: | major facilitator superfamily (MFS) antibiotic efflux pump (ARO:0010002) | ||||||||||
| Target: | phenicol antibiotic (ARO:3000387) | ||||||||||
| Protein Sequence: | MKKDSKSKEM IQSEKRGSTR LLMMVLSLSV LVGAITADLV NPVLPLISKD LEASKSQVSW IVSGIALVLA IGVPIYGRIS DFFELRKLYI FAIMILASGS LLCAIAPNLP LLVLGRMVQG AGMSAIPVLS IIAISKVFPQ GKRGGALGII AGSIGVGTAA GPIFGGVVGQ YLGWNALFWS TFLLAIMIVI GAYYALPTIK PAESVGSNKN FDFIGGLFLG LTVGLLLFGI TQGETSGFSS FSSLTSLIGS VVALVGFIWR IVTAENPFVP PVLFNNKDYV NTVIIAFFSM FAYFAVLVFV PLLVVEVNGL SSGQAGMILL PGGVAVAILS PFVGRLSDRF GDKRLIITGM TLMGLSTLFL STYASGASPL LVSVGVLGVG IAFAFTNSPA NNAAVSALDA DKVGVGMGIF QGALYLGAGT GAGMIGALLS ARRDATEPIN PLYILDAMSY SDAFLAATGA ILIALIAGLG LKKRG |
||||||||||
| TnCentral Accession | TE Name | Type | Coordinates | Strand | Length |
|---|---|---|---|---|---|
| TnSau9-AM408573.1 | TnSau9 | transposon | 3411-13004 | + | 9594 |
| ISSau9-AM086211 | ISSau9 | insertion sequence | 3411-5862 | + | 2452 |
| ISSau9.1-AM408573 | ISSau9.1 | insertion sequence | 10553-13004 | + | 2452 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IRR | ISSau9 | 3411-3437 | + | 27 | TGTATTTCGC AACTGAAAAT TGAGCCA |
| IRL | ISSau9 | 5836-5862 | - | 27 | TGTATATGTT AACTTAAAAC TGAGCCA |
1. Kehrenberg C, Aarestrup FM, Schwarz S.
IS21-558 insertion sequences are involved in the mobility of the multiresistance gene cfr.. Antimicrob Agents Chemother. 2007 Feb;51(2):483-7. doi: 10.1128/AAC.01340-06. Epub 2006 Dec 4. PubMed ID:
17145796
.