Mobile element type:  Transposon
Name:  Tn5393.9
Synonyms: 
Accession:  Tn5393.9-KU987453.1
Family:  Tn3
Group:  Tn5393
First isolate:  ND
Partial:  ND
Evidence of transposition:  Yes

Host Organism:  Klebsiella pneumoniae
Date of Isolation:  2016
Country:  South korea
Molecular Source:  plasmid F5111

Name Coordinates Direction Length Sequence
IRL 1-40 + 40 GGGGTCGTTT GCGGGAGAGG GCGAAATCCT ACGCTAAGGC
IRRl 22240-22320 - 81 GGGGTCGTTT GCGGGAGGGG GCGGAATCCT ACGCTAAGGC TTTGGCCAGC GATATTCTCC GGTGAGATTG ATGTGTTCCC A
IRR 22281-22320 - 40 GGGGTCGTTT GCGGGAGGGG GCGGAATCCT ACGCTAAGGC

Name Associated TE Coordinates Orientation Length Sequence
res Tn2 1800-1920 + 121 AAATGTACCT TAAATCGAAT ATCGGACAAC TCATGTCTAT TATTACAAAT TTACGATTTA ATAGACATAT TAATGTAACA GTTTTACGAT GTCCGATAAT TTATAACATT TCGTACGGTT G
res_site_III Tn2 1803-1825 + 23 TGTACCTTAA ATCGAATATC GGA
res_site_II Tn2 1833-1866 + 34 TGTCTATTAT TACAAATTTA CGATTTAATA GACA
res_site_I Tn2 1889-1917 + 29 TGTCCGATAA TTTATAACAT TTCGTACGG
res Tn5393.9 19180-19401 + 222 TGTCCCGTTC GACACCTGCG GCGCGCAAGG CGTCGTGCTG CAGGTCGAGA GACTGCGAGC CATCGGCTTT GGAGACGCGG GCATATCCGA TCAGCATGTA TCACAAACGT TGGTTTGAGG CGGCGCTTCG GCCACGATTG CATTGACCTC TGGAAATGTA TCTCAACCAG CTTCATAAAC AAAGCGTCTT GAACGCTATC AGATTTTGAA AAAGGAACAT GT

ORF Summary
Name Associated TE Coordinates Orientation Class Subclass
bla TEM-1 (ARO:3000873) Tn2 197-1057 - Passenger Gene Antibiotic Resistance
tnpR Tn2 1240-1797 - Accessory Gene Resolvase
tnpA Tn2 1961-4966 + Transposase
tnpA ISEc29 5551-6735 - Transposase
armA (ARO:3000858) Tn5393.9 7451-8266 - Passenger Gene Antibiotic Resistance
tnp ISEc28 8550-9389 - Transposase
tnp ISCR1 9623-11164 - Transposase
tnp IS5708 12272-13294 - Transposase
APH(6)-Id (ARO:3002660) Tn5393.9 13452-14297 - Passenger Gene Antibiotic Resistance
APH(3'')-Ib (ARO:3002639) Tn5393.9 14288-15091 - Passenger Gene Antibiotic Resistance
rtase type_II_intron 15737-17245 - Passenger Gene Other
tnpR Tn5393.9 18665-19276 - Accessory Gene Resolvase
tnpA Tn5393.9 19402-22287 + Transposase
ORF Details
Gene Name Protein Name Associated TE Gene Length Coordinates Strand
bla TEM-1 (ARO:3000873) Bla TEM-1 Tn2 286 197-1057 -
Class: Passenger Gene
Subclass: Antibiotic Resistance
Function: antibiotic inactivation (ARO:0001004)
Sequence Family: TEM beta-lactamase (ARO:3000014)
Target: penam (ARO:3000008)||monobactam (ARO:0000004)||cephalosporin (ARO:0000032)||penem (ARO:3003706)
Comment: 100 % identity with reference sequence ARO:3000873 (bitscore=591)
Protein Sequence: MSIQHFRVAL IPFFAAFCLP VFAHPETLVK VKDAEDQLGA RVGYIELDLN SGKILESFRP EERFPMMSTF KVLLCGAVLS RVDAGQEQLG RRIHYSQNDL VEYSPVTEKH LTDGMTVREL CSAAITMSDN TAANLLLTTI GGPKELTAFL HNMGDHVTRL DRWEPELNEA IPNDERDTTM PAAMATTLRK LLTGELLTLA SRQQLIDWME ADKVAGPLLR SALPAGWFIA DKSGAGERGS RGIIAALGPD GKPSRIVVIY TTGSQATMDE RNRQIAEIGA SLIKHW

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpR TnpR Tn2 185 1240-1797 -
Class: Accessory Gene
Subclass: Resolvase
Function: resolvase||serine site-specific recombinase (GO:0000150)
Sequence Family: Serine Site-Specific Recombinase
Transposase Chemistry: Serine
Protein Sequence: MRLFGYARVS TSQQSLDLQV RALKDAGVKA NRIFTDKASG SSTDREGLDL LRMKVEEGDV ILVKKLDRLG RDTADMIQLI KEFDAQGVAV RFIDDGISTD GDMGQMVVTI LSAVAQAERR RILERTNEGR QEAKLKGIKF GRRRTVDRNV VLTLHQKGTG ATEIAHQLSI ARSTVYKILE DERAS

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA Tn2 1001 1961-4966 +
Class: Transposase
Function: transposase activity (GO:0004803)
Transposase Chemistry: DDE
Comment: identical to tnpA (Tn1)
Protein Sequence: MPVDFLTTEQ TESYGRFTGE PDELQLARYF HLDEADKEFI GKSRGDHNRL GIALQIGCVR FLGTFLTDMN HIPSGVRHFT ARQLGIRDIT VLAEYGQREN TRREHAALIR QHYQYREFAW PWTFRLTRLL YTRSWISNER PGLLFDLATG WLMQHRIILP GATTLTRLIS EVREKATLRL WNKLALIPSA EQRSQLEMLL GPTDCSRLSL LESLKKGPVT ISGPAFNEAI ERWKTLNDFG LHAENLSTLP AVRLKNLARY AGMTSVFNIA RMSPQKRMAV LVAFVLAWET LALDDALDVL DAMLAVIIRD ARKIGQKKRL RSLKDLDKSA LALASACSYL LKEETPDESI RAEVFSYIPR QKLAEIITLV REIARPSDDN FHEEMVEQYG RVRRFLPHLL NTVKFSSAPA GVTTLNACDY LSREFSSRRQ FFDDAPTEII SRSWKRLVIN KEKHITRRGY TLCFLSKLQD SLRRRDVYVT GSNRWGDPRA RLLQGADWQA NRIKVYRSLG HPTDPQEAIK SLGHQLDSRY RQVAARLCEN EAVELDVSGP KPRLTISPLA SLDEPDSLKR LSKMISDLLP PVDLTELLLE INAHTGFADE FFHASEASAR VDDLPVSISA VLMAEACNIG LEPLIRSNVP ALTRHRLNWT KANYLRAETI TSANARLVDF QATLPLAQIW GGGEVASADG MRFVTPVRTI NAGPNRKYFG NNRGITWYNF VSDQYSGFHG IVIPGTLRDS IFVLEGLLEQ ETGLNPTEIM TDTAGASELV FGLFWLLGYQ FSPRLADAGA SVFWRMDHDA DYGVLNDIAR GQSDPRKIVL QWDEMIRTAG SLKLGKVQVS VLVRSLLKSE RPSGLTQAII EVGRINKTLY LLNYIDDEDY RRRILTQLNR GESRHAVARA ICHGQKGEIR KRYTDGQEDQ LGTLGLVTNA VVLWNTIYMQ AALDHLRAQG ETLNDEDIAR LSPLCHGHIN MLGHYSFTLA ELVTKGHLRP LKEASEAENV A

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA ISEc29 394 5551-6735 -
Class: Transposase
Function: transposase activity (GO:0004803)
Transposase Chemistry: DDE
Protein Sequence: MLTMNVKAML ADFLTFVTPK SMHKARFSVL LDAVTALAKD ACCTVTAIGR AMPGSSDKVS IKRADRLLNN PNLQRELPLI YAALTASIVG HKTKPMILVD WSNADTAKRH FILRASIAAD GRALTLLQKI AAAEDYTCPH LHGAFLKQLK AMLPKDCKPV IVTDAGFKVP WLKQVRKLGW HYVARVRGNV KLKLAEQDKF ISVNQLYRQA KKDPKSVGKI MLAQTQHYET QAVLVGKGYK LLKRDKNKTY KEPWLLVSSL ADCHGYADKI AKCYSSRMQI EESFRDQKSH RYGLGSDLHG TKKKSRLEIL LLLAALVNWF HYLLGSAAEK AGLHLRYQAN TVKNRRVLAL NFLGILLCKE PKQRIRRQYY QQGLKQILQW VVQWDWAVIK QADS

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
armA (ARO:3000858) ArmA Tn5393.9 271 7451-8266 -
Class: Passenger Gene
Subclass: Antibiotic Resistance
Function: antibiotic target alteration (ARO:0001001)
Sequence Family: 16S rRNA methyltransferase (G1405) (ARO:3004271)
Target: aminoglycoside antibiotic (ARO:0000016)
Comment: 100 % identity with reference sequence (ARO:3000858) (bitscore=517)
Protein Sequence: MTVPIKYLTC RFFQMDKNDV VKKILESKKY ENLDSDIVEK VVSISEKKYK LKEVENYSKK KLHQIWGSYY SAYPNWDKLL KKYNQGQLSI EDLLKIHSST NERVATLNDF YTYVFGNIKH VSSILDFGCG FNPLALYQWN ENEKIIYHAY DIDRAEIAFL SSIIGKLKTT IKYRFLNKES DVYKGTYDVV FLLKMLPVLK QQDVNILDFL QLFHTQNFVI SFPIKSLSGK EKGMEENYQL WFESFTKGWI KILDSKVIGN ELVYITSGFQ K

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnp Tnp ISEc28 279 8550-9389 -
Class: Transposase
Transposase Chemistry: DDE
Comment: possibly 5' truncated
Protein Sequence: WMDEQAIKQW HCLVHHGRRG RGFHYSDTAI ETALMLKGLF KLPLRALEGF INSLFQLMAV PLQSPDYSCI SKRAKTVDIK YRLPSQGPVA HLVIDATGLK VYGEGEWKIR KHGKEKRRVW RKLHLAVDAT THAVIAAEVS LETVADNEVL PTLLNPLRRK IKQVSADGAY DTKACHALLK KKGAKATIPP RKNAAPWEEG HPRNEAVTAL KAGELKQWKK DSGYHQRSIA ETAMYRFKQL IGPTLSLRNY NAQVGEILAG VKVMNKLIGL GMPVRQPVN

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnp Tnp ISCR1 513 9623-11164 -
Class: Transposase
Sequence Family: IS91 tnp
Transposase Chemistry: HUH
Comment: CRof ISCR1
Protein Sequence: MSLARNATAS QSPTQTNGYE RHQPDQTLLY QLVEQHYPAF KASLEAQGQH LPRYIQQEFN DLLQCGRLEY GFMRVRCEDC HHERLVAFSC KRRGFCPSCG ARRMAESAAL LIDEVFPKEP IRQWVLSFPF QLRFLLARHP QLMGQVLSIV YRTLSTHLIK KAGYTKASAQ TGSVTLIQRF GSALNLNVHY HMLFLDGVYA EDDYGKQRFH RVKAPTYDEL NTLAHTLSHR IARCMEKRGI LERDAENTWL TLEEGEDDTL TQLHGASVTY RIAVGPQQGR KVFTLQTLPG REDKADSSSR VANHAGFSLH AGVMAEAHQR DKLERLCRYI SRPAVSEKRL ALTANGQVRY ELKTPYRNGT THVIFEPLDF IAKLAALVPK PRVNLTRFHG VFAPNSKHRV QVTPAKRGKK PDKSEGLDTN WRDKSPAERH RAMTWMQRLK RVFNIDIEVC EHCGGHVKVI ASIEDPKVIE QILKHLKQKT AKANAAKQRE LPPERAPPLT PSLFDPSQSR LFD

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnp Tnp IS5708 340 12272-13294 -
Class: Transposase
Transposase Chemistry: DDE
Protein Sequence: MTITTVGIDL AKNVFAVHCI DQNGKAVLVK PKVSRAALSE LIAGLPPCVI GMEACSGAHY WARLFRQYGH DVRLMAPKFV SPYRMAGKTG KNDAADAIAI CEAVQRPHMR FVPVKDESQQ AMQCLHRTRQ GFIQERTATY NRLRGLISEF GVIAPQSTDA LRHVVSDQKE TLPVQVRLCI DDLLTHVTNI EEKIAEYDRV LSRVAKTDHR SQQLMELKGV GPTTASALVA SIGNAHDFKN GRQLAAWLGL TPSQYSSGGK SKLGRITKAG DAYLRTLLVQ GARSVMVGAE NRTDPFSRWV CSLIGRRGYW RAVVAIAAKN ARLCWASLHY GDDFRLYSTT

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
APH(6)-Id (ARO:3002660) APH(6)-Id Tn5393.9 281 13452-14297 -
Class: Passenger Gene
Subclass: Antibiotic Resistance
Function: antibiotic inactivation (ARO:0001004)
Sequence Family: APH(6) (ARO:3000151)
Target: aminoglycoside antibiotic (ARO:0000016)
Comment: strB, orfI || strict match to reference sequence for ARO:3002660 (bitscore: 568)
Protein Sequence: MGLMFMPPVF PAHWHVSQPV LIADTFSSLV WKVSLPDGTP AIVKGLKPIE DIADELRGAD YLVWRNGRGA VRLLGRENNL MLLEYAGERM LSHIVAEHGD YQATEIAAEL MAKLYAASEE PLPSALLPIR DRFAALFQRA RDDQNAGCQT DYVHAAIIAD QMMSNASELR GLHGDLHHEN IMFSSRGWLV IDPVGLVGEV GFGAANMFYD PADRDDLCLD PRRIAQMADA FSRALDVDPR RLLDQAYAYG CLSAAWNADG EEEQRDLAIA AAIKQVRQTS Y

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
APH(3'')-Ib (ARO:3002639) APH(3'')-Ib Tn5393.9 267 14288-15091 -
Class: Passenger Gene
Subclass: Antibiotic Resistance
Function: antibiotic inactivation (ARO:0001004)
Sequence Family: APH(3'') (ARO:3000127)
Target: aminoglycoside antibiotic (ARO:0000016)
Comment: strA, orfH || perfect match to referencesequence for ARO: 3002639
Protein Sequence: MNRTNIFFGE SHSDWLPVRG GESGDFVFRR GDGHAFAKIA PASRRGELAG ERDRLIWLKG RGVACPEVIN WQEEQEGACL VITAIPGVPA ADLSGADLLK AWPSMGQQLG AVHSLSVDQC PFERRLSRMF GRAVDVVSRN AVNPDFLPDE DKSTPQLDLL ARVERELPVR LDQERTDMVV CHGDPCMPNF MVDPKTLQCT GLIDLGRLGT ADRYADLALM IANAEENWAA PDEAERAFAV LFNVLGIEAP DRERLAFYLR LDPLTWG

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
rtase Rtase type_II_intron 502 15737-17245 -
Class: Passenger Gene
Subclass: Other
Function: RNA-directed DNA polymerase activity (GO:0003964)
Sequence Family: RVT_1 (Pfam:PF00078)
Comment: group II intron reverse transcriptase/maturase OZP64963.1
Protein Sequence: MQRKLATWAA TDPSLRIQRL LRLITQPEWL AEAARITLSS KGAHTPGVDG VNKTMLQARL AVELQILRDE LLSGHYQPLP ARRVYIPKSN GKLRPLGIPA LRDRIVQRAM LMAMEPIWES DFHTLSYGFR PERSVHHAIR TVKLQLTDCG ETRGRWVIEG DLSSYFDTVH HRLLMKAVRR RISDARFMTL LWKTIKAGHI DVGLFRAASE GVPQGGVISP LLSNIMLNEF DQYLHERYLS GKARKDRWYW NNSIQRGRST AVRENWQWKP AVAYCRYADD FVLIVKGTKA QAEAIREECR GVLEGSLKLR LNMDKTKITH VNDGFIFLGH RIIRKRSRYG EMRVVSTIPQ EKARNFAASL TALLSGNYSE SKVDMAEQLN RKLKGWAMFY QFVDFKAKVF SYIDRVVFWK LAHWLARKYR TGIASLMRWW CKSPKPGQSK TWVLFGKTNH GKLSGEILYR LVGQGKKLFR WRLPEGNPYL RTETRNTYTS RFTEVAMAFA SI

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpR TnpR Tn5393.9 204 18665-19276 -
Class: Accessory Gene
Subclass: Resolvase
Function: recombinaseactivity (GO:0000150)
Sequence Family: Serine Site-Specific Recombinase
Transposase Chemistry: Serine
Protein Sequence: MLIGYARVSK ADGSQSLDLQ HDALRAAGVE RDNIYDDLAS GGRDDRPGLT ACLKSLRDGD VLVVWKLDRL GRSLAHLVNT VKELSDRKIG LRVLTGKGAQ IDTTTASGRM VFGIFATLAE FERDLIRERT MAGLASARAR GRKGGRKFAL TKAQVRLAQA AMAQRDTSVS DLCKELGIER VTLYRYVGPK GELRDHGKHV LGLT

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA Tn5393.9 961 19402-22287 +
Class: Transposase
Function: transposase activity (GO:0004803)
Transposase Chemistry: DDE
Protein Sequence: MPRRVTLTDR QKDALLRLPT SQTDLLKHYT LSDEDLGHIR LRRRAHNRFG FALQLCVLRY PGRVLAPGEL IPAEVIEFIG AQLGLGADDL VDYAAREETR HEHLAELRGL YGFRTFSGRG ASELKEWLFR EAEMAVSNED IARRFVAECR RTRTVLPATS TIERLCAAAL VDAERRIETR IASRLPMSIR EQLLALLEET ADDRVTRFVW LRQFEPGSNS SSANRLLDRL EYLQRIDLPE DLLAGVPAHR VTRLRRQGER YYADGMRDLP EDRRLAILAV CVSEWQAMLA DAVVETHDRI VGRLYRASER ICHAKVADEA GVVRDTLKSF AEIGGALVDA QDDGQPLGDV IASGSGWDGL KTLVAMATRL TATMADDPLN HVLDGYHRFR RYAPRMLRLL DLRAAPVALP LLEAVTALRT GLNDAAMTSF LRPSSKWHRH LRAQRAGDAR LWEIAVLFHL RDAFRSGDVW LTRSRRYGDL KHALVPAQSI AEGGRLAVPL RPEEWLADRQ ARLDMRLREL GRAARAGTIP GGSIENGVLH IEKLEAAAPT GAEDLVLDLY KQIPPTRITD LLLEVDAATG FTEAFTHLRT GAPCADRIGL MNVILAEGIN LGLRKMADAT NTHTFWELIR IGRWHVEGEA YDRALAMVVE AQAALPMARF WGMGTSASSD GQFFVATEQG EAMNLVNAKY GNTPGLKAYS HVSDQYAPFA TQVIPATASE APYILDGLLM NDAGRHIREQ FTDTGGFTDH VFAACAILGY RFAPRIRDLP SKRLYAFNPS AAPAHLRALI GGKVNQAMIE RNWPDILRIA ATIAAGTVAP SQILRKLASY PRQNELATAL REVGRVERTL FMIDWILDAE LQRRAQIGLN KGEAHHALKR AISFHRRGEI RDRSAEGQHY RIAGMNLLAA IIIFWNTMKL GEVVANQKRD GKLLSPDLLA HVSPLGWEHI NLTGEYRWPK P

TnCentral Accession TE Name Type Coordinates Strand Length
Tn2-KT002541 Tn2 transposon 50-4999 + 4950
ISEc29-MK649825 ISEc29 transposon 5517-6841 + 1325
ISEc28-FJ187822 ISEc28 insertion sequence 8494-9390 + 897
ISCR1-L06822 ISCR1 transposon 9391-11544 + 2154
IS5708-AJ010745 IS5708 transposon 12015-13377 + 1363
IS1133_type_II_intron-KU987453.1 IS1133_type_II_intron insertion sequence 15160-18661 + 3502
type_II_intron-KU987453 type_II_intron other 15647-17916 + 2270

Name Associated TE Coordinates Direction Length Sequence
IRL Tn2 50-87 + 38 GGGGTCTGAC GCTCAGTGGA ACGAAAACTC ACGTTAAG
IRR Tn2 4962-4999 - 38 GGGGTCTGAC GCTCAGTGGA ACGAAAACTC ACGTTAAG
IRR ISEc29 5517-5538 + 22 CTGAGGGATC CCCACAAAAT TT
IRL ISEc29 6820-6841 - 22 CTGAGGTATC CCCAGAAATT CT
IRL ISEc28 9374-9390 - 17 CTGGATGGAC GAACAAG
IRL IS5708 13328-13377 - 50 GAATGGAAGG GACTTCCCCT AGATATGCGC CTGATTAACT TTCGTGCAAT