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 |