Mobile element type:
Transposon
Name:
Tn5393.10
Synonyms:
Accession:
Tn5393.10-CP019905.1
Family:
Tn3
Group:
Tn163
First isolate:
ND
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Escherichia coli MDR_56
Date of Isolation:
2017
Country:
Molecular Source:
plasmid unamed 6
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| IRLl | 1-81 | + | 81 | GGGGTCGTTT GCGGGAGAGG GCGAAATCCT ACGCTAAGGC TTTGGCCAAC GATATTCTCC GGTAAGATTG ATGTGTTCCC A |
| IRL | 1-40 | + | 40 | GGGGTCGTTT GCGGGAGAGG GCGAAATCCT ACGCTAAGGC |
| IRRl | 13699-13779 | - | 81 | GGGGTCGTTT GCGGGAGGGG GCGGAATCCT ACGCTAAGGC TTTGGCCAGC GATATTCTCC GGTGAGATTG ATGTGTTCCC A |
| IRR | 13740-13779 | - | 40 | GGGGTCGTTT GCGGGAGGGG GCGGAATCCT ACGCTAAGGC |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| res | Tn5393.10 | 3565-3786 | + | 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 |
|---|---|---|---|---|---|
| APH(6)-Id (ARO:3002660) | Tn5393.10 | 107-952 | - | Passenger Gene | Antibiotic Resistance |
| APH(3'')-Ib (ARO:3002639) | Tn5393.10 | 943-1746 | - | Passenger Gene | Antibiotic Resistance |
| orfAB | IS1133 | 1853-2982 | - | Transposase | |
| orfB | IS1133 | 1853-2710 | - | Transposase | |
| orfA | IS1133 | 2707-2982 | - | Accessory Gene | Regulator |
| tnpR | Tn5393.10 | 3050-3661 | - | Accessory Gene | Resolvase |
| tnpA N-ter | Tn5393.10 | 3787-4149 | + | Transposase | |
| ABC-F | Tn5393.10 | 5713-7368 | - | Passenger Gene | Other |
| NAD(P)-dependent oxidoreductase | Tn5393.10 | 7421-8296 | - | Passenger Gene | Other |
| tnp_truncated | IS50L | 10500-11852 | - | Transposase | |
| inh_truncated | IS50L | 10500-11687 | - | Accessory Gene | Inhibitor |
| tnpA C-ter | Tn5393.10 | 11947-13746 | + | Transposase |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | APH(6)-Id (ARO:3002660) | APH(6)-Id | Tn5393.10 | 281 | 107-952 | - |
|---|
| 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 AIVKELKPIE 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 | Tn5393.10 | 267 | 943-1746 | - |
|---|
| 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: | MNRTNIFFGK 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 | orfAB | OrfAB | IS1133 | 376 | 1853-2982 | - |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | fusion protein from -1 programmed frameshifting between orfA and orfB | ||||||||||
| Protein Sequence: | MSLKHSDEFK RDAVRIALTS GLTRRQVASD LSIGLSTLGK WIASISDETK IPTQDTDLLR ENERLRKENR ILREEREILK KAAIFFAVQK L*DFSLLRIT VALSHVHAYV V*WA*QIVVY VHGNAVLHHC ASVVILYF*R IYVSSIGCVW GAMVGRV*QK S*KRWACRLG SVGLDV*CAR ITLQLFERVN SNGQRIVIIP STLHRTY*NK TLAQAHPTRN GQAISLMFGP EKDGSILLLS LTCIPVA*LA GQQVID*SRI LH*GH*IWRW LYANHHRVVF NTQTVGANIA LMNIKSYCSN INCCRP*AGK AIVLITPQ*K ASLNH*RLS* FGADTGKQGE ILRLQSSNI* MAFIIHAEDI QHSAGNRRWH LRKKPL |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | orfB | OrfB | IS1133 | 285 | 1853-2710 | - |
|---|
| Class: | Transposase | ||||||||||
| Function: | Nucleic acid binding (GO:0003676) | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | frameshiftrequired| 5'-end of tnp gene | ||||||||||
| Protein Sequence: | MRFQFITDYR GSLSRSRICR LMGVTDRGLR AWKRRPPSLR QRRDLILLAH IREQHRLCLG SYGRPRMTEE LKALGLQVGQ RRVGRLMRQN NITVVRTRKF KRTTDSHHTF NIAPNLLKQD FSASAPNQKW AGDITYVWTR EGWVYLAVIL DLYSRRVIGW ATGDRLKQDL ALRALNMALA LRKPPPGCIQ HTDRGSQYCA HEYQKLLLKH QLLPSMSGKG NCFDNSAVES FFKSLKAELI WRRHWQTRRD IEIAIFEYIN GFYNPRRRHS TLGWKSPVAF EKKAA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | orfA | OrfA | IS1133 | 91 | 2707-2982 | - |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Regulator | ||||||||||
| Function: | transposase activity (GO:0004803) | ||||||||||
| Comment: | orfA, together with orfB, encodes a fusion protein formed by translational frame-shifting that is the transposase forIS1133 | ||||||||||
| Protein Sequence: | MSLKHSDEFK RDAVRIALTS GLTRRQVASD LSIGLSTLGK WIASISDETK IPTQDTDLLR ENERLRKENR ILREEREILK KAAIFFAVQK L |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpR | TnpR | Tn5393.10 | 204 | 3050-3661 | - |
|---|
| 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 N-ter | TnpA N-ter | Tn5393.10 | 121 | 3787-4149 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MPRRVTLTDR QKDALLRLPT SQTDLLKHYT LSDEDLGHIR LRRRAHNRFG FALQLCVLRY PGRVLAPGEL IPAEVIEFIG AQLGLGADDL VDYAAREETR HEHLAELRGL YGFRTFSGRG A |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | ABC-F | ABC-F | Tn5393.10 | 551 | 5713-7368 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Comment: | ribosomal protection protein | ||||||||||
| Protein Sequence: | MFINLIARKG GDCMELIKMR GIEKYFGGKL LFTFDKLTVF KNDIIGVVGL NGSGKTTLLE IINNDIAPDK GNVEVKGDIS YYKQFGQYHE SVDSWQLKEF RSSSTISEGW FSGGEKTRLR LAETFSKSSS ILLLDEPTAN LDTKGIQLLK RNLGKYNTMM IISHDTNLLD ELCNRIIEID NNTINCFDGN YTAYKQQKEH QIHTEKREYE NYQAKKKQLE EAYLQKKRQA EAITDKPRNM SNSEIRARSF ISTYKSFGGR QKAIAKQAKA VQSRIEQLDV KEQVEEQANI RINFELTNPP KNKILIRGEE VTFGYDNHLI FNHASFEIRN KQKVAVLGDN GSGKSTLFSL IRNKYEGIYA VPKLKIGYLY QEFENLQPDK TLLESVLSDS VQENHTVYTV LMNLLFTIED FDKKVAVLSG GEKIRLSFAK LIVSDYNLLI LDEPTNYLDL PSIEVVKSVL KEYEGTIIFA SHDEAFINEL STELFIIDNK KLQGYRGNLE EFKNKTDANI EQLQQEIEQI QLSQAKLLME NETNPRKIEK IKKRYEEMTR V |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | NAD(P)-dependent oxidoreductase | NAD(P)-dependent oxidoreductase | Tn5393.10 | 291 | 7421-8296 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Sequence Family: | Short-chain dehydrogenase/reductase SDR (IPR002347) | ||||||||||
| Protein Sequence: | MTFNNNENTR VWFITGASSG LGYEFTKKAL ESGEKVVGVA RNIEKLNELK CQFEGMLLPL SLDVTDRSAV STTVETAIKH FGRLDIVINN AGNMVMGMIE EFSEDEVRSQ METNFFGTVW VSQAVMPYLR AQESGHIIQI SSIGGLISGP MSGIYSASKF ALEGFSEALA QEAAHFGIKV SIVEPGGYWT NLYLKMSFTT QKKEYDSLRE KLAQQYSNES VDSDPKLAAE AIMKLVNSEN PPLRLVLGSL VYDLAVENAE KRIFTWKEWE SVSRSSEHGI PAPEGYGIIE E |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp_truncated | Tnp_truncated | IS50L | 450 | 10500-11852 | - |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | truncated to 421 amino acids by ochre mutation in C-terminal region which creates a promoter for aphA2 expression||non-functional | ||||||||||
| Protein Sequence: | MITSALHRAA DWAKSVFSSA ALGDPRRTAR LVNVAAQLAK YSGKSITISS EGSEAMQEGA YRFIRNPNVS AEAIRKAGAM QTVKLAQEFP ELLAIEDTTS LSYRHQVAEE LGKLGSIQDK SRGWWVHSVL LLEATTFRTV GLLHQEWWMR PDDPADADEK ESGKWLAAAA TSRLRMGSMM SNVIAVCDRE ADIHAYLQDK LAHNERFVVR SKHPRKDVES GLYLYDHLKN QPELGGYQIS IPQKGVVDKR GKRKNRPARK ASLSLRSGRI TLKQGNITLN AVLAEEINPP KGETPLKWLL LTSEPVESLA QALRVIDIYT HRWRIEEFHK AWKTGAGAER QRMEEPDNLE RMVSILSFVA VRLLQLRESF TLPQALRAQG LLKEAEHVES QSAETVLTPD ECQLLGYLDK GKRKRKEKAG SLQWAYMAIA RLGGFMDSKR TGIASWGALW |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | inh_truncated | Inh_truncated | IS50L | 395 | 10500-11687 | - |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Inhibitor | ||||||||||
| Comment: | truncated by ochre mutation in C-terminal end | ||||||||||
| Protein Sequence: | MQEGAYRFIR NPNVSAEAIR KAGAMQTVKL AQEFPELLAI EDTTSLSYRH QVAEELGKLG SIQDKSRGWW VHSVLLLEAT TFRTVGLLHQ EWWMRPDDPA DADEKESGKW LAAAATSRLR MGSMMSNVIA VCDREADIHA YLQDKLAHNE RFVVRSKHPR KDVESGLYLY DHLKNQPELG GYQISIPQKG VVDKRGKRKN RPARKASLSL RSGRITLKQG NITLNAVLAE EINPPKGETP LKWLLLTSEP VESLAQALRV IDIYTHRWRI EEFHKAWKTG AGAERQRMEE PDNLERMVSI LSFVAVRLLQ LRESFTLPQA LRAQGLLKEA EHVESQSAET VLTPDECQLL GYLDKGKRKR KEKAGSLQWA YMAIARLGGF MDSKRTGIAS WGALW |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA C-ter | TnpA C-ter | Tn5393.10 | 599 | 11947-13746 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | LVAMATRLTA TMADDPLNHV LDGYHRFRRY APRMLRLLDL RAAPVALPLL EAVTALRTGL NDAAMTSFLR PSSKWHRHLR AQRAGDARLW EIAVLFHLRD AFRSGDVWLT RSRRYGDLKH ALVPAQSIAE GGRLAVPLRP EEWLADRQAR LDMRLRELGR AARAGTIPGG SIENGVLHIE KLEAAAPTGA EDLVLDLYKQ IPPTRITDLL LEVDAATGFT EAFTHLRTGA PCADRIGLMN VILAEGINLG LRKMADATNT HTFWELIRIG RWHVEGEAYD RALAMVVEAQ AALPMARFWG MGTSASSDGQ FFVATEQGEA MNLVNAKYGN TPGLKAYSHV SDQYAPFATQ VIPATASEAP YILDGLLMND AGRHIREQFT DTGGFTDHVF AACAILGYRF APRIRDLPSK RLYAFNPSAA PAHLRALIGG KVNQAMIERN WPDILRIAAT IAAGTVAPSQ ILRKLASYPR QNELATALRE VGRVERTLFM IDWILDAELQ RRAQIGLNKG EAHHALKRAI SFHRRGEIRD RSAEGQHYRI AGMNLLAAII IFWNTMKLGE VVANQKRDGK LLSPDLLAHV SPLGWEHINL TGEYRWPKP |
||||||||||
| TnCentral Accession | TE Name | Type | Coordinates | Strand | Length |
|---|---|---|---|---|---|
| IS1133-Z12167 | IS1133 | insertion sequence | 1815-3046 | + | 1232 |
| IS50L-U00004.1 | IS50L | insertion sequence | 10411-11944 | + | 1534 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IRR | IS1133 | 1815-1841 | + | 27 | TGGACTTGCA CCGGTTGTGT TCCGGTC |
| IRL | IS1133 | 3020-3046 | - | 27 | TGGACTTGCC TCGGTTTCGT TCCGGTC |
| IRL | IS50L | 11936-11944 | - | 9 | CTGACTCTT |