Mobile element type:
Transposon
Name:
Tn5393
Synonyms:
Accession:
Tn5393-M95402.1
Family:
Tn3
Group:
Tn163
First isolate:
Yes
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Erwinia amylovora
Date of Isolation:
1993
Country:
Molecular Source:
plasmidpEa34
| 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 | 6625-6705 | - | 81 | GGGGTCGTTT GCGGGAGGGG GCGGAATCCT ACGCTAAGGC TTTGGCCAGC GATATTCTCC GGTGAGATTG ATGTGTTCCC A |
| IRR | 6666-6705 | - | 40 | GGGGTCGTTT GCGGGAGGGG GCGGAATCCT ACGCTAAGGC |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| res | Tn5393 | 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 | 107-952 | - | Passenger Gene | Antibiotic Resistance |
| APH(3'')-Ib (ARO:3002639) | Tn5393 | 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 | 3050-3661 | - | Accessory Gene | Resolvase |
| tnpA | Tn5393 | 3787-6672 | + | Transposase |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | APH(6)-Id (ARO:3002660) | APH(6)-Id | Tn5393 | 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 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 | 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: | 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 | 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 | 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 | TnpA | Tn5393 | 961 | 3787-6672 | + |
|---|
| 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 ARLDMRLRDV GRAARAGTIP GGSIENGVLH IEKLEAAAPT GAEDLVLDLY KQIPPTRITD LLLEVDAATG FTEAFTHLRT GAPCADRIGL MNVILAEGIN LGLRKMADRT 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 KGERHHALKR AISFHRRGEI RDRSAEGQHY RIAGMNLLAA IIIFWNTMKL GEVVANQKRD GKLLSPDLLA HVSPLGWEHI NLTGEYRWPK P |
||||||||||
| TnCentral Accession | TE Name | Type | Coordinates | Strand | Length |
|---|---|---|---|---|---|
| IS1133-Z12167 | IS1133 | insertion sequence | 1815-3046 | + | 1232 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IRR | IS1133 | 1815-1841 | + | 27 | TGGACTTGCA CCGGTTGTGT TCCGGTC |
| IRL | IS1133 | 3020-3046 | - | 27 | TGGACTTGCC TCGGTTTCGT TCCGGTC |
1. Chiou CS, Jones AL.
Nucleotide sequence analysis of a transposon (Tn5393) carrying streptomycin resistance genes in Erwinia amylovora and other gram-negative bacteria.. J Bacteriol. 1993 Feb;175(3):732-40. doi: 10.1128/jb.175.3.732-740.1993. PubMed ID:
8380801
.