Mobile element type:
Integron
Name:
In_Tn6025
Synonyms:
Accession:
In_Tn6025-GU562437
Family:
Tn402
Group:
Class 1
First isolate:
Yes
Partial:
ND
Evidence of transposition:
Yes
Host Organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Date of Isolation:
2010
Country:
Australia
Molecular Source:
plasmid pSRC125
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| IRt | 1-33 | + | 33 | TGTCATTTTC AGAAGACGAC TGCACCAGTT GAT |
| repeat t1 | 9-27 | + | 19 | TCAGAAGACG ACTGCACCA |
| repeat t2 | 49-67 | - | 19 | TCAGGAGCTG GCTGCACAA |
| repeat t3 | 78-97 | + | 20 | TCAGAAGTGA TCTGCACCAA |
| repeat t4 | 110-128 | + | 19 | TCAATACTCG TGTGCACCA |
| IRt | 1123-1155 | - | 33 | TGTCATTTTC AGAAGACGAC TGCACCAGTT GAT |
| IRi | 5279-5311 | - | 33 | TGTCGTTTTC AGAAGACGGC TGCACTGAAC GTC |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| attC qacH_sul1 | In_Tn6025 | 2078-2111 , 3386-3392 | + | 41 | CCGCTAGCGG GCGGCCGGAA GGTGAATGCT AGGCATCTAA C |
| attC qacH_sul1 core | In_Tn6025 | 2078-2111 | + | 34 | CCGCTAGCGG GCGGCCGGAA GGTGAATGCT AGGC |
| attC dfrA5 | In_Tn6025 | 3386-3472 , 3954-3959 | + | 93 | ATCTAACGCC GTTATCAATT GCGGTAAGAA GCGTAGCAAG CGAAGCGAAC GAAGCTTTTT ACCGTCAATT GCATAGCTTT GTTAACCGGT TAA |
| attC dfrA5 | In_Tn6025 | 3386-3472 | + | 87 | ATCTAACGCC GTTATCAATT GCGGTAAGAA GCGTAGCAAG CGAAGCGAAC GAAGCTTTTT ACCGTCAATT GCATAGCTTT GTTAACC |
| attI | In_Tn6025 | 3960-4015 | + | 56 | CTTTGTTTTA GGGCGACTGC CCTGCTGCGT AACATCGTTG CTGCTCCATA ACATCA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tniA interrupted | In_Tn6025 | 106-152 , 1034-1046 | + | Transposase | |
| tnp | IS6100 | 207-971 | - | Transposase | |
| WP_001424634.1 | In_Tn6025 | 1167-1454 | - | Passenger Gene | Hypothetical |
| GNAT_fam | In_Tn6025 | 1478-1978 | - | Passenger Gene | Antibiotic Resistance |
| sul1 (ARO:3000410) | In_Tn6025 | 2106-2942 | - | Passenger Gene | Antibiotic Resistance |
| qacEdelta1 (ARO:3005010) | In_Tn6025 | 2936-3283 | - | Passenger Gene | Antibiotic Resistance |
| dfrA5 (ARO:3002861) | In_Tn6025 | 3467-3940 | - | Passenger Gene | Antibiotic Resistance |
| intI1 | In_Tn6025 | 4096-5109 | + | Integron Integrase | Class 1 |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniA interrupted | TniA interrupted | In_Tn6025 | 19 | 106-152 , 1034-1046 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | IS6100 insertion | ||||||||||
| Protein Sequence: | MLNTRVHQSE VSMATEHEY |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp | Tnp | IS6100 | 254 | 207-971 | - |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MTDFKWRHFQ GDVILWAVRW YCRYPISYRD LEEMLAERGI SVDHTTIYRW VQCYAPEMEK RLRWFWRRGF DPSWRLDETY VKVRGKWTYL YRAVDKRGDT IDFYLSPTRS AKAAKRFLGK ALRGLKHWEK PATLNTDKAP SYGAAITELK REGKLDRETA HRQVKYLNNV IEADHGKLKI LIKPVRGFKS IPTAYATIKG FEVMRALRKG QARPWCLQPG IRGEVRLVER AFGIGPSALT EAMGMLNHHF AAAA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | WP_001424634.1 | WP_001424634.1 | In_Tn6025 | 95 | 1167-1454 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Hypothetical | ||||||||||
| Protein Sequence: | MSGWDGPVAS RSLAVRPRCL GCARGCRYPP LPSSTLDNAA AVIAADARAG LFGPVRLARP SACLGEISGG RINGGASPPF VRVKAEDSSL KNIRL |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | GNAT_fam | GNAT_fam | In_Tn6025 | 166 | 1478-1978 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Sequence Family: | Acetyltransf_1 (Pfam:PF00583) | ||||||||||
| Target: | aminoglycoside antibiotic (ARO:0000016) | ||||||||||
| Comment: | putative acetyltransferase ADU64769.1 | ||||||||||
| Protein Sequence: | MDSEEPPNVR VACSGDIDEV VRLMHDAAAW MSAKGTPAWD VARIDRTFAE TFVLRSELLV ASCSDGIVGC CTLSAEDPEF WPDALKGEAA YLHKLAVRRT HAGRGVSSAL IEACRHAART QGCAKLRLDC HPNLRGLYER LGFTHVDTFN PGWDPTFIAE RLELEI |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | sul1 (ARO:3000410) | Sul1 | In_Tn6025 | 278 | 2106-2942 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic target replacement (ARO:0001002) | ||||||||||
| Sequence Family: | sulfonamide resistant sul (ARO:3004238) | ||||||||||
| Transposase Chemistry: | dihydropteroate synthase | ||||||||||
| Target: | sulfonamide antibiotic (ARO:3000282)||sulfone antibiotic (ARO:3003401) | ||||||||||
| Comment: | perfect match to reference sequence for ARO:3000410 | ||||||||||
| Protein Sequence: | MVTVFGILNL TEDSFFDESR RLDPAGAVTA AIEMLRVGSD VVDVGPAASH PDARPVSPAD EIRRIAPLLD ALSDQMHRVS IDSFQPETQR YALKRGVGYL NDIQGFPDPA LYPDIAEADC RLVVMHSAQR DGIATRTGHL RPEDALDEIV RFFEARVSAL RRSGVAADRL ILDPGMGFFL SPAPETSLHV LSNLQKLKSA LGLPLLVSVS RKSFLGATVG LPVKDLGPAS LAAELAIGNG ADYVRTHAPG DLRSAITFSE TLAKFRSRDA RDRGLDHA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | qacEdelta1 (ARO:3005010) | QacEdelta1 | In_Tn6025 | 115 | 2936-3283 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic efflux (ARO:0010000) | ||||||||||
| Sequence Family: | major facilitator superfamily (MFS) antibiotic efflux pump (ARO:0010002) | ||||||||||
| Target: | disinfecting agents and antiseptics(ARO:3005386) | ||||||||||
| Comment: | subunit of the qac multidrug efflux pump||perfect match to reference sequence for ARO:3005010 (bitscore:219) | ||||||||||
| Protein Sequence: | MKGWLFLVIA IVGEVIATSA LKSSEGFTKL APSAVVIIGY GIAFYFLSLV LKSIPVGVAY AVWSGLGVVI ITAIAWLLHG QKLDAWGFVG MGLIIAAFLL ARSPSWKSLR RPTPW |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | dfrA5 (ARO:3002861) | DfrA5 | In_Tn6025 | 157 | 3467-3940 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic target replacement (ARO:0001002) | ||||||||||
| Sequence Family: | trimethoprim resistant dihydrofolate reductase dfr (ARO:3001218) | ||||||||||
| Transposase Chemistry: | antibiotic target replacement (ARO:0001002) | ||||||||||
| Target: | diaminopyrimidine antibiotic (ARO:3000171) | ||||||||||
| Protein Sequence: | MKVSLMAAKA KNGVIGCGPH IPWSAKGEQL LFKALTYNQW LLVGRKTFES MGALPNRKYA VVTRSAWTAD NDNVIVFPSI EEAMYGLAEL TDHVIVSGGG EIYRETLPMA STLHISTIDI EPEGDVFFPN IPNTFEVVFE QHFSSNINYC YQIWQKG |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1 | IntI1 | In_Tn6025 | 337 | 4096-5109 | + |
|---|
| Class: | Integron Integrase | ||||||||||
| Subclass: | Class 1 | ||||||||||
| Sequence Family: | Class 1 Integron Tyrosine Integrase | ||||||||||
| Transposase Chemistry: | Tyrosine | ||||||||||
| Protein Sequence: | MKTATAPLPP LRSVKVLDQL RERIRYLHYS LRTEQAYVNW VRAFIRFHGV RHPATLGSSE VEAFLSWLAN ERKVSVSTHR QALAALLFFY GKVLCTDLPW LQEIGRPRPS RRLPVVLTPD EVVRILGFLE GEHRLFAQLL YGTGMRISEG LQLRVKDLDF DHGTIIVREG KGSKDRALML PESLAPSLRE QLSRARAWWL KDQAEGRSGV ALPDALERKY PRAGHSWPWF WVFAQHTHST DPRSGVVRRH HMYDQTFQRA FKRAVEQAGI TKPATPHTLR HSFATALLRS GYDIRTVQDL LGHSDVSTTM IYTHVLKVGG AGVRSPLDAL PPLTSER |
||||||||||
| TnCentral Accession | TE Name | Type | Coordinates | Strand | Length |
|---|---|---|---|---|---|
| IS6100-X53635 | IS6100 | insertion sequence | 153-1032 | + | 880 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IR | IS6100 | 153-166 | + | 14 | GGCTCTGTTG CAAA |
| IR | IS6100 | 1019-1032 | - | 14 | GGCTCTGTTG CAAA |
1. Cain AK, Liu X, Djordjevic SP, Hall RM.
Transposons related to Tn1696 in IncHI2 plasmids in multiply antibiotic resistant Salmonella enterica serovar Typhimurium from Australian animals.. Microb Drug Resist. 2010 Sep;16(3):197-202. doi: 10.1089/mdr.2010.0042. PubMed ID:
20701539
.
2. Cain AK, Hall RM. Transposon Tn5393e carrying the aphA1-containing transposon Tn6023 upstream of strAB does not confer resistance to streptomycin.. Microb Drug Resist. 2011 Sep;17(3):389-94. doi: 10.1089/mdr.2011.0037. Epub 2011 Jun 24. PubMed ID: 21702681 .
2. Cain AK, Hall RM. Transposon Tn5393e carrying the aphA1-containing transposon Tn6023 upstream of strAB does not confer resistance to streptomycin.. Microb Drug Resist. 2011 Sep;17(3):389-94. doi: 10.1089/mdr.2011.0037. Epub 2011 Jun 24. PubMed ID: 21702681 .