Mobile element type:
Integron
Name:
In_Tn21.1
Synonyms:
Accession:
In_Tn21.1-MH257753
Family:
Tn402
Group:
Class 1
First isolate:
ND
Partial:
ND
Evidence of transposition:
Yes
Host Organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Date of Isolation:
Country:
Molecular Source:
plasmid pST1007-1A
| 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 |
| repeat i4 | 12049-12067 | - | 19 | TCAGCGGACG CAGGGAGGA |
| repeat i3 | 12077-12095 | - | 19 | TCAGGCAACG ACGGGCTGC |
| repeat i2 | 12119-12137 | - | 19 | TCAGAAGCCG ACTGCACTA |
| IRi | 12136-12168 | - | 33 | TGTCGTTTTC AGAAGACGGC TGCACTGAAC GTC |
| repeat i1 | 12142-12160 | - | 19 | TCAGAAGACG GCTGCACTG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| attC cmlA6 | In_Tn21.1 | 7508-7571 , 9051-9056 | + | 70 | CGCCTGAGCT CAGCCGACCG AAACCGCGTA GCGGTTTTGG GTCGGCTGCA GCGATTTGTT GGGCGCCCAA |
| attC cmlA6 core | In_Tn21.1 | 7508-7571 | + | 64 | CGCCTGAGCT CAGCCGACCG AAACCGCGTA GCGGTTTTGG GTCGGCTGCA GCGATTTGTT GGGC |
| attC-cmlA6 3'-end | In_Tn21.1 | 9051-9056 | + | 6 | GCCCAA |
| attC aadA2 | In_Tn21.1 | 9057-9110 , 9907-9912 | + | 60 | CGCCGGAGTT AAGCCGCCGC GCGTAGCGCG GTCGGCTTGA ACGAATTGTT AGACGTCTAA |
| attC aadA3 core | In_Tn21.1 | 9057-9110 | + | 54 | CGCCGGAGTT AAGCCGCCGC GCGTAGCGCG GTCGGCTTGA ACGAATTGTT AGAC |
| attC orfD core | In_Tn21.1 | 9918-9965 | + | 48 | GAGGTAAGCC GACCGCAGAA TGCGGGTCGG CTTGACCGAA ATGTTAGA |
| attC dfrA12 core | In_Tn21.1 | 10233-10316 | + | 84 | CGTTGGACGT AACGAGAGCC GGAGCGCAGC GGAGGGAACC AAAATGCGCA GCATTTTGGC GTCCCGTTGA CGGAATGGTT AGCC |
| attI | In_Tn21.1 | 10817-10872 | + | 56 | CTTTGTTTTA GGGCGACTGC CCTGCTGCGT AACATCGTTG CTGCTCCATA ACATCA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tniA 5'-end | In_Tn21.1 | 106-1410 | + | Transposase | |
| tnpA | IS26 | 1457-2161 | + | Transposase | |
| SDR family oxidoreductase | In_Tn21.1 | 2619-3482 | + | Passenger Gene | Other |
| GrpB domain protein | In_Tn21.1 | 3520-3765 | + | Passenger Gene | Other |
| sul3 (ARO:3000413) | In_Tn21.1 | 4234-5025 | + | Passenger Gene | Antibiotic Resistance |
| tnp IS256 family | In_Tn21.1 | 5350-5958 | + | Transposase | |
| qacL (ARO:3005098) | In_Tn21.1 | 6205-6537 | - | Passenger Gene | Antibiotic Resistance |
| aadA (ARO:3002601) | In_Tn21.1 | 6707-7498 | - | Passenger Gene | Antibiotic Resistance |
| cmlA6 (ARO:3002696) | In_Tn21.1 | 7591-8850 | - | Passenger Gene | Antibiotic Resistance |
| aadA2 (ARO:3002602) | In_Tn21.1 | 9112-9891 | - | Passenger Gene | Antibiotic Resistance |
| DUF1010 family protein | In_Tn21.1 | 9909-10199 | - | Passenger Gene | Other |
| dfrA12 (ARO:3002858) | In_Tn21.1 | 10311-10808 | - | Passenger Gene | Antibiotic Resistance |
| intI1 | In_Tn21.1 | 10953-11966 | + | Integron Integrase | Class 1 |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniA 5'-end | TniA 5'-end | In_Tn21.1 | 434 | 106-1410 | + |
|---|
| Class: | Transposase | ||||||||||
| Function: | integrase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | Contains the first 429 amino acids of tniA (In2)||probably truncated by insertion of IS26 | ||||||||||
| Protein Sequence: | MLNTRVHQSE VSMATDTPRI PEQGVATLPD EAWERARRRA EIISPLAQSE TVGHEAADMA AQALGLSRRQ VYVLIRRARQ GSGLVTDLVP GQSGGGKGKG RLPEPVERVI HELLQKRFLT KQKRSLAAFH REVTQVCKAQ KLRVPARNTV ALRIASLDPR KVIRRREGQD AARDLQGVGG EPPAVTAPLE QVQIDHTVID LIVVDDRDRQ PIGRPYLTLA IDVFTRCVLG MVVTLEAPSA VSVGLCLVHV ACDKRPWLEG LNVEMDWQMS GKPLLLYLDN AAEFKSEALR RGCEQHGIRL DYRPLGQPHY GGIVERIIGT AMQMIHDELP GTTFSNPDQR GDYDSENKAA LTLRELERWL TLAVGTYHGS VHNGLLQPPA ARWAEAVARV GVPAVVTRAT SFLVDFLPIL RRTLTRTGFV IDHIHYYADG HCCK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA | TnpA | IS26 | 234 | 1457-2161 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MNPFKGRHFQ RDIILWAVRW YCKYGISYRE LQEMLAERGV NVDHSTIYRW VQRYAPEMEK RLRWYWRNPS DLCPWHMDET YVKVNGRWAY LYRAVDSRGR TVDFYLSSRR NSKAAYRFLG KILNNVKKWQ IPRFINTDKA PAYGRALALL KREGRCPSDV EHRQIKYRNN VIECDHGKLK RIIGATLGFK SMKTAYATIK GIEVMRALRK GQASAFYYGD PLGEMRLVSR VFEM |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | SDR family oxidoreductase | SDR family oxidoreductase | In_Tn21.1 | 287 | 2619-3482 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Sequence Family: | WP_000612791.1 | ||||||||||
| Protein Sequence: | MIPNSENKRV WFITGASKGL GYAFTCAALK AGDKVVAVAR TIDNLAKLEE TYQESLLPLN LDVTDREAVF STVETAVKHF GRLDIVVNNA GIMTMGMIEE LNESDARKLM DTNFFGALWV CQAVMPYLRS QRSGHIIQIT SIGAIISGPM SGIYSASKFA LEGMSEALAK EAEHFGVKLT MVEPGGYWTD LYTSMSYSNP LDSYGTLRDE LAKQYSEDSV DSDPSLAAEA LMKLVASNNP PLRLILGSMV YDLAMDTLKA RMATWEEWEA VSRASEKAIP APERYGV |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | GrpB domain protein | GrpB domain protein | In_Tn21.1 | 81 | 3520-3765 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Sequence Family: | GrpB (Pfam:PF04229) | ||||||||||
| Protein Sequence: | MKIEIMEYNP DWTKNFEEEK IKLLHFFGSH AVAIEHIGST AIPNQRAKPV IDIFIGVSPF AELPFISAFL MQRSITTLRQ I |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | sul3 (ARO:3000413) | Sul3 | In_Tn21.1 | 263 | 4234-5025 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic target replacement (ARO:0001002) | ||||||||||
| Sequence Family: | sulfonamide resistant sul (ARO:3004238) | ||||||||||
| Target: | sulfone antibiotic (ARO:3003401)||sulfonamide antibiotic (ARO:3000282) | ||||||||||
| Comment: | perfect match to reference sequence for ARO:3000413 | ||||||||||
| Protein Sequence: | MSKIFGIVNI TTDSFSDGGL YLDTDKAIEH ALHLVEDGAD VIDLGAASSN PDTTEVGVVE EIKRLKPVIK ALKEKGISIS VDTFKPEVQS FCIEQKVDFI NDIQGFPYPE IYSGLAKSDC KLVLMHSVQR IGAATKVETN PEEVFTSMME FFKERIAALV EAGVKRERII LDPGMGFFLG SNPETSILVL KRFPEIQEAF NLQVMIAVSR KSFLGKITGT DVKSRLAPTL AAEMYAYKKG ADYLRTHDVK SLSDALKISK ALG |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp IS256 family | Tnp IS256 family | In_Tn21.1 | 202 | 5350-5958 | + |
|---|
| Class: | Transposase | ||||||||||
| Function: | tranposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MEFYPSCIEK GMRSERALKL AIAEMYVKGV STRRVSDIVE ILCGTEVSSS QVSRLAKELD EEITSWKAQP VGQIQYLVLD ATYESVRVGS HVVKQALLVA IGVDYSGNRH ILDAEVANSE AEVNWRSFLE GLVRRGMHGL RMITSDDHSG LRAAIDAVFP GILWQRCQFH LQQNAHSYVT KKDEIPLIAA DIRKVFNRNM SR |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | qacL (ARO:3005098) | QacL | In_Tn21.1 | 110 | 6205-6537 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic efflux (ARO:0010000) | ||||||||||
| Sequence Family: | small multidrug resistance (SMR) antibiotic efflux pump (ARO:0010003) | ||||||||||
| Target: | disinfecting agents and antiseptics(ARO:3005386) | ||||||||||
| Comment: | subunit of the qac multidrug efflux pump||strict match to reference sequence for ARO:3005098 (bitscore: 202) | ||||||||||
| Protein Sequence: | MKNWLFLAIA IFGEVVATSA LKSSHGFTKL VPSVVVVAGY GLAFYFLSLA LKSIPVGIAY AVWAGLGIVL VAAIAWIFHG QKLDLWAFVG MGLIVSGVAV LNLLSKVSAH |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | aadA (ARO:3002601) | AadA | In_Tn21.1 | 263 | 6707-7498 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | ANT(3'') (ARO:3004275) | ||||||||||
| Transposase Chemistry: | aminoglycoside nucleotidyltransferase | ||||||||||
| Target: | aminoglycoside antibiotic (ARO:0000016) | ||||||||||
| Comment: | perfect match to reference sequence for ARO:3002601||Synonyms: aadA1-pm aadA, aadA1, aad(3'')(9) | ||||||||||
| Protein Sequence: | MREAVIAEVS TQLSEVVGVI ERHLEPTLLA VHLYGSAVDG GLKPHSDIDL LVTVTVRLDE TTRRALINDL LETSASPGES EILRAVEVTI VVHDDIIPWR YPAKRELQFG EWQRNDILAG IFEPATIDID LAILLTKARE HSVALVGPAA EELFDPVPEQ DLFEALNETL TLWNSPPDWA GDERNVVLTL SRIWYSAVTG KIAPKDVAAD WAMERLPAQY QPVILEARQA YLGQEEDRLA SRADQLEEFV HYVKGEITKV VGK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | cmlA6 (ARO:3002696) | CmlA6 | In_Tn21.1 | 419 | 7591-8850 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic efflux (ARO:0010000) | ||||||||||
| Sequence Family: | major facilitator superfamily (MFS) antibiotic efflux pump (ARO:0010002) | ||||||||||
| Target: | phenicol antibiotic (ARO:3000387) | ||||||||||
| Comment: | strict match to reference sequence for ARO:3002696 (bitscore: 819) | ||||||||||
| Protein Sequence: | MSSKNFSWRY SLAATVLLLS PFDLLASLGM DMYLPAVPFM PNALGTTAST IQLTLTTYLV MIGAGQLLFG PLSDRLGRRP VLLGGGLAYV VASMGLALTS SAEVFLGLRI LQACGASACL VSTFATVRDI YAGREESNVI YGILGSMLAM VPAVGPLLGA LVDMWLGWRA IFAFLGLGMI AASAAAWRFW PETRVQRVAG LQWSQLLLPV KCLNFWLYTL CYAAGMGSFF VFFSIAPGLM MGRQGVSQLG FSLLFATVAI AMVFTARFMG RVIPKWGSPS VLRMGMGCLI AGAVLLAITE IWALQSVLGF IAPMWLVGIG VATAVSVAPN GALRGFDHVA GTVTAVYFCL GGVLLGSIGT LIISLLPRNT AWPVVVYCLT LATVVLGLSC VSRVKGSRGQ GEHDVVALQS AESTSNPNR |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | aadA2 (ARO:3002602) | AadA2 | In_Tn21.1 | 259 | 9112-9891 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | ANT(3'') (ARO:3004275) | ||||||||||
| Target: | aminoglycoside antibiotic (ARO:0000016) | ||||||||||
| Comment: | strict match to reference sequence for ARO:3002602 (bitscore: 520) | ||||||||||
| Protein Sequence: | VTIEISNQLS EVLSVIERHL ESTLLAVHLY GSAVDGGLKP YSDIDLLVTV AVKLDETTRR ALLNDLMEAS AFPGESETLR AIEVTLVVHD DIIPWRYPAK RELQFGEWQR NDILAGIFEP AMIDIDLAIL LTKAREHSVA LVGPAAEEFF DPVPEQDLFE ALRETLKLWN SQPDWAGDER NVVLTLSRIW YSAITGKIAP KDVAADWAIK RLPAQYQPVL LEAKQAYLGQ KEDHLASRAD HLEEFIRFVK GEIIKSVGK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | DUF1010 family protein | DUF1010 family protein | In_Tn21.1 | 96 | 9909-10199 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Other | ||||||||||
| Sequence Family: | DUF1010 (Pfam:PF06231) | ||||||||||
| Protein Sequence: | MFIQTAFSFS GVIQCLFCLF SGLRLHGLRR FSVFLASSPC VASASSYRFC SAVPPRWRSV FSRLAPVAKF KLSVLASGSN ISVKPTRILR SAYLAR |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | dfrA12 (ARO:3002858) | DfrA12 | In_Tn21.1 | 165 | 10311-10808 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic target replacement (ARO:0001002) | ||||||||||
| Sequence Family: | trimethoprim resistant dihydrofolate reductase dfr (ARO:3001218) | ||||||||||
| Target: | diaminopyrimidine antibiotic (ARO:3000171) | ||||||||||
| Comment: | 100% identity with reference sequence for ARO:3002858 (bitscore: 339)||Synonyms: | ||||||||||
| Protein Sequence: | MNSESVRIYL VAAMGANRVI GNGPNIPWKI PGEQKIFRRL TEGKVVVMGR KTFESIGKPL PNRHTLVISR QANYRATGCV VVSTLSHAIA LASELGNELY VAGGAEIYTL ALPHAHGVFL SEVHQTFEGD AFFPMLNETE FELVSTETIQ AVIPYTHSVY ARRNG |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1 | IntI1 | In_Tn21.1 | 337 | 10953-11966 | + |
|---|
| Class: | Integron Integrase | ||||||||||
| Subclass: | Class 1 | ||||||||||
| Function: | Integrase | ||||||||||
| Sequence Family: | Class 1 Integron Tyrosine Integrase | ||||||||||
| Transposase Chemistry: | Tyrosine | ||||||||||
| Protein Sequence: | MKTATAPLPP LRSVKVLDQL RERIRYLHYS LPTEQAYVHW 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 |
|---|---|---|---|---|---|
| IS26-MH257753 | IS26 | insertion sequence | 1394-2213 | + | 820 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IRL | IS26 | 1394-1407 | + | 14 | GGCACTGTTG CAAA |
| IRR | IS26 | 2200-2213 | - | 14 | GGCACTGTTG CAAA |