Mobile element type:
Integron
Name:
In36
Synonyms:
Accession:
In36-AY259085
Family:
Tn402
Group:
Class 1
First isolate:
Yes
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Escherichia coli
Date of Isolation:
2003
Country:
China
Molecular Source:
plasmid pHSH1
| 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 t3 | 1059-1078 | - | 20 | TCAGAAGTGA TCTGCACCAA |
| repeat t2 | 1089-1107 | + | 19 | TCAGGAGCTG GCTGCACAA |
| IRt | 1123-1155 | - | 33 | TGTCATTTTC AGAAGACGAC TGCACCAGTT GAT |
| repeat t1 | 1129-1147 | - | 19 | TCAGAAGACG ACTGCACCA |
| repeat i4 | 11428-11446 | - | 19 | TCAGCGGACG CAGGGAGGA |
| repeat i3 | 11456-11474 | - | 19 | TCAGGCAACG ACGGGCTGC |
| repeat i2 | 11498-11516 | - | 19 | TCAGAAGCCG ACTGCACTA |
| IRi | 11515-11547 | - | 33 | TGTCGTTTTC AGAAGACGGC TGCACTGAAC GTC |
| repeat i1 | 11521-11539 | - | 19 | TCAGAAGACG GCTGCACTG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| attC aadA3 | In36 | 8752-8805 , 9602-9607 | + | 60 | CGCCGGAGTT AAGCCGCCGC GCGTAGCGCG GTCGGCTTGA ACGAATTGTT AGACGTCTAA |
| attC aadA3 core | In36 | 8752-8805 | + | 54 | CGCCGGAGTT AAGCCGCCGC GCGTAGCGCG GTCGGCTTGA ACGAATTGTT AGAC |
| attC dfr16 | In36 | 9608-9706 , 10190-10195 | + | 105 | CGCCCGCCTC AACTGCCGGA GGTTAATGGC GCCTTTTTTG CAGCTCCACC GCAAAAAAAG GTGACAGTAA CCGGAGGTCA GATTGCAGGC GCTTGTTAAA GTTAA |
| attC dfr16 core | In36 | 9608-9706 | + | 99 | CGCCCGCCTC AACTGCCGGA GGTTAATGGC GCCTTTTTTG CAGCTCCACC GCAAAAAAAG GTGACAGTAA CCGGAGGTCA GATTGCAGGC GCTTGTTAA |
| attI | In36 | 10196-10251 | + | 56 | CTTTGTTTTA GGGCGACTGC CCTGCTGCGT AACATCGTTG CTGCTCCATA ACATCA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tniA interrupted | In36 | 106-152 , 1034-1046 | + | Transposase | |
| tnp | IS6100 | 207-971 | - | Transposase | |
| WP_001424634.1 | In36 | 1167-1454 | - | Passenger Gene | Hypothetical |
| GNAT_fam | In36 | 1478-1978 | - | Passenger Gene | Antibiotic Resistance |
| sul1 (ARO:3000410) | In36 | 2106-2945 | - | Passenger Gene | Antibiotic Resistance |
| qacEdelta1_p (ARO:3005010) | In36 | 2939-3146 | - | Passenger Gene | Antibiotic Resistance |
| bla NmcR (ARO:3003665) | In36 | 3536-4411 | - | Passenger Gene | Antibiotic Resistance |
| QnrA1 (ARO:3002707) | In36 | 4597-5253 | - | Passenger Gene | Antibiotic Resistance |
| tnp | ISCR1 | 5517-7058 | - | Transposase | |
| sul1 (ARO:3000410) | In36 | 7463-8302 | - | Passenger Gene | Antibiotic Resistance |
| qacEdelta1 (ARO:3005010) | In36 | 8296-8643 | - | Passenger Gene | Antibiotic Resistance |
| aadA3 (ARO:3002603) | In36 | 8807-9598 | - | Passenger Gene | Antibiotic Resistance |
| dfrA16 (ARO:3003014) | In36 | 9703-10176 | - | Passenger Gene | Antibiotic Resistance |
| intI1 | In36 | 10332-11345 | + | Integron Integrase | Class 1 |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniA interrupted | TniA interrupted | In36 | 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 | In36 | 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 | In36 | 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 | In36 | 279 | 2106-2945 | - |
|---|
| 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 LAAELHAIGN GADYVRTHAP GDLRSAITFS ETLAKFRSRD ARDRGLDHA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | qacEdelta1_p (ARO:3005010) | N/A | In36 | 68 | 2939-3146 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic efflux (ARO:0010000) | ||||||||||
| Sequence Family: | major facilitator superfamily (MFS) antibiotic efflux pump (ARO:0010002) | ||||||||||
| Transposase Chemistry: | antibiotic efflux (ARO:0010000) | ||||||||||
| Target: | acridine dye (ARO:3000054)||quaternary ammonium salts | ||||||||||
| Comment: | perfect match C-temrinal 68 amino acis of reference sequence for ARO:3005010 (bitscore:133) | ||||||||||
| Protein Sequence: | SLVLKSIPVG VAYAVWSGLG VVIITAIAWL LHGQKLDAWG FVGMGLIIAA FLLARSPSWK SLRRPTPW |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | bla NmcR (ARO:3003665) | Bla NmcR | In36 | 291 | 3536-4411 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | NmcA beta-lactamase (ARO:3004195) | ||||||||||
| Transposase Chemistry: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Target: | penam (ARO:3000008)||cephamycin (ARO:0000044)||carbapenem (ARO:0000020)||cephalosporin (ARO:0000032) | ||||||||||
| Comment: | poor match 46% to referencesequence for ARO:3003665 (bitscore: 275)||Synonyms: | ||||||||||
| Protein Sequence: | MVRRYLPLNP LRAFEAAARH LSFTRAAIEL NVTHAAVSQQ VRALEEQLGC VLFTRVSRGL VLTHEGEGLL PVLNEAFDRI ADTLECFSHG QFRERVKVGA VGTFAAGWLL PRLAGFYDSH PHIDLHISTH NNHVDPAAEG HDYTIRFGNG AWHESDAELI FSAPHAPLCS PAIAEQLQQP DDVHRFTLLR SFRRDEWSRW LDCAGGTPPS PSQPVMVFDT SLAMAEAAQL GAGVAIAPVC MFSRLLQSGA LVQPFAAEIT LGGYWLTRLQ SRTETPAMQQ FARWLLNTAA A |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | QnrA1 (ARO:3002707) | QnrA1 | In36 | 218 | 4597-5253 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic target protection (ARO:0001003) | ||||||||||
| Sequence Family: | quinolone resistance protein (qnr) (ARO:3000419) | ||||||||||
| Transposase Chemistry: | antibiotic target protection (ARO:0001003) | ||||||||||
| Target: | fluoroquinolone antibiotic (ARO:0000001) | ||||||||||
| Comment: | strict match to reference sequence for ARO:3002707 (bitscore: 446)||Synonyms: | ||||||||||
| Protein Sequence: | MDIIDKVFQQ EDFSRQDLSD SRFRRCRFYQ CDFSHCQLQD ASFEDCSFIE SGAVEGCHFS YADLRDASFK ACRLSLANFS GANCFGIEFR ECDLKGANFS RARFYNQVSH KMYFCSAYIS GCNLAYTNLS GQCLEKCELF ENNWSNANLS GASLMGSDLS RGTFSRDCWQ QVNLRGCDLT FADLDGLDPR RVNLEGVKIC AWQQEQLLEP LGVIVLPD |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp | Tnp | ISCR1 | 513 | 5517-7058 | - |
|---|
| 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 | sul1 (ARO:3000410) | Sul1 | In36 | 279 | 7463-8302 | - |
|---|
| 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 LAAELHAIGN GADYVRTHAP GDLRSAITFS ETLAKFRSRD ARDRGLDHA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | qacEdelta1 (ARO:3005010) | QacEdelta1 | In36 | 115 | 8296-8643 | - |
|---|
| 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 | aadA3 (ARO:3002603) | AadA3 | In36 | 263 | 8807-9598 | - |
|---|
| 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:3002603 (bitscore: 522) | ||||||||||
| Protein Sequence: | MRVAVTIEIS NQLSEVLSVI ERHLESTLLA VHLYGSAVDG GLKPYSDIDL LVTVAVKLDE TTRRALLNDL MEASAFPGES ETLRAIEVTL VVHDDIIPWR YPAKRELQFG EWQRNDILAG IFEPAMIDID LAILLTKARE HSVALVGPAA EEFFDPVPEQ DLFEALRETL KLWNSQPDWA GDERNVVLTL SRIWYSAITG KIAPKDVAAD WAIKRLPAQY QPVLLEAKQA YLGQKEDHLA SRADHLEEFI RFVKGEIIKS VGK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | dfrA16 (ARO:3003014) | DfrA16 | In36 | 157 | 9703-10176 | - |
|---|
| 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) | ||||||||||
| Comment: | strict match to reference sequence for ARO:3003014 (bitscore: 325) | ||||||||||
| Protein Sequence: | MKLSLMAAKS KNGIIGNGPD IPWSAKGEQL LFKAITYNQW LLVGRKTFES MGALPNRKYA VVTRSNFSTN DEGVMVFSSI QDALINLEEI TDHVIVSGGG EIYKSLISKV DTLHISTVDI ERDGDIVFPE IPDTFKLVFE QDFESNINYC YQIWQKS |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1 | IntI1 | In36 | 337 | 10332-11345 | + |
|---|
| Class: | Integron Integrase | ||||||||||
| Subclass: | Class 1 | ||||||||||
| Sequence Family: | Class 1 Integron Tyrosine Integrase | ||||||||||
| Transposase Chemistry: | Tyrosine | ||||||||||
| Protein Sequence: | MKTATAPLPP LRSVKVLDQL RERIRYLHYS LRTEQAYVHW 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-U12338.3 | IS6100 | insertion sequence | 153-1032 | + | 880 |
| ISCR1-L06822 | ISCR1 | transposon | 5285-7438 | + | 2154 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IR | IS6100 | 153-166 | + | 14 | GGCTCTGTTG CAAA |
| IR | IS6100 | 1019-1032 | - | 14 | GGCTCTGTTG CAAA |
1. Wang M, Tran JH, Jacoby GA, Zhang Y, Wang F, Hooper DC.
Plasmid-mediated quinolone resistance in clinical isolates of Escherichia coli from Shanghai, China.. Antimicrob Agents Chemother. 2003 Jul;47(7):2242-8. doi: 10.1128/AAC.47.7.2242-2248.2003. PubMed ID:
12821475
.