Mobile element type:
Integron
Name:
In_TnAs3
Synonyms:
In_Tn7145
Accession:
In_TnAs3-CP000645.1
Family:
Tn402
Group:
Class 1
First isolate:
Yes
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Aeromonas salmonicida subsp. salmonicida A449
Date of Isolation:
2007
Country:
Canada
Molecular Source:
plasmid 4
| 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 | 9944-9962 | - | 19 | TCAGCGGACG CAGGGAGGA |
| repeat i3 | 9972-9990 | - | 19 | TCAGGCAACG ACGGGCTGC |
| repeat i2 | 10014-10032 | - | 19 | TCAGAAGCCG ACTGCACTA |
| IRi | 10031-10063 | - | 33 | TGTCGTTTTC AGAAGACGGC TGCACTGAAC GTC |
| repeat i1 | 10037-10055 | - | 19 | TCAGAAGACG GCTGCACTG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| attC qacH_sul1 | In_TnAs3 | 3380-3413 , 4691-4697 | + | 41 | CCGCTAGCGG GCGGCCGGAA GGTGAATGCT AGGCATCTAA C |
| attC qacH_sul1 core | In_TnAs3 | 3380-3413 | + | 34 | CCGCTAGCGG GCGGCCGGAA GGTGAATGCT AGGC |
| attC aadA1a core | In_TnAs3 | 4697-4750 | + | 54 | CGCTTGAGTT AAGCCGCGCC GCGAAGCGGC GTCGGCTTGA ACGAATTGTT AGAC |
| attI | In_TnAs3 | 5553-5608 | + | 56 | CTTTGTTTTA GGGCGACTGC CCTGCTGCGT AACATCGTTG CTGCTCCATA ACATCA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tniA | In_TnAs3 | 142-1821 | + | Transposase | |
| tniB_p | In_TnAs3 | 1824-2723 | + | Accessory Gene | |
| GNAT_fam | In_TnAs3 | 2780-3280 | - | Passenger Gene | Antibiotic Resistance |
| sul1 (ARO:3000410) | In_TnAs3 | 3408-4247 | - | Passenger Gene | Antibiotic Resistance |
| qacEdelta1 (ARO:3005010) | In_TnAs3 | 4241-4588 | - | Passenger Gene | Antibiotic Resistance |
| aadA (ARO:3002601) | In_TnAs3 | 4752-5543 | - | Passenger Gene | Antibiotic Resistance |
| intI1_p | In_TnAs3 | 5689-6243 | + | Integron Integrase | Class 1 |
| tnp | In_TnAs3 | 6414-7616 | + | Transposase | |
| Ccol_ACT_CHL (ARO:3004454) | In_TnAs3 | 7891-8517 | - | Passenger Gene | Antibiotic Resistance |
| intI1 | In_TnAs3 | 8848-9861 | + | Integron Integrase | Class 1 |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniA | TniA | In_TnAs3 | 559 | 142-1821 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Comment: | can be extended upstream by 12 amino acids| identical to tniA (Tn1721 and In2)| 25% amino acid sequence identity to TnsB from Tn7 | ||||||||||
| Protein Sequence: | MATDTPRIPE QGVATLPDEA WERARRRAEI ISPLAQSETV GHEAADMAAQ ALGLSRRQVY VLIRRARQGS GLVTDLVPGQ SGGGKGKGRL PEPVERVIHE LLQKRFLTKQ KRSLAAFHRE VTQVCKAQKL RVPARNTVAL RIASLDPRKV IRRREGQDAA RDLQGVGGEP PAVTAPLEQV QIDHTVIDLI VVDDRDRQPI GRPYLTLAID VFTRCVLGMV VTLEAPSAVS VGLCLVHVAC DKRPWLEGLN VEMDWQMSGK PLLLYLDNAA EFKSEALRRG CEQHGIRLDY RPLGQPHYGG IVERIIGTAM QMIHDELPGT TFSNPDQRGD YDSENKAALT LRELERWLTL AVGTYHGSVH NGLLQPPAAR WAEAVARVGV PAVVTRATSF LVDFLPILRR TLTRTGFVID HIHYYADALK PWIARRERWP SFLIRRDPRD ISRIWVLEPE GQHYLEIPYR TLSHPAVTLW EQRQALAKLR QQGREQVDES ALFRMIGQMR EIVTSAQKAT RKARRDADRR QHLKTSARPD KPVPPDTDIA DPQADNLPPA KPFDQIEEW |
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| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniB_p | TniB_p | In_TnAs3 | 299 | 1824-2723 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Sequence Family: | ATP binding protein | ||||||||||
| Comment: | 3' deletion| similar function to Tn7 tnsC and MuB | ||||||||||
| Protein Sequence: | VDEYPIIDLS HLLPAAQGLA RLPADERIQR LRADRWIGYP RAVEALNRLE ALYAWPNKQR MPNLLLVGPT NNGKSMIVEK FRRTHPASSD ADQEHIPVLV VQMPSEPSVI RFYVALLAAM GAPLRPRPRL PEMEQLALAL LRKVGVRMLV IDELHNVLAG NSVNRREFLN LLRFLGNELR IPLVGVGTRD AYLAIRSDDQ LENRFEPMML PVWEANDDCC SLLASFAASL PLRRPSPIAT LDMARYLLTR SEGTIGELAH LLMAAAIVAV ESGEEAINHR TLSISTTSRA TKTSRSDCK |
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| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | GNAT_fam | GNAT_fam | In_TnAs3 | 166 | 2780-3280 | - |
|---|
| 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_TnAs3 | 279 | 3408-4247 | - |
|---|
| 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 |
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| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | qacEdelta1 (ARO:3005010) | QacEdelta1 | In_TnAs3 | 115 | 4241-4588 | - |
|---|
| 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 |
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| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | aadA (ARO:3002601) | AadA | In_TnAs3 | 263 | 4752-5543 | - |
|---|
| 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 RIAPKDVAAD WAMERLPAQY QPVILEARQA YLGQEEDRLA SRADQLEEFV HYVKGEITKV VGK |
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| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1_p | IntI1_p | In_TnAs3 | 184 | 5689-6243 | + |
|---|
| 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 KGRRIGRTFS RAVR |
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| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp | Tnp | In_TnAs3 | 400 | 6414-7616 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | HUH | ||||||||||
| Protein Sequence: | MAESARHLVD EVFGPRPVRQ WVLSFPYPLR FLFASKPEAI GPVLGIVHRV IAGWLADQAG VPRDTAQCGA VTLIQRFGSA LNLNVHFHML WLDGVYDANV EPPRRKPRLR RARAPTSAQL TQLANTIAHR VCRHLSRRGW LEGEDESVFL SDSAGSDDGM DGLRMSSMTY RIATGRDAGR KVVTLQTLPG DAGSLEGDAG KVGGFSLHAG VAAEAHESHK LEKLCRYITR PAISEQRLSI SPQGRVRYQL KTPWRNGTTH VEWDAVDFIA KLAALVPPPR AHLTRFHGVF APNANLRAQL TPSGRGKRPA GDAAPVDVSA HDEPRSPEQK RRAMSWAQRL KRVFSIDITI CAHCGGAVRI VASIEEPTAI RAILAHFEKH GAREEAHYRP AARAPPGEAA |
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| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | Ccol_ACT_CHL (ARO:3004454) | Ccol_ACT_CHL | In_TnAs3 | 208 | 7891-8517 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | chloramphenicol acetyltransferase (ARO:3000122) | ||||||||||
| Target: | phenicol antibiotic (ARO:3000387) | ||||||||||
| Comment: | 96% match to reference sequence for ARO:3004454 (bitscore: 420)||Synonyms: | ||||||||||
| Protein Sequence: | MMQFTKIDIN NWTRKEYFDH YFDNTPCTYS MTVKLDISKL KKDGKKLYPT LLYGVTTILN RHEEFRTALD KNGQVGVFSE MLPCYTIFHK ETETFSSIWT EFTADYTEFL QNYQKDIDAY GERKGMFAKP NPPENTFPVS MIPWTSFEGF NLNLKKGYDY LLPIFTFGKY YEDGGKYYIP LSIQVHHAVC DGFHVCRFLD ELQDLLNK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1 | IntI1 | In_TnAs3 | 337 | 8848-9861 | + |
|---|
| 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 |
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