Mobile element type:
Integron
Name:
In33
Synonyms:
Tn2521, Tn1405
Accession:
In33-AF313471
Family:
Tn402
Group:
Class 1
First isolate:
Yes
Partial:
ND
Evidence of transposition:
Yes
Host Organism:
Pseudomonas aeuroginosa
Date of Isolation:
1982
Country:
Australia
Molecular Source:
plasmid R18-18
| 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 | 1380-1399 | - | 20 | TCAGAAGTGA TCTGCACCAA |
| repeat t2 | 1410-1428 | + | 19 | TCAGGAGCTG GCTGCACAA |
| repeat t1 | 1450-1468 | - | 19 | TCAGAAGACG ACTGCACCA |
| repeat i4 | 6848-6866 | - | 19 | TCAGCGGACG CAGGGAGGA |
| repeat i3 | 6876-6894 | - | 19 | TCAGGCAACG ACGGGCTGC |
| repeat i2 | 6918-6936 | - | 19 | TCAGAAGCCG ACTGCACTA |
| IRi | 6935-6967 | - | 33 | TGTCGTTTTC AGAAGACGGC TGCACTGAAC GTC |
| repeat i1 | 6941-6959 | - | 19 | TCAGAAGACG GCTGCACTG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| attC qacH_sul1 | In33 | 2399-2432 , 3710-3716 | + | 41 | CCGCTAGCGG GCGGCCGGAA GGTGAATGCT AGGCATCTAA C |
| attC qacH_sul1 core | In33 | 2399-2432 | + | 34 | CCGCTAGCGG GCGGCCGGAA GGTGAATGCT AGGC |
| attC aadA1a core | In33 | 3716-3769 | + | 54 | CGCTTGAGTT AAGCCGCGCC GCGAAGCGGC GTCGGCTTGA ACGAATTGTT AGAC |
| attC bla CARB-1 core | In33 | 4572-4676 | + | 105 | CGCCGCCATA AGTTGCGGCT TTGGAGTTGA TTGTTTTGTG GTAGCGTAGC GTTAAACCAC AAAACAAGCG ACGGAAAAGC CGTCAACTTG ATGGCCTTGT TAGCC |
| attI | In33 | 5616-5671 | + | 56 | CTTTGTTTTA GGGCGACTGC CCTGCTGCGT AACATCGTTG CTGCTCCATA ACATCA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tnp | IS6100 | 528-1292 | - | Transposase | |
| WP_001424634.1 | In33 | 1488-1775 | - | Passenger Gene | Hypothetical |
| GNAT_fam | In33 | 1799-2299 | - | Passenger Gene | Antibiotic Resistance |
| sul1 (ARO:3000410) | In33 | 2427-3266 | - | Passenger Gene | Antibiotic Resistance |
| qacEdelta1 (ARO:3005010) | In33 | 3260-3607 | - | Passenger Gene | Antibiotic Resistance |
| aadA (ARO:3002601) | In33 | 3771-4562 | - | Passenger Gene | Antibiotic Resistance |
| bla CARB-1 (ARO:3002240) | In33 | 4680-5546 | - | Passenger Gene | Antibiotic Resistance |
| intI1 | In33 | 5752-6765 | + | Integron Integrase | Class 1 |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp | Tnp | IS6100 | 254 | 528-1292 | - |
|---|
| 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 | In33 | 95 | 1488-1775 | - |
|---|
| 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 | In33 | 166 | 1799-2299 | - |
|---|
| 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 | In33 | 279 | 2427-3266 | - |
|---|
| 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 | In33 | 115 | 3260-3607 | - |
|---|
| 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 | aadA (ARO:3002601) | AadA | In33 | 263 | 3771-4562 | - |
|---|
| 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 | bla CARB-1 (ARO:3002240) | Bla CARB-1 | In33 | 288 | 4680-5546 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | CARB beta-lactamase (ARO:3000091) | ||||||||||
| Target: | penam (ARO:3000008) | ||||||||||
| Comment: | strict match to reference sequence for ARO:3002240 (bitscore: 593)||Synonyms: NDM-1, PSE-4, BlaP1a | ||||||||||
| Protein Sequence: | MKFLLAFSLL IPSVVFASSS KFQQVEQDVK AIEVSLSARI GVSVLDTQNG EYWDYNGNQR FPLTSTFKTI ACAKLLYDAE QGKVNPNSTV EIKKADLVTY SPVIEKQVGQ AITLDDACFA TMTTSDNTAA NIILSAVGGP KGVTDFLRQI GDKETRLDRI EPDLNEGKLG DLRDTTTPKA IASTLNKFLF GSALSEMNQK KLESWMVNNQ VTGNLLRSVL PAGWNIADRS GAGGFGARSI TAVVWSEHQA PIIVSIYLAQ TQASMEERND AIVKIGHSIF DVYTSQSR |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1 | IntI1 | In33 | 337 | 5752-6765 | + |
|---|
| 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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| TnCentral Accession | TE Name | Type | Coordinates | Strand | Length |
|---|---|---|---|---|---|
| IS6100-U12338.3 | IS6100 | insertion sequence | 474-1353 | + | 880 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IR | IS6100 | 474-487 | + | 14 | GGCTCTGTTG CAAA |
| IR | IS6100 | 1340-1353 | - | 14 | GGCTCTGTTG CAAA |
1. Partridge SR, Brown HJ, Hall RM.
Characterization and movement of the class 1 integron known as Tn2521 and Tn1405.. Antimicrob Agents Chemother. 2002 May;46(5):1288-94. doi: 10.1128/AAC.46.5.1288-1294.2002. PubMed ID:
11959558
.