Mobile element type:
Integron
Name:
In28
Synonyms:
Accession:
In28-AF313472
Family:
Tn402
Group:
Class 1
First isolate:
Yes
Partial:
ND
Evidence of transposition:
Yes
Host Organism:
Pseudomonas aeuroginosa RPL11
Date of Isolation:
2006
Country:
Australia
Molecular Source:
plasmid RPL11
| 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 i4 | 6147-6165 | - | 19 | TCAGCGGACG CAGGGAGGA |
| repeat i3 | 6175-6193 | - | 19 | TCAGGCAACG ACGGGCTGC |
| repeat i2 | 6217-6235 | - | 19 | TCAGAAGCCG ACTGCACTA |
| IRi | 6234-6266 | - | 33 | TGTCGTTTTC AGAAGACGGC TGCACTGAAC GTC |
| repeat i1 | 6240-6258 | - | 19 | TCAGAAGACG GCTGCACTG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| attC aadA1a core | In28 | 1466-1519 | + | 54 | CGCTTGAGTT AAGCCGCGCC GCGAAGCGGC GTCGGCTTGA ACGAATTGTT AGAC |
| attC cmlA6 | In28 | 2322-2385 , 3865-3870 | + | 70 | CGCCTGAGCT CAGCCGACCG AAACCGCGTA GCGGTTTTGG GTCGGCTGCA GCGATTTGTT GGGCGCCCAA |
| attC cmlA6 core | In28 | 2322-2385 | + | 64 | CGCCTGAGCT CAGCCGACCG AAACCGCGTA GCGGTTTTGG GTCGGCTGCA GCGATTTGTT GGGC |
| attC bla CARB-1 core | In28 | 3871-3975 | + | 105 | CGCCGCCATA AGTTGCGGCT TTGGAGTTGA TTGTTTTGTG GTAGCGTAGC GTTAAACCAC AAAACAAGCG ACGGAAAAGC CGTCAACTTG ATGGCCTTGT TAGCC |
| attI | In28 | 4915-4970 | + | 56 | CTTTGTTTTA GGGCGACTGC CCTGCTGCGT AACATCGTTG CTGCTCCATA ACATCA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tnp | IS6100 | 207-971 | - | Transposase | |
| qacEdelta1 (ARO:3005010) | In28 | 1004-1357 | - | Passenger Gene | Antibiotic Resistance |
| aadA (ARO:3002601) | In28 | 1521-2312 | - | Passenger Gene | Antibiotic Resistance |
| cmlA6 (ARO:3002696) | In28 | 2405-3664 | - | Passenger Gene | Antibiotic Resistance |
| bla CARB-1 (ARO:3002240) | In28 | 3979-4845 | - | Passenger Gene | Antibiotic Resistance |
| intI1 | In28 | 5051-6064 | + | Integron Integrase | Class 1 |
ORF Details
| 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 | qacEdelta1 (ARO:3005010) | QacEdelta1 | In28 | 117 | 1004-1357 | - |
|---|
| 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: | perfect match to first 108 aminoacids of reference sequence for ARO:3005010 (bitscore: 204)||Synonyms: | ||||||||||
| Protein Sequence: | MKGWLFLVIA IVGEVIATSA LKSSEGFTKL APSAVVIIGY GIAFYFLSLV LKSIPVGVAY AVWSGLGVVI ITAIAWLLHG QKLDAWGFVG MGLIIAAFLL ARSPSWKSRL CCKNREA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | aadA (ARO:3002601) | AadA | In28 | 263 | 1521-2312 | - |
|---|
| 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 | In28 | 419 | 2405-3664 | - |
|---|
| 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: | MRSKNFSWRY SLAATVLLLS PFDLLASLGM DMYLPAVPFM PNALGTTAST IQLTLTTYLV MIGAGQLLFG PLSDRLGRRP VLLGGGLAYV VASMGLALTS SAEVFLGLRI LQACGASACL VSTFATVRDI YAGREESNVI YGILGSMLAI 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 | bla CARB-1 (ARO:3002240) | Bla CARB-1 | In28 | 288 | 3979-4845 | - |
|---|
| 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 TQASMAERND AIVKIGHSIF DVYTSQSR |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1 | IntI1 | In28 | 337 | 5051-6064 | + |
|---|
| 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 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IR | IS6100 | 153-166 | + | 14 | GGCTCTGTTG CAAA |
| IR | IS6100 | 1019-1032 | - | 14 | GGCTCTGTTG CAAA |
1. Partridge SR, Recchia GD, Stokes HW, Hall RM.
Family of class 1 integrons related to In4 from Tn1696.. Antimicrob Agents Chemother. 2001 Nov;45(11):3014-20. doi: 10.1128/AAC.45.11.3014-3020.2001. PubMed ID:
11600350
.
2. Stokes HW, Elbourne LD, Hall RM. Tn1403, a multiple-antibiotic resistance transposon made up of three distinct transposons.. Antimicrob Agents Chemother. 2007 May;51(5):1827-9. doi: 10.1128/AAC.01279-06. Epub 2007 Jan 29. PubMed ID: 17261631 .
2. Stokes HW, Elbourne LD, Hall RM. Tn1403, a multiple-antibiotic resistance transposon made up of three distinct transposons.. Antimicrob Agents Chemother. 2007 May;51(5):1827-9. doi: 10.1128/AAC.01279-06. Epub 2007 Jan 29. PubMed ID: 17261631 .