Mobile element type:
Integron
Name:
In6_p
Synonyms:
Accession:
In6_p-L06822
Family:
Tn402
Group:
Class 1
First isolate:
ND
Partial:
Yes
Evidence of transposition:
ND
Host Organism:
Staphylococcus aureus
Date of Isolation:
1993
Country:
Molecular Source:
plasmid pSA
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| repeat i4 | 10818-10836 | - | 19 | TCAGCGGACG CAGGGAGGA |
| repeat i3 | 10846-10864 | - | 19 | TCAGGCAACG ACGGGCTGC |
| repeat i2 | 10888-10906 | - | 19 | TCAGAAGCCG ACTGCACTA |
| IRi | 10905-10937 | - | 33 | TGTCGTTTTC AGAAGACGGC TGCACTGAAC GTC |
| repeat i1 | 10911-10929 | - | 19 | TCAGAAGACG GCTGCACTG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| attC qacH_sul1 core | In6_p | 1244-1277 | + | 34 | CCGCTAGCGG GCGGCCGGAA GGTGAATGCT AGGC |
| attC aadA3 core | In6_p | 8091-8144 | + | 54 | CGCCGGAGTT AAGCCGCCGC GCGTAGCGCG GTCGGCTTGA ACGAATTGTT AGAC |
| attC AAC(6')-Ib core | In6_p | 8947-9012 | + | 66 | CGTTTGACAT GAGGGGCGGC CAAGGGCGCC AGCCCTTGGA CGTCCCCCTC GATGGAAGGG TTAGGC |
| attI | In6_p | 9586-9641 | + | 56 | CTTTGTTTTA GGGCGACTGC CCTGCTGCGT AACATCGTTG CTGCTCCATA ACATCA |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| GNAT_fam | In6_p | 644-1144 | - | Passenger Gene | Antibiotic Resistance |
| sul1 (ARO:3000410) | In6_p | 1272-2111 | - | Passenger Gene | Antibiotic Resistance |
| qacEdelta1_p (ARO:3005010) | In6_p | 2105-2312 | - | Passenger Gene | Antibiotic Resistance |
| catII (ARO:3002684) | In6_p | 3058-3699 | - | Passenger Gene | Antibiotic Resistance |
| tnp | ISCR1 | 4856-6397 | - | Transposase | |
| sul1 (ARO:3000410) | In6_p | 6802-7641 | - | Passenger Gene | Antibiotic Resistance |
| qacEdelta1 (ARO:3005010) | In6_p | 7635-7982 | - | Passenger Gene | Antibiotic Resistance |
| aadA3 (ARO:3002603) | In6_p | 8146-8937 | - | Passenger Gene | Antibiotic Resistance |
| AAC(6')-Ib8 (ARO:3002579) | In6_p | 9007-9558 | - | Passenger Gene | Antibiotic Resistance |
| intI1 | In6_p | 9722-10735 | + | Integron Integrase | Class 1 |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | GNAT_fam | GNAT_fam | In6_p | 166 | 644-1144 | - |
|---|
| 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 | In6_p | 279 | 1272-2111 | - |
|---|
| 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 | In6_p | 68 | 2105-2312 | - |
|---|
| 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: | disinfecting agents and antiseptics(ARO:3005386) | ||||||||||
| 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 | catII (ARO:3002684) | CatII | In6_p | 213 | 3058-3699 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | chloramphenicol acetyltransferase (CAT) (ARO:3000122) | ||||||||||
| Transposase Chemistry: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Target: | phenicol antibiotic (ARO:3000387) | ||||||||||
| Comment: | perfect match to reference sequence from Escherichia cili for ARO:3004656 (bitscore: 449) | ||||||||||
| Protein Sequence: | MNFTRIDLNT WNRREHFALY RQQIKCGFSL TTKLDITALR TALAETGYKF YPLMIYLISR AVNQFPEFRM ALKDNELIYW DQSDPVFTVF HKETETFSAL SCRYFPDLSE FMAGYNAVTA EYQHDTRLFP QGNLPENHLN ISSLPWVSFD GFNLNITGND DYFAPVFTMA KFQQEGDRVL LPVSVQVHHA VCDGFHAARF INTLQLMCDN ILK |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp | Tnp | ISCR1 | 513 | 4856-6397 | - |
|---|
| 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 | In6_p | 279 | 6802-7641 | - |
|---|
| 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 | In6_p | 115 | 7635-7982 | - |
|---|
| 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 | In6_p | 263 | 8146-8937 | - |
|---|
| 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 | AAC(6')-Ib8 (ARO:3002579) | AAC(6')-Ib8 | In6_p | 183 | 9007-9558 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | AAC(6') (ARO:3000345) | ||||||||||
| Target: | aminoglycoside antibiotic (ARO:0000016) | ||||||||||
| Comment: | strict match to reference sequence for ARO:3002579 missing 43 aa N-ter (bitscore: 379) | ||||||||||
| Protein Sequence: | TNSTDSVTLR LMTEHDLAML YEWLNRSHIV EWWGGEEARP TLADVQEQYL PSVLAQESVT PYIAMLNGEP IGYAQSYVAL GSGDGWWEEE TDPGVRGIDQ SLANASQLGK GLGTKLVRAL VELLFNDPEV TKIQTDPSPS NLRAIRCYEK AGFERQGTVT TPDGPAVYMV QTRQAFERTR SDA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | intI1 | IntI1 | In6_p | 337 | 9722-10735 | + |
|---|
| Class: | Integron Integrase | ||||||||||
| Subclass: | Class 1 | ||||||||||
| Sequence Family: | Class 1 Integron Tyrosine Integrase | ||||||||||
| Transposase Chemistry: | Tyrosine | ||||||||||
| Protein Sequence: | MKTATAPLPP LRSVKVLDQL RERIRYLHYS LRTEQAYVNW 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 |
|---|---|---|---|---|---|
| ISCR1-L06822 | ISCR1 | transposon | 4624-6777 | + | 2154 |
1. Stokes HW, Tomaras C, Parsons Y, Hall RM.
The partial 3'-conserved segment duplications in the integrons In6 from pSa and In7 from pDGO100 have a common origin.. Plasmid. 1993 Jul;30(1):39-50. doi: 10.1006/plas.1993.1032. PubMed ID:
8378445
.
2. Bito A, Susani M. Revised analysis of aadA2 gene of plasmid pSa.. Antimicrob Agents Chemother. 1994 May;38(5):1172-5. doi: 10.1128/AAC.38.5.1172. PubMed ID: 7915099 .
3. Valentine CR, Heinrich MJ, Chissoe SL, Roe BA. DNA sequence of direct repeats of the sulI gene of plasmid pSa.. Plasmid. 1994 Sep;32(2):222-7. doi: 10.1006/plas.1994.1059. PubMed ID: 7846147 .
4. Hall RM, Brown HJ, Brookes DE, Stokes HW. Integrons found in different locations have identical 5' ends but variable 3' ends.. J Bacteriol. 1994 Oct;176(20):6286-94. doi: 10.1128/jb.176.20.6286-6294.1994. PubMed ID: 7929000 .
5. Collis CM, Hall RM. Expression of antibiotic resistance genes in the integrated cassettes of integrons.. Antimicrob Agents Chemother. 1995 Jan;39(1):155-62. doi: 10.1128/AAC.39.1.155. PubMed ID: 7695299 .
6. Partridge SR, Hall RM. In34, a complex In5 family class 1 integron containing orf513 and dfrA10.. Antimicrob Agents Chemother. 2003 Jan;47(1):342-9. doi: 10.1128/AAC.47.1.342-349.2003. PubMed ID: 12499211 .
2. Bito A, Susani M. Revised analysis of aadA2 gene of plasmid pSa.. Antimicrob Agents Chemother. 1994 May;38(5):1172-5. doi: 10.1128/AAC.38.5.1172. PubMed ID: 7915099 .
3. Valentine CR, Heinrich MJ, Chissoe SL, Roe BA. DNA sequence of direct repeats of the sulI gene of plasmid pSa.. Plasmid. 1994 Sep;32(2):222-7. doi: 10.1006/plas.1994.1059. PubMed ID: 7846147 .
4. Hall RM, Brown HJ, Brookes DE, Stokes HW. Integrons found in different locations have identical 5' ends but variable 3' ends.. J Bacteriol. 1994 Oct;176(20):6286-94. doi: 10.1128/jb.176.20.6286-6294.1994. PubMed ID: 7929000 .
5. Collis CM, Hall RM. Expression of antibiotic resistance genes in the integrated cassettes of integrons.. Antimicrob Agents Chemother. 1995 Jan;39(1):155-62. doi: 10.1128/AAC.39.1.155. PubMed ID: 7695299 .
6. Partridge SR, Hall RM. In34, a complex In5 family class 1 integron containing orf513 and dfrA10.. Antimicrob Agents Chemother. 2003 Jan;47(1):342-9. doi: 10.1128/AAC.47.1.342-349.2003. PubMed ID: 12499211 .