Mobile element type:
Transposon
Name:
TnXorYNA12
Synonyms:
Tn7226
Accession:
TnXorYNA12-HQ662557.1
Family:
Tn402
Group:
First isolate:
Yes
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Xanthomonas oryzae pv. oryzae strain YNA12-2
Date of Isolation:
2013
Country:
China
| 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 | 7503-7521 | - | 19 | TCAGCGGACG CAGGGAGGA |
| repeat i3 | 7531-7549 | - | 19 | TCAGGCAACG ACGGGCTGC |
| repeat i2 | 7573-7591 | - | 19 | TCAGAAGCCG ACTGCACTA |
| IRi | 7590-7622 | - | 33 | TGTCATTTTC AGAAGACGGC TGCACTGAAC GTC |
| repeat i1 | 7596-7614 | - | 19 | TCAGAAGACG GCTGCACTG |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| r6 | TnXorYNA12 | 3824-3837 | + | 14 | TTGGAACGGT TGCG |
| r5 | TnXorYNA12 | 3870-3883 | + | 14 | AATTTCTGTC ACAT |
| r4 | TnXorYNA12 | 3875-3888 | - | 14 | AGGTAATGTG ACAG |
| r3 | TnXorYNA12 | 3926-3939 | + | 14 | GGGTTAAGTG ACAA |
| res | TnXorYNA12 | 3967-4001 | + | 35 | ACACTGTCAC ATAATCGAAC GTATACGTGA CGGGT |
| r2 | TnXorYNA12 | 3970-3983 | - | 14 | CGATTATGTG ACAG |
| attC aadA1 core | TnXorYNA12 | 4728-4787 | + | 60 | GTTCAACGCT TGAGTTAAGC CGCGCCGCGA AGCGGCGTCG GCTTGAACGA ATTGTTAGAC |
| attC arr-3 | TnXorYNA12 | 5584-5697 , 6187-6193 | + | 121 | GTTTAACGCC GCCATAAACG GCGACAGGGT GGCGCGCCTA TTGCGCATAA AATGGCGAAG CCATGCGCAA CAGGCGCGGA ATCTCTGGCG TCCGGTTTGA TGGCTTTGTT ATGCGCATAA C |
| attC arr-3 core | TnXorYNA12 | 5591-5697 | + | 107 | GCCGCCATAA ACGGCGACAG GGTGGCGCGC CTATTGCGCA TAAAATGGCG AAGCCATGCG CAACAGGCGC GGAATCTCTG GCGTCCGGTT TGATGGCTTT GTTATGC |
| attC AAC(6')-IIa | TnXorYNA12 | 6187-6246 , 6815-6820 | + | 66 | GCATAACACC TGAATTAAGC CGCGCCGCGA AGCGGCGTCG GCTTGAATGA GTTGTTAGGC GCCTAA |
| attC AAC(6')-IIa core | TnXorYNA12 | 6187-6246 | + | 60 | GCATAACACC TGAATTAAGC CGCGCCGCGA AGCGGCGTCG GCTTGAATGA GTTGTTAGGC |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tniA | TnXorYNA12 | 142-1821 | + | Transposase | |
| tniB | TnXorYNA12 | 1824-2732 | + | Accessory Gene | |
| tniQ | TnXorYNA12 | 2729-3946 | + | Accessory Gene | Target Site Selection |
| tniR | TnXorYNA12 | 4008-4631 | + | Accessory Gene | Resolvase |
| aadA (ARO:3002601) | TnXorYNA12 | 4789-5580 | - | Passenger Gene | Antibiotic Resistance |
| arr-3 (ARO:3002848) | TnXorYNA12 | 5704-6195 | - | Passenger Gene | Antibiotic Resistance |
| AAC(6')-IIa (ARO:3002594) | TnXorYNA12 | 6241-6795 | - | Passenger Gene | Antibiotic Resistance |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniA | TniA | TnXorYNA12 | 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 |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniB | TniB | TnXorYNA12 | 302 | 1824-2732 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Sequence Family: | ATP binding protein? | ||||||||||
| Comment: | identical to tniB (Tn1721)| similar function to Tn7 tnsC and MuB | ||||||||||
| Protein Sequence: | MDEYPIIDLS 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 TLSMAVYTGP SERRRQFERE LM |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniQ | TniQ | TnXorYNA12 | 405 | 2729-3946 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Target Site Selection | ||||||||||
| Comment: | identical to tniQ (Tn1721)|similar function to Tn7 tnsD? | ||||||||||
| Protein Sequence: | MKPAPRWPLH PAPKEGEALS SWLNRVALCY HMEEPDLLEH DLGHGQVDDL DTAPPLSLLA LLSQRSGIEL DRLRCMSFAG WVPWLLDSLD DQIPDALETY AFQLSVLLPR LRRKTRSITS WRAWLPSQPI NRACPLCLSD PENQAVLLAW KLPLMLSCPL HGCWLESYWG VPGRFLGWEN ADAEPRTASD AIAAMDQRTW QALTTGHVEL PRRRIHAGLW FRLLRTLLDE LNTPLSACGT CAGYPRQVWE GCGHPLRAGQ SLWRPYETLN PIVRLQMLEA AATAISLIEV RDISPPGEQA KLFWSEPQTG FTSGLPTKAP KPEPINHWQR AVQAIDEAII EARHNPETAR SLFALASYGR RDPASLERLR ATFVKEGIPP EFLSHYLPDA PFACLKQNDG LSDKF |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tniR | TniR | TnXorYNA12 | 207 | 4008-4631 | + |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Resolvase | ||||||||||
| Sequence Family: | Serine Site-Specific Recombinase | ||||||||||
| Transposase Chemistry: | Serine | ||||||||||
| Comment: | resolution of cointegrates || Protein: ACE81792.1 || identical to tniR(Tn1721) | ||||||||||
| Protein Sequence: | MLIGYMRVSK ADGSQSTNLQ RDALIAAGVS LAHLYEDLAS GRRDDRPGLA ACLKALREGD TLIVWKLDRL GRDLRHLINT VHDLTARSVG LKVLTGHGAA VDTTTAAGKL VFGIFAALAE FERELISERT VAGLISARAR GRKGGRPFKM TAAKLRLAMA SMGQPETKVG DLCEELGITR QTLYRHVSPK GELRPDGVKL LSLGSAA |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | aadA (ARO:3002601) | AadA | TnXorYNA12 | 263 | 4789-5580 | - |
|---|
| 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: | MREAMIAEVS TQLSEVVGVI ERHLEPTLLA VHLYGSAVDG GLKPHSDIDL LVTVTVRLDE TTRRALINDL LETSASPGGS 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 | arr-3 (ARO:3002848) | Arr-3 | TnXorYNA12 | 163 | 5704-6195 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | rifampin ADP-ribosyltransferase (Arr) (ARO:3000390) | ||||||||||
| Target: | rifamycin antibiotic (ARO:3000157) | ||||||||||
| Comment: | perfect match to reference sequence for ARO:3002848 from Escherichia coli||Synonyms: arr-6 | ||||||||||
| Protein Sequence: | MLCSQIPTIK GLKMVKDWIP ISHDNYKQVQ GPFYHGTKAN LAIGDLLTTG FISHFEDGRI LKHIYFSALM EPAVWGAELA MSLSGLEGRG YIYIVEPTGP FEDDPNLTNK RFPGNPTQSY RTCEPLRIVG VVEDWEGHPV ELIRGMLDSL EDLKRRGLHV IED |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | AAC(6')-IIa (ARO:3002594) | AAC(6')-IIa | TnXorYNA12 | 184 | 6241-6795 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antibiotic Resistance | ||||||||||
| Function: | antibiotic inactivation (ARO:0001004) | ||||||||||
| Sequence Family: | AAC(6') (ARO:3000345) | ||||||||||
| Target: | aminoglycoside antibiotic (ARO:0000016) | ||||||||||
| Comment: | perfect match to referencesequence for ARO:3002594 from Salmonella enterica (Bitscore: 379)||Synonyms: | ||||||||||
| Protein Sequence: | MSASTPPITL RLMTERDLPM LHDWLNRPHI VEWWGGDEER PTLDEVLEHY LPRAMAEESV TPYIAMLGEE PIGYAQSYVA LGSGDGWWED ETDPGVRGID QSLADPTQLN KGLGTRLVRA LVELLFSDPT VTKIQTDPTP NNHRAIRCYE KAGFVREKII TTPDGPAVYM VQTRQAFERK RGVA |
||||||||||
1. Xu Y, Luo QQ, Zhou MG.
Identification and characterization of integron-mediated antibiotic resistance in the phytopathogen Xanthomonas oryzae pv. oryzae.. PLoS One. 2013;8(2):e55962. doi: 10.1371/journal.pone.0055962. Epub 2013 Feb 21. PubMed ID:
23437082
.