Transposon
Name: TnXc4.2       (Synonyms: Tn7212)
Family: Tn3        Group: Tn3
Evidence of Transposition: no
 Host     

Host Organism:Xanthomonas citri pv. citri 03-1638-1-1 Molecular Source:plasmid pP2
Place of Origin:Bella Vista Corrientes, Argentina Date of Isolation:2018
Other Geographic Information:copper tolerant A group strain isolated from Red Blush Grapefruit (C. paradiseMacf.) 2003

 Map     



 Terminal Inverted Repeats (IR)     

IRL (Length: 38 bp)GGGGTTCGGGGAGCAATGGAACAGGGAAGTCAGTTAAG
IRR (Length: 38 bp)GGGGTTCGGGGAGCAATGGAACAGGGAAGTCAGTTAAG

 Sequence     
DNA SequenceLength  5184 
--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTTCGGG GAGCAATGGA ACAGGGAAGT CAGTTAAGCC TTCACCAGTG CCGGTCTGTA CCTTCCATGC GGGCGTGGCT CTCTGAGAAA CAGTGGCGGT 100
CATCCGCACC GCAGGCGATG TCGGTTAGCA AATCGTTCAC GGCTTCATCC AGCTCTTCAT CCGTGTCATA GGGCACCTTC AGTTCATATT CCCCGTTCGG 200
CCGCCGCGTG GCATCGTATT GGGCAAGATC AAAAAACTCG ACATGCTCGA TCGAGCGCTT CTTTCCGCGC ACGAACTTGC TATTGTTCTC GATGCGCAAG 300
GTCAGCAGGA TGGTGGCGAC CTTCGGCTGG TCAGCGTTTC CGCTCTCGAC CACGGAGACG TTTATCGGCG ACTGCGCCGA TTGTTTGTAC GGGCCGATCT 400
CTACGCCGCG ATGCCGCAGG TAGCTGTACA GCGTGCTCTT GGACAAGTGC AGTTTCTGCG CAATGGCAGC GACCGACAGC TTGCGCTCGC GGTATAGGGT 500
CTCGGCCGCC AGCGCTGTCG CTTCGGCCTG CGGCGACAGG CCCTTGGGTC GCCCACCGAC CCTGCCACGC GCCCGCGCGG CCGTCAGCCC GGCCTGGGTG 600
CGCTCGCGAA TTAGCTCGCG CTCGAACTCG GCCAGCGTGG CGAACAGGTT GAACACGAAC CGCCCTTGGG CGCTGGTGGT GTCGATGGGG TCATTCAGGC 700
TGAGCAGCCC GACCTTGCGT TCCATCAGGC TACCCACCAA CTCAACCAGG TGCTTGAGTG AGCGTCCCAT GCGGTCGAGT TTCCAGATCA CCAGCACGTC 800
GCCGCCACGC AACTGGCCCA GCAGTTCATC GAGCGCTGGG CGCGCGGTCT TCGCGCCGCT CGCAACGTCC TGATAAATGC GCTCGCAGCC GGCCGCCTTG 900
AGGGAGTCCA CCTGCAAGGC TGGGTTCTGT TCGCGCGTGG ATACGCGCGC ATAGCCGATT TTCATCGTAA TAGCAAAAAA AACCGCTTAA AGAGTGTATA 1000
AACACCGATG TGCATAAACT CTGATTGGAG AGAGCTTCAT GAATACCGTG CGCTGGAACA TCGCCGTATC GCCGGACGTG GATCAGTCCG TCCGCATGTT 1100
CATCGCCGCG CAAGGCGGCG GTCGCAAGGG CGACCTGTCA CGCTTCATCG AGGATGCGGT GCGCGCCTAC CTCTTCGAGC GGGCTGTGGA ACAAGCCAAA 1200
GCCGCTACGG TGGGTATGGG TGAGACAGAA CTGAACGACC TCATTGATGA GGCGGTGCAA TGGGCGCGTG AGCATTAATG CGGGTCGTCC TCGACACCAA 1300
CGTATTGCTG GCCGCGCTGA TCTCGTCGCA CAGCCCACCC GACATCATCT ATCGCGGTTG GCTTGCAGCA CGCTTTGAAC TGGTGACAGG GACGGCGCAG 1400
CTTGATGAAC TGCGCCGCGT GAGCCGTTAC CCGAAGATCA AGGCAATCCT GCCCGCGCAT CGCGTCGGCA CGATGATCAA CAACATGCAG CGCGCCGTTG 1500
TGCTGCATGT ATTGCCGCCT CTGCCTGATC GCATCGAGGT CAATGATCCG AACGATGCGT TCCTGCTGGC GATGGCACTG GCCAGCGAGG CCGATTACCT 1600
TGTGACTGGC GACCGCCGCG CTGGGCTGCT GCAACGCGGT AGCATTGGCC GCACGCGCAT CGTCACGCCA GTCACCTTCT GCGCCGAGGC GCTTTGACGC 1700
CATGCCGGTC AGCTTCCTGT CCACCACACA ACGGGAACGC TACGGCCGCT ATCCAGACAC GCTTTCCAGC GAAGAGCTGG CGCGCTATTT CCACCTGGAC 1800
GACGATGACC GCGAGTGGAT CGCCACCAAG CGACGCGACA GCAGTCGCCT CGGTTATGCG CTGCAACTGA CCACGGCGCG GTTTCTCGGC ACCTTTCTGG 1900
AAGACCCTAC CGCCGTGCCA AGCCCGGTGC TGCATACGCT GTCGTCGCAA CTTGGCATCG CCGACCCTTC CGATTGCGTC ATTGACTACC GGACAACTCG 2000
GCAGCGCTGG CAGCACACGA GCGAGATTCG CACCCGCTAT GGCTACCGCG AGTTCACGGG TACCGGCGTC CAGTTCCGCC TTGGCCGCTG GTTGTGCGCG 2100
TTGTGCTGGA CGGGCACTGA CCGCCCGAGT GCGCTGTTCG ACTACGCCAA CGGCTGGCTG GTCGGCCACA AGGTGCTGCT ACCCGGCGTC ACCTTGCTGG 2200
AGCGCTTTAT CGCCTAGATA CGCTCACGCA TGGAGTCGCG TCTGTGGCGA CTACTGGTGC ACGGCGTGAC ACCCGAGCAG CGACAACGCC TCGATGACTT 2300
GCTCAAGCTT GTCGAAGGCA GCCGGCAGTC TTGGCTGGAT CGATTGCGCA AGGGGCCGGT ACGCGTCAGC GCTCCGGCGC TCGTTGCGGC CTTGCTGCGA 2400
ATCGAAACCG TGCGTGGCTT GGGCATTAAG CTGCCAGGCA CCCATGTGCC GCCGAGCCGC ATCGCAGCGC TGGCCCGCTT CGCCAGTACT GCCAAGGTAT 2500
CCGCCGTGGC TCGATTGCCG GAGGTGCGAC GCATCGCCAC GCTAGTGGCC TTCGTCCACT GCCTGGAAGC CAGCGCGCAA GACGATGCCA TCGATGTGCT 2600
CGACCTGCTG CTGCGCGAGC TGTTCACCAA GGCTGAGAAA GAAGATCGTA AGGTCAGGCA GCGCTCCCTC AAGGATCTGG ATCGGGCCGC CTCGACGCTG 2700
GCCGAGGCAT GCCGGATGCT GCTCGATCCG GCCCTGCCGG ACGGCGAACT GCGCGAGCGC GTCTATGCCG CCATCGGCCA CGATGAACTG GCCCAGGCGC 2800
TCAATGAAGT GCGCGGTCTG GTGCGCCCGC CCAACGATGT GTTCTACACC GAACTGGAAG CCCGCAAGGC CACCGTCTCG CGCTTCCTGC CGGCGTTGCT 2900
GCGCGTCATC CGCTTTGACG CCAATCCGGC CGCGCAACCT TTGGCGCAGG CGTTGCAATG GCTGCATGAG AAGCCCGACC ATGATCCGCC CACGGCCATC 3000
GTCGGCAAGG CGTGGCAACG CCATGTCGTT CAGGATGATG GCCGCATCAA TGCCACAGCC TATTCGTTCT GCGCGCTCGA CAAGCTGCGC AGTGCGATTC 3100
GCCGCCGCGA CGTGTTCATC AGCCCGAGTT GGCGCTACGC CGATCCACGC GCCGGGCTGC TGGCCGGAGC TGAATGGGAG GCCTCGCGGC CTATCGTCTG 3200
CCGCTCGCTG AGCCTGTCGG CGCAGCCCGA GGCCACGTTG TCCGAGCTGA CGCGCGAGCT GGACGAAACC TACCGCCGCG TCGCCGCGCG CCTGCCCCAG 3300
AACGACGCAG TGCGCTTCGA GAACGTTGGC GACAAGACGG AACTGGTGCT CAGTCCGCTT GAAGCATTGG AGGAGCCGCC TTCATTGATC GCGCTGCGCA 3400
ACGAAATCAA GGCGCGCATG CCGCGCGTCG ATCTTCCGGA AATCCTGCTG GAAGTCGCCG GTCGTACTGG CTGCATGGAA GCGTTCACGC ACCTGACTGA 3500
ACGCACCGCG CGCGCGGCCG ACCTGACCAC CAGCCTGTGC GCGGTGCTGA TGGCCGAAGC CTGCAACACC GGCCCGGAAC CACTGGTGCG GCCAGACACT 3600
CCGGCGCTCA AGCGCGACCG GCTGATGTGG GTCGATCAGA ACTATGTGCG TGACGACACG CTGACAGCCT GCAATGCCGT GCTGGTGGCC GCGCAAAGTC 3700
GTATCGCACT GGCGCGAACC TGGGGAGGTG GCGATGTGGC TTCGGCCGAC GGCATGCGAT TCGTGGTGCC GGTGCGCACG ATCCACGCTG GACCGAACCC 3800
AAAGTATTTC AATCGCGGGC GCGGCGTCAC TTGGTACAAC TTGCTTTCCG ATCAGCGCAC CGGACTGAAC GCGATCACTG TGCCTGGCAC GCTGCGCGAC 3900
AGTTTGATTT TGCTAGCGGT TGTGCTGGAG CAGCAAACGG AGTTGCAGCC GACCCAGATC ATGACCGACA CCGGCGCGTA CAGCGATTTG GTGTTCGGTT 4000
TGTTCCGCCT CTCCAACTAT CGATTCTGCC CGCGCCTGGC CGATGTTGGC GGTACCCGTT TCTGGCGCGT CGATCCCGAC GCCGACTATG GCGACCTCAA 4100
TGCGCTGGCC CGGCAGCGTG TGAATCTCGA CCGTATCACC CCGCATTGGG ATGATGTGCT GCGTCTGGTC GGCTCGCTCA AGCTCGGTCT GGTTCCGGCG 4200
ATGGGCATCA TGCGCACCTT ACAGGTCGAT GAACGGCCCA CCAGCCTGGC GCAAGCCATC GCCGAAATCG GCCGTATCGA CAAGACCATC CACACGTTGA 4300
ATTTCATCGA CGACGAAGCC CGCCGTCGCG CCACGCTGCT GCAACTGAAT CTCGGTGAAG GCCGCCACAG CCTGGCGCGC GAGGTTTTCC ACGGCAAGCG 4400
CGGCGAGCTG TTCCAGCGCT ACCGCGAAGG GCAGGAAGAC CAGTTGAGCG CGCTCGGCCT GGTCGTGAAC ATGATCGTGC TTTGGAACAC GCTGTACATG 4500
GATGCGGTGC TGACGCAGTT GCGCAGCGAA GGCTACCCCG TGAAGCCAGA AGACGAGGCA CGGCTGTCGC CGTTCGGCCA CGAGCACATC AACATGCTCG 4600
GACGCTATTC GTTCTCGGTG CCGGAAGCTG TCGCGCGCGG CGAGCCAAGC CGCCGAAATT CTTGGCTTGG TCATGCGGCA CTGGAACACG ATTGCATCAG 4700
AATTGTTCCG CACTCTGGAG AAAGACGATG TCTACCTTCC CGTGCTACTC GAAGATGCGG ATGGGGCCGT ACACGGTAAC GACTGGGCAC GTGGTTTCAT 4800
GCGCGGCATT CAATTACGGC CCAATAGTTG GCAAGAGTTG ATCGGCAGCG AAGAATTTGG CGGGCCCATG CTGCCAATCA TGATCTTGAC CCATGAACAT 4900
GATCCTGATC CCGCCATGCG CCCGCCAGAG ATTGCGCCGG ACAAACGCGA TGAGTTGCTT CAGTCCCTGA TTGCCGGACT GACGCACATC TATCGCTACT 5000
TTGCCTCACA TCGCCAATTG GCAACCCAAG GGTCTTTACG CAGACAAGGT CCTAAGATTG GGAGAAATGA TCAGTGCCCA TGTGGCAGTG GGCGGAAGTA 5100
CAAGCATTGC TGTGCTACCA GCGCTCCGAC ATTTCATTGA TACCGGCTTA ACTGACTTCC CTGTTCCATT GCTCCCCGAA CCCC

 ORFs     
ORF Summary
Gene Name Associated TE Coordinates Class Sub Class Orientation
tnpR TnXc4.2 42-965 Accessory Gene Resolvase -
RHH_6 TnXc4.2 1039-1278 Passenger Gene Antitoxin +
PIN_3 TnXc4.2 1278-1697 Passenger Gene Toxin +
tnpA TnXc4.2 1795-4779 Transposase   +
secC_p TnXc4.2 4673-5140 Passenger Gene Plant Pathogenicity +

ORF Details
Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpR TnpR TnXc4.2 924 42-965 -
Class:   Accessory Gene
Sub Class:   Resolvase
Transpoase Chemistry:   Serine
Sequence Family:  Serine Site-Specific Recombinase
Protein Sequence:  
MKIGYARVST REQNPALQVD SLKAAGCERI YQDVASGAKT ARPALDELLG QLRGGDVLVI WKLDRMGRSL KHLVELVGSL MERKVGLLSL NDPIDTTSAQ
GRFVFNLFAT LAEFERELIR ERTQAGLTAA RARGRVGGRP KGLSPQAEAT ALAAETLYRE RKLSVAAIAQ KLHLSKSTLY SYLRHRGVEI GPYKQSAQSP
INVSVVESGN ADQPKVATIL LTLRIENNSK FVRGKKRSIE HVEFFDLAQY DATRRPNGEY ELKVPYDTDE ELDEAVNDLL TDIACGADDR HCFSESHARM
EGTDRHW

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
RHH_6 RHH_6 TnXc4.2 240 1039-1278 +
Class:   Passenger Gene
Sub Class:   Antitoxin
Sequence Family:  RHH_6 (Pfam:PF16762)
Protein Sequence:  
MNTVRWNIAV SPDVDQSVRM FIAAQGGGRK GDLSRFIEDA VRAYLFERAV EQAKAATVGM GETELNDLID EAVQWAREH

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
PIN_3 PIN_3 TnXc4.2 420 1278-1697 +
Class:   Passenger Gene
Sub Class:   Toxin
Target:   single stranded RNA
Sequence Family:  PIN_3 (Pfam:PF13470)
Comment:   tRNA(fMet)-specific endonuclease
Protein Sequence:  
MRVVLDTNVL LAALISSHSP PDIIYRGWLA ARFELVTGTA QLDELRRVSR YPKIKAILPA HRVGTMINNM QRAVVLHVLP PLPDRIEVND PNDAFLLAMA
LASEADYLVT GDRRAGLLQR GSIGRTRIVT PVTFCAEAL

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
tnpA TnpA TnXc4.2 2985 1795-4779 +
Class:   Transposase
Transpoase Chemistry:   DDE
Comment:   missing 135 bp at 3' (C-ter) end
Protein Sequence:  
LDDDDREWIA TKRRDSSRLG YALQLTTARF LGTFLEDPTA VPSPVLHTLS SQLGIADPSD CVIDYRTTRQ RWQHTSEIRT RYGYREFTGT GVQFRLGRWL
CALCWTGTDR PSALFDYANG WLVGHKVLLP GVTLLERFIA *IRSRMESRL WRLLVHGVTP EQRQRLDDLL KLVEGSRQSW LDRLRKGPVR VSAPALVAAL
LRIETVRGLG IKLPGTHVPP SRIAALARFA STAKVSAVAR LPEVRRIATL VAFVHCLEAS AQDDAIDVLD LLLRELFTKA EKEDRKVRQR SLKDLDRAAS
TLAEACRMLL DPALPDGELR ERVYAAIGHD ELAQALNEVR GLVRPPNDVF YTELEARKAT VSRFLPALLR VIRFDANPAA QPLAQALQWL HEKPDHDPPT
AIVGKAWQRH VVQDDGRINA TAYSFCALDK LRSAIRRRDV FISPSWRYAD PRAGLLAGAE WEASRPIVCR SLSLSAQPEA TLSELTRELD ETYRRVAARL
PQNDAVRFEN VGDKTELVLS PLEALEEPPS LIALRNEIKA RMPRVDLPEI LLEVAGRTGC MEAFTHLTER TARAADLTTS LCAVLMAEAC NTGPEPLVRP
DTPALKRDRL MWVDQNYVRD DTLTACNAVL VAAQSRIALA RTWGGGDVAS ADGMRFVVPV RTIHAGPNPK YFNRGRGVTW YNLLSDQRTG LNAITVPGTL
RDSLILLAVV LEQQTELQPT QIMTDTGAYS DLVFGLFRLS NYRFCPRLAD VGGTRFWRVD PDADYGDLNA LARQRVNLDR ITPHWDDVLR LVGSLKLGLV
PAMGIMRTLQ VDERPTSLAQ AIAEIGRIDK TIHTLNFIDD EARRRATLLQ LNLGEGRHSL AREVFHGKRG ELFQRYREGQ EDQLSALGLV VNMIVLWNTL
YMDAVLTQLR SEGYPVKPED EARLSPFGHE HINMLGRYSF SVPEAVARGE PSRRNSWLGH AALEHDCIRI VPHSGERRCL PSRATRRCGW GRTR

Gene Name Protein Name Associated TE Gene Length Coordinates Strand
secC_p SecC_p TnXc4.2 468 4673-5140 +
Class:   Passenger Gene
Sub Class:   Plant Pathogenicity
Comment:   C-terminal segment
Protein Sequence:  
MRHWNTIASE LFRTLEKDDV YLPVLLEDAD GAVHGNDWAR GFMRGIQLRP NSWQELIGSE EFGGPMLPIM ILTHEHDPDP AMRPPEIAPD KRDELLQSLI
AGLTHIYRYF ASHRQLATQG SLRRQGPKIG RNDQCPCGSG RKYKHCCATS APTFH

 References     

Gochez AM, Huguet-Tapia JC, Minsavage GV, Shantaraj D, Jalan N, Strauß A, Lahaye T, Wang N, Canteros BI, Jones JB, Potnis N. Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains. BMC Genomics. 2018 Jan 4;19(1):16. doi: 10.1186/s12864-017-4408-9. PubMed ID: 29301493