Mobile element type:
Transposon
Name:
TnXc5
Synonyms:
Tn7214
Accession:
TnXc5-Z73593
Family:
Tn3
Group:
Tn3
First isolate:
Yes
Partial:
ND
Evidence of transposition:
ND
Host Organism:
Xanthomonas campestris pv. citri XAS450 1
Date of Isolation:
1989
Country:
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| IRL | 1-38 | + | 38 | GGGGTTCGGG GAGCAATGGA ACAGGGAAGT CAGTTAAG |
| IRR | 6899-6937 | - | 39 | GGGTTCGGGG AGCAATGGAA CAGGGAAGTC AGTTAAGCC |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| res | TnXc5 | 973-1112 | + | 140 | TTTTGCTTTA CTCGTTAATT TTTAATAATA TCAAACTTTG ATTGTACAAA CCACTATTAC AGACTGCTTG TTGGCTTACG GACACCTCGC GCCGATCGCC CCATCAGAGT TCATAAAAAC GATCGTTTTA TTGAACCGTT |
| res_site_III | TnXc5 | 973-1001 | + | 29 | TTTTGCTTTA CTCGTTAATT TTTAATAAT |
| res_site_II | TnXc5 | 1005-1040 | + | 36 | AAACTTTGAT TGTACAAACC ACTATTACAG ACTGCT |
| res_site_I | TnXc5 | 1080-1112 | + | 33 | AGTTCATAAA AACGATCGTT TTATTGAACC GTT |
| None | TnXc5 | 4836-4976 , 6325-6894 | + | 711 | ATGCAACAAA TGACGCAACA ACCGTTGAAC GATGCCCAGC TTGATCGGCT GGGCGACTTT CTCGAAGGAG TCGGCGCACC TGCAATGAAT CTCGAAATGC TCGATGGGTT CTTTGCCGCA CTCATTTGTG GTCCAGAAAC TGGTCCAGAA ACGGTTTTGC CCAGCGAACA CTTGCCACAA GTATTCGGGG AAGACCATTG CTTCGACAGC AATGACCAAG CCGCCGAAAT TCTTGGCTTG GTCATGCGGC ACTGGAACAC GATTGCATCA GAATTGTTCC GCACTCTGGA GAAAGACGAT GTCTACCTTC CCGTGCTACT CGAAGATGCG GATGGGGCCG TACACGGTAA CGACTGGGCA CGTGGTTTCA TGCGCGGCAT TCAATTACGG CCCAATAGTT GGCAAGAGTT GATCGGCAGC GAAGAATTTG GCGGGCCCAT GCTGCCAATC ATGATCTTGA CCCATGAACA TGATCCTGAT CCCGCCATGC GCCCGCCAGA GATTGCGCCG GACAAACGCG ATGAGTTGCT TCAGTCCCTG ATTGCCGGAC TGACGCACAT CTATCGCTAC TTTGCCTCAC ATCGCCAATT GGCAACCCAA GGGCCTTTAC GCAGACAAGG TCCTAAGATT GGGAGAAATG ATCAGTGCCC ATGTGGCAGT GGGCGGAAGT ACAAGCATTG CTGTGCTACC AGCGCTCCGA CATTTCATTG A |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tnpR | TnXc5 | 42-965 | - | Accessory Gene | Resolvase |
| RHH_6 | TnXc5 | 1179-1418 | + | Passenger Gene | Antitoxin |
| PIN_3 | TnXc5 | 1418-1837 | + | Passenger Gene | Toxin |
| tnpA | TnXc5 | 1842-4817 | + | Transposase | |
| secC 5'-end | TnXc5 | 4836-4975 | + | Passenger Gene | Plant Pathogenicity |
| tnp | ISXac1 | 5092-6306 | + | Transposase | |
| secC 3'-end | TnXc5 | 6326-6894 | + | Passenger Gene | Plant Pathogenicity |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpR | TnpR | TnXc5 | 307 | 42-965 | - |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Resolvase | ||||||||||
| Sequence Family: | Serine Site-Specific Recombinase | ||||||||||
| Transposase Chemistry: | Serine | ||||||||||
| 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 | TnXc5 | 79 | 1179-1418 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | 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 | TnXc5 | 139 | 1418-1837 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Toxin | ||||||||||
| Sequence Family: | PIN_3 (Pfam:PF13470) | ||||||||||
| Target: | single stranded RNA | ||||||||||
| 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 | TnXc5 | 991 | 1842-4817 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MPVSFLSTTQ RERYGRYPDT LSSEELARYF HLDDDDREWI ATKRRDSSRL GYALQLTTAR FLGTFLEDPT AVPSPVLHTL SSQLGIADPS DCVIDYRTTR QRWQHTSEIR TRYGYREFTG TGVQFRLGRW LCALCWTGTD RPSALFDYAN GWLVGHKVLL PGVTLLERFI AEIRSRMESR LWRLLVHGVT PEQRQRLDDL LKLVEGSRQS WLDRLRKGPV RVSAPALVAA LLRIETVRGL GIKLPGTHVP PSRIAALARF ASTAKVSAVA RLPEVRRIAT LVAFVHCLEA SAQDDAIDVL DLLLRELFTK AEKEDRKVRQ RSLKDLDRAA STLAEACRML LDPALPDGEL RERVYAAIGH DELAQALNEV RGLVRPPNDV FYTELEARKA TVSRFLPALL RVIRFDANPA AQPLAQALQW LHEKPDHDPP TAIVGKAWQR HVVQDDGRIN ATAYSFCALD KLRSAIRRRD VFISPSWRYA DPRAGLLAGA EWEASRPIVC RSLSLSAQPE ATLSELTREL DETYRRVAAR LPQNDAVRFE NVGDKTELVL SPLEALEEPP SLIALRNEIK ARMPRVDLPE ILLEVAGRTG CMEAFTHLTE RTARAADLTT SLCAVLMAEA CNTGPEPLVR PDTPALKRDR LMWVDQNYVR DDTLTACNAV LVAAQSRIAL ARTWGGGDVA SADGMRFVVP VRTIHAGPNP KYFNRGRGVT WYNLLSDQRT GLNAITVPGT LRDSLILLAV VLEQQTELQP TQIMTDTGAY SDLVFGLFRL SNYRFCPRLA DVGGTRFWRV DPDADYGDLN ALARQRVNLD RITPHWDDVL RLVGSLKLGL VPAMGIMRTL QVDERPTSLA QAIAEIGRID KTIHTLNFID DEARRRATLL QLNLGEGRHS LAREVFHGKR GELFQRYREG QEDQLSALGL VVNMIVLWNT LYMDAVLTQL RSEGYPVKPE DEARLSPFGH EHINMLGRYS FSVPEAVARG ELRPLTKPND P |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | secC 5'-end | N/A | TnXc5 | 46 | 4836-4975 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Plant Pathogenicity | ||||||||||
| Comment: | interrupted by ISXac1 insertion | ||||||||||
| Protein Sequence: | MQQMTQQPLN DAQLDRLGDF LEGVGAPAMN LEMLDGFFAA LICGPE |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnp | Tnp | ISXac1 | 404 | 5092-6306 | + |
|---|
| Class: | Transposase | ||||||||||
| Function: | transposition | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MRASEVLQKC LSNSLSGMHA LRQRTLLGAV EALVHGGRLT LIDIARAWPG ATRVRAPLKA CDRLLCNRTL QAERSMIERD MAHWLLRGDQ PVIVIDWSDL KPDKSWCLLR AAVPIGGRTL TLLDMVVAGK QQGSPGAEKR FLQQLRRMIP DDVRPILVTD AGFRTPWFRA VSAMGWDWVG RLRGRTQVKP QDVPDDAAQW IDSRRLHALA SNRACELPPM QANRSDPLDC RLVLYAKTRL GRQQRNRRSP AKVSRASSSL KAAAREREPW LIVASPQLQA PSAKHLVNLY ARRMQIELAF RDLKSHRYGQ AMEDSLTRRG ERLQILLLLN TLATFASWLA GLGCEATGIA QWLSPRSSTR KLYSTLRVGR QALARRWPME PVSRWLERLR TLPEAVREQM TLVL |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | secC 3'-end | N/A | TnXc5 | 189 | 6326-6894 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Plant Pathogenicity | ||||||||||
| Comment: | interrupted by ISXac1 insertion | ||||||||||
| Protein Sequence: | VQKRFCPANT CHKYSGKTIA STAMTKPPKF LAWSCGTGTR LHQNCSALWR KTMSTFPCYS KMRMGPYTVT TGHVVSCAAF NYGPIVGKS* SAAKNLAGPC CQS*S*PMNM ILIPPCARQR LRRTNAMSCF SP*LPD*RTS IATLPHIANW QPKGLYADKV LRLGEMISAH VAVGGSTSIA VLPALRHFI |
||||||||||
| TnCentral Accession | TE Name | Type | Coordinates | Strand | Length |
|---|---|---|---|---|---|
| ISXac1-NC_003919 | ISXac1 | insertion sequence | 4976-6325 | + | 1350 |
| Name | Associated TE | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|---|
| IRL | ISXac1 | 4976-5025 | + | 50 | TGAGGTTTCC CCACATTTCT TCCTGCGAGA TCAAGCGCTT GGTGGGCCAG |
| IRR | ISXac1 | 6276-6325 | - | 50 | CTTAGGTATC CCCACGTTTT TAAAGCACCA GCGTCATCTG CTCACGCACT |
1. Liu CC, Wang HR, Chou HC, Chang WT, Tu J.
Analysis of the genes and gene products of Xanthomonas transposable elements ISXc5 and ISXc4.. Gene. 1992 Oct 12;120(1):99-103. doi: 10.1016/0378-1119(92)90015-h. PubMed ID:
1327971
.