Mobile element type:
Transposon
Name:
Tn5563a
Synonyms:
Accession:
Tn5563a-KJ920395.1
Family:
Tn3
Group:
Tn3
First isolate:
Yes
Partial:
ND
Evidence of transposition:
Yes
Host Organism:
Pseudomonas mendocina strain LM7
Date of Isolation:
2014
Country:
Poland
| Name | Coordinates | Direction | Length | Sequence |
|---|---|---|---|---|
| IR | 1-39 | + | 39 | GGGGTTTGGG GAGCAATGGA ACCAAAAACC AACGTAAGC |
| IR | 6215-6253 | - | 39 | GGGGTTTGGG GAGCAATGGA ACCAAAAACC AACGTAAGC |
| Name | Associated TE | Coordinates | Orientation | Length | Sequence |
|---|---|---|---|---|---|
| res_site_III | Tn5563a | 985-1026 | + | 42 | ACTCGACTAC GTTAGTAATA GTTGAACTTT GATTAAGCGT AC |
| res_site_II | Tn5563a | 1029-1059 | + | 31 | GTTATTTGAA CCGTAGCGCG GGGAGCTTAA C |
| res_site_I | Tn5563a | 1083-1110 | + | 28 | GTTCGGCAAA ACCTTCGTTT TGTCGAAC |
ORF Summary
| Name | Associated TE | Coordinates | Orientation | Class | Subclass |
|---|---|---|---|---|---|
| tnpR | Tn5563a | 41-970 | - | Accessory Gene | Resolvase |
| RHH_6 | Tn5563a | 1172-1411 | + | Passenger Gene | Antitoxin |
| PIN_3 | Tn5563a | 1411-1821 | + | Passenger Gene | Toxin |
| tnpA | Tn5563a | 1825-4818 | + | Transposase | |
| merP | Tn5563a | 5051-5326 | - | Passenger Gene | Heavy Metal Resistance |
| merT | Tn5563a | 5339-5695 | - | Passenger Gene | Heavy Metal Resistance |
| merR | Tn5563a | 5764-6162 | + | Passenger Gene | Heavy Metal Resistance |
ORF Details
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpR | TnpR | Tn5563a | 309 | 41-970 | - |
|---|
| Class: | Accessory Gene | ||||||||||
| Subclass: | Resolvase | ||||||||||
| Sequence Family: | Serine Site-Specific Recombinase | ||||||||||
| Transposase Chemistry: | Serine | ||||||||||
| Protein Sequence: | MKIGYARVST RDQKADLQVD ALKQAGCERI YQDIASGAKS ARPELDKLLA NVRPGDAVVI WKLDRLGRSL KHLVELVGEL AERKVGLQSL NDPIDTTHAQ GRLVFNLFAS LAEFERELIR ERTQAGLSAA RARGRIGGRP KGLPAKAEAT AMAAETLYRE GRLSVSAIGE KLHISKSTLY SYLRHRGVEI GAYQKSARSR DQQPSAASPA EPPAAERVAT VTLRLAVVNN SKFVRGRKRA TENIERYCLE PYGMKRLDAG HYELTIPYRS DDELDKSVHD LLTEISQEAD MRNCFVEMGA WEEDTEKRW |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | RHH_6 | RHH_6 | Tn5563a | 79 | 1172-1411 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Antitoxin | ||||||||||
| Function: | antitoxin||binds to DNA(IPR031914) | ||||||||||
| Sequence Family: | RHH_6 (Pfam:PF16762) | ||||||||||
| Comment: | Pfam PF16762.4 | ||||||||||
| Protein Sequence: | MNTIRWNVAV SADTDQSLRM FLASQGGGRK GDLSRFIEEA VRAHILELSA EQAKAANAHL SEAELTNAVD EALDWARKR |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | PIN_3 | PIN_3 | Tn5563a | 136 | 1411-1821 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Toxin | ||||||||||
| Function: | cleave single stranded RNA (Pfam:PF13470) | ||||||||||
| Sequence Family: | PIN_3 (Pfam:PF13470) | ||||||||||
| Target: | single stranded RNA | ||||||||||
| Protein Sequence: | MRVVLDTNIL FSALISPHGA PDAIYRAWRA ARFEVVTSRM QLDEIRRASR YPKLQAILQP AKVGAMINNL QRAVVLERLT IEVEADDPDD SFLLAMALAG DADYLVTGDR RAGLLQRGHI ERTRIVTPAV FCVEVL |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | tnpA | TnpA | Tn5563a | 997 | 1825-4818 | + |
|---|
| Class: | Transposase | ||||||||||
| Transposase Chemistry: | DDE | ||||||||||
| Protein Sequence: | MPVGFLTQEQ RDGFGRYVDS PSREELERYF HLSDEDREAI QVLRGNHNRL GYAVLLTTVR FVGVLPDKPA AVPVEVLQVL CRQLAIPDPD CLQRYSDHRR WIHATDIQNR FGYRHFTDPG IGFRLSRWLY ALCWTGTDRP GVLFERATSW LFTQKVLLPG VSQLERFIAQ LRSRVEERLW FTLGRSVTEE QRLQLQDLLT VAEGNRSSRL DQLRSGPVMV SGPALIRALR RLDDVRGIGI TLPAAAHIPP SRIAALARFA NTAKVTAINR LPASRRMATL VAFALCLEAT AHDDALEVLE ALLRDLFSNA EKADKKARMR SLKDLDRSAA TLAAACKVVL DSSISDDNVR ARLFNDLPRT TLEKALEEVN ALIRPVDDVY FLALEARYRS VRRFLPDLLK HIRFGFSPAG KGVAASLEWL QLNLPRRKPE DDAPQEIVAK AWQKHITRED GSLDMGAYVF CTLDALRTAL RRRDVFVSPS WRYADPRLGL LDGAEWLAAR PIICRSLGLT IDAKTTLDAL SVELDATWLA VAARLPDNPA IQLSENTEGK TELSLGALDK LDEPCSLLQL RAAVSDLMPR VDLPEILLEI AARTGFSEAF THVSERNARA DNLVTSLCAV LLGGACNTGL EPLIRTDNPA LRRDRLSWVS QNYIRDDTLS AANAILVGAQ SQLELAQVWG GGEVASADGM RFVVPVRTVH AGPNPKYFGT GRGVTWYNLI SDQFSGLNAI TVPGTLRDSL VLLAVVLEQQ TELQPTQIMT DTGAYSDVVF GLFRLLGYHF SPRLADVGGT RFWRTRPDAD YGKLNGLARQ SVKLDLIAEH WDDLLRLAGS LKLGRVPATG IMRTLQTGDR PTRLAQALAE FGRIEKTLHT LTYIDDESKR RATLTQLNRG EGRHSLARAV FHGKRGELRQ RYREGQEDQL GALGLVVNII VLWNTLYMTA AVERLKQHGY PVLEEDLARL SPLIYEHINM LGRYSFAVPE EVARGELRPL RNPDDDL |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | merP | MerP | Tn5563a | 91 | 5051-5326 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Heavy Metal Resistance | ||||||||||
| Target: | Mercury | ||||||||||
| Comment: | periplasmic binding protein | ||||||||||
| Protein Sequence: | MRKLLIAVLF ALPFVALAAP PKTVTLDVQN MTCGLCPITV KKSLEKVSGV SDVQVNFDQK TATVTYDPDK AQPEALTEAT ANAGYPSTVQ K |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | merT | MerT | Tn5563a | 118 | 5339-5695 | - |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Heavy Metal Resistance | ||||||||||
| Target: | Mercury | ||||||||||
| Comment: | transport protein | ||||||||||
| Protein Sequence: | MGMGMQLTGK GSLVASSLTA IGASVCCVGP LVLLALGVGG TWVGALTMME PLRPLFIGLT LLFLGLAFRK LYLVPQVCTP GTPCADPRTL VRQRLVFWIV SVLLLGLLAV PWLAPLFY |
||||||||||
| Gene Name | Protein Name | Associated TE | Gene Length | Coordinates | Strand | merR | MerR | Tn5563a | 132 | 5764-6162 | + |
|---|
| Class: | Passenger Gene | ||||||||||
| Subclass: | Heavy Metal Resistance | ||||||||||
| Target: | Mercury | ||||||||||
| Comment: | regulatory protein | ||||||||||
| Protein Sequence: | MATELTIGKL ADAAGVNVET IRYYQRRGLL DEPAKPLGGH RRYPVDMVKR LRFIKRAQAL GFTLSEVGGL LTLDESCACA ETRARAARKL ALIEQKMADL VVMQQLLGEL VQQCDAGDGG TICPIIEALI RE |
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1. Szuplewska M, Ludwiczak M, Lyzwa K, Czarnecki J, Bartosik D.
Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs).. PLoS One. 2014 Aug 14;9(8):e105010. doi: 10.1371/journal.pone.0105010. eCollection 2014. PubMed ID:
25121765
.