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Internal Transposable Elements | |
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| Name: Tn5393c |
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| Family: Tn3 Group: Tn163 |
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| Evidence of Transposition: no |
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| Host |
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| Host Organism: | Pseudomonas syringae pv. syringae A2 | Molecular Source: | plasmid pPSR1 |
| Place of Origin: | United States | Date of Isolation: | 2003 |
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| Map |
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| Terminal Inverted Repeats (IR) |
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| IRL (Length: 81 bp) |  | GGGGTCGTTTGCGGGAGAGGGCGAAATCCTACGCTAAGGCTTTGGCCAACGATATTCTCCGGTAAGATTGATGTGTTCCCA |
| IRR (Length: 40 bp) | | GGGGTCGTTTGCGGGAGGGGGCGGAATCCTACGCTAAGGC |
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| Sequence |
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--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTCGTTT GCGGGAGAGG GCGAAATCCT ACGCTAAGGC TTTGGCCAAC GATATTCTCC GGTAAGATTG ATGTGTTCCC AGGGGATAGG AGAAGTCGCT 100
TGATATCTAG TATGACGTCT GTCGCACCTG CTTGATCGCG GCCGCGATAG CTAGATCGCG TTGCTCCTCT TCTCCATCCG CGTTCCAAGC TGCGGAAAGG 200
CACCCATAAG CGTACGCCTG GTCGAGCAGG CGACGCGGAT CGACGTCCAG CGCACGAGAG AATGCGTCCG CCATCTGTGC AATGCGTCTA GGATCGAGAC 300
AAAGGTCGTC TCTGTCAGCC GGATCGTAGA ACATATTGGC GGCGCCAAAG CCCACTTCAC CGACCAGACC GACGGGATCT ATCACCAGCC AGCCGCGACT 400
GGAGAACATG ATGTTTTCAT GATGCAGATC GCCATGTAGC CCACGCAGTT CCGAGGCATT GCTCATCATT TGATCGGCTA TAATCGCCGC GTGGACGTAG 500
TCAGTTTGAC AACCTGCGTT TTGATCATCG CGCGCCCGCT GAAACAAAGC TGCAAAGCGA TCCCGGATCG GGAGAAGGGC AGAAGGCAGG GGTTCCTCAG 600
ATGCGGCATA CAGCTTCGCC ATTAGTTCCG CTGCAATTTC GGTCGCCTGG TAGTCGCCGT GCTCGGCAAC GATGTGAGAG AGCATTCGCT CCCCGGCATA 700
TTCGAGCAAC ATCAGATTGT TCTCACGACC GAGCAACCGG ACTGCTCCCC TCCCATTGCG CCATACCAGA TAGTCGGCCC CGCGCAGTTC ATCAGCAATG 800
TCTTCTATAG GTTTCAATCC CTTGACGATT GCAGGAGTCC CGTCTGGCAA TGAAACTTTC CAAACGAGGC TGGAAAAGGT GTCCGCAATG AGAACAGGTT 900
GCGAAACGTG CCAATGAGCA GGAAAAACAG GCGGCATGAA CATCAACCCC AAGTCAGAGG GTCCAATCGC AGATAGAAGG CAAGGCGTTC GCGGTCGGGG 1000
GCTTCGATCC CCAATACATT GAATAGGACA GCGAAGGCGC GCTCTGCTTC ATCTGGCGCT GCCCAGTTCT CTTCGGCGTT AGCAATCATG AGTGCCAAAT 1100
CGGCATAGCG ATCTGCTGTT CCGAGCCGCC CAAGGTCGAT CAGACCCGTG CATTGAAGAG TTTTAGGGTC CACCATGAAG TTCGGCATGC AGGGATCACC 1200
ATGGCAAACA ACCATATCGG TGCGCTCTTG GTCGAGCCGC ACCGGTAGCT CTCGTTCGAC ACGAGCCAAA AGATCGAGCT GCGGCGTACT CTTGTCCTCG 1300
TCCGGTAAGA AGTCGGGATT GACGGCATTG CGGGACACCA CATCAACGGC GCGTCCGAAC ATTCGCGACA GCCTGCGCTC AAACGGACAT TGATCAACCG 1400
ATAGGCTGTG AACAGCGCCA AGTTGCTGCC CCATTGACGG CCACGCTTTG AGCAAATCCG CTCCAGACAG ATCAGCCGCC GGTACTCCCG GAATTGCCGT 1500
TATCACCAAG CATGCACCCT CCTGTTCCTC CTGCCAGTTG ATCACCTCGG GGCAAGCCAC ACCTCGACCT TTGAGCCAAA TGAGGCGGTC ACGCTCTCCA 1600
GCGAGCTCAC CGCGGCGGGA AGCAGGTGCG ATTTTCGCGA AGGCATGCCC GTCACCACGT CGAAAAACAA AATCACCAGA TTCTCCGCCT CTGACAGGCA 1700
ACCAGTCAGA ATGCGATTCA CCAAAAAAAA TATTAGTTCG ATTCAATGGA GGTTCCTTCA GTTTTCTGAT GAAGCGCGGA GGTGGCTCAA CCTGCGAAAA 1800
GAAACGAGTT GCTACGTAAG TCCGAGAACA TGCTTTCCAT GGTCTCTGAG CTCGCCTTTG GGACCGACAT ATCGGTAGAG AGTGACGCGC TCGATGCCGA 1900
GTTCCTTGCA GAGATCGGAA ACTGAAGTAT CGCGCTGGGC CATGGCGGCT TGCGCGAGAC GCACCTGAGC TTTGGTGAGC GCGAATTTTC GTCCGCCCTT 2000
GCGACCGCGC GCTCTCGCGG AGGCGAGACC CGCCATGGTG CGCTCTCGGA TCAGATCCCG CTCGAACTCG GCCAAGGTGG CGAAGATTCC GAACACCATG 2100
CGACCGGACG CAGTCGTGGT GTCGATCTGA GCGCCCTTTC CAGTCAGAAC CCGCAGGCCG ATCTTGCGGT CTGACAGCTC CTTCACCGTG TTGACCAGAT 2200
GGGCAAGCGA TCGTCCGAGG CGATCGAGCT TCCAGACCAC CAGCACATCG CCGTCACGCA ATGACTTGAG GCAGGCAGTC AAGCCAGGGC GATCATCACG 2300
ACCGCCGGAA GCAAGATCAT CATAGATATT GTCCCGTTCG ACACCTGCGG CGCGCAAGGC GTCGTGCTGC AGGTCGAGAG ACTGCGAGCC ATCGGCTTTG 2400
GAGACGCGGG CATATCCGAT CAGCATGTAT CACAAACGTT GGTTTGAGGC GGCGCTTCGG CCACGATTGC ATTGACCTCT GGAAATGTAT CTCAACCAGC 2500
TTCATAAACA AAGCGTCTTG AACGCTATCA GATTTTGAAA AAGGAACATG TATGCCGCGT CGCGTCACTC TAACCGATCG GCAGAAAGAC GCGCTGTTGC 2600
GCTTGCCGAC TTCACAGACG GATTTGCTCA AGCACTATAC GCTGAGTGAT GAAGACCTTG GGCATATCAG GCTGCGTCGG CGCGCTCACA ACAGGTTCGG 2700
CTTCGCCCTG CAATTGTGTG TCCTGCGCTA TCCCGGCCGG GTGCTGGCTC CAGGCGAACT GATCCCTGCA GAGGTCATCG AATTTATCGG AGCGCAGCTT 2800
GGCCTGGGTG CCGACGATCT CGTAGACTAT GCTGCCCGCG AGGAAACACG GCACGAGCAT CTTGCCGAGT TACGGGGGCT CTACGGCTTC CGCACCTTCT 2900
CCGGACGTGG TGCGAGCGAG CTGAAGGAAT GGTTGTTCCG AGAAGCCGAG ATGGCGGTGT CGAACGAGGA TATCGCCCGT CGCTTCGTAG CCGAGTGCCG 3000
ACGCACCCGC ACTGTCCTTC CCGCGACATC CACGATCGAG CGGCTTTGTG CCGCGGCTCT CGTCGATGCC GAGCGACGCA TCGAGACGAG GATCGCCAGT 3100
CGGCTGCCTA TGTCGATCCG AGAACAGTTG CTGGCATTGC TCGAGGAGAC GGCTGATGAT CGGGTGACCC GTTTTGTGTG GCTGCGCCAG TTCGAGCCTG 3200
GCTCGAACTC TTCGTCGGCC AACCGGCTGC TCGACCGGCT CGAATATCTG CAACGCATCG ATCTCCCCGA GGATCTGCTT GCCGGCGTTC CTGCCCATCG 3300
GGTGACTCGT CTGCGCAGGC AGGGTGAACG GTATTATGCC GACGGCATGC GCGATCTCCC GGAGGACAGG CGGCTTGCGA TCTTGGCTGT TTGCGTCTCG 3400
GAATGGCAGG CGATGTTGGC CGACGCAGTG GTCGAAACCC ACGACCGGAT CGTCGGCCGT CTCTACCGTG CTTCGGAGCG TATTTGCCAT GCAAAGGTCG 3500
CAGACGAAGC GGGGGTGGTG CGTGACACCC TGAAATCCTT CGCCGAGATC GGGGGCGCCC TGGTCGATGC ACAGGATGAT GGCCAGCCGC TGGGCGATGT 3600
CATCGCGAGT GGGTCAGGGT GGGACGGCTT AAAAACCCTT GTTGCAATGG CAACCAGGCT GACCGCCACC ATGGCCGACG ATCCGCTCAA TCATGTGCTC 3700
GACGGTTATC ACCGCTTCCG CCGATACGCT CCACGCATGT TGCGCCTGCT CGATCTGCGA GCTGCGCCCG TTGCACTGCC GCTTCTGGAA GCGGTGACGG 3800
CCCTTCGTAC CGGTTTGAAC GATGCCGCGA TGACCAGCTT CTTGCGGCCC AGCTCGAAAT GGCATCGCCA CCTTCGGGCC CAGAGGGCTG GCGACGCTCG 3900
CCTATGGGAG ATCGCGGTGC TGTTCCATCT GCGCGATGCG TTCCGCTCCG GAGATGTCTG GCTTACTAGG TCCCGGCGCT ATGGCGATCT GAAACACGCA 4000
CTCGTTCCGG CACAATCCAT CGCGGAAGGC GGTCGTCTCG CTGTGCCATT GCGGCCGGAG GAATGGCTGG CAGACCGGCA AGCTCGCCTC GACATGCGGT 4100
TGCGCGACGT TGGCCGTGCC GCTCGCGCAG GCACGATCCC GGGCGGGTCG ATTGAAAACG GCGTTCTGCA TATCGAGAAA CTCGAAGCCG CCGCGCCGAC 4200
AGGCGCCGAA GATCTGGTGC TCGATCTCTA CAAGCAGATC CCGCCCACGC GCATCACCGA TCTCCTGCTG GAGGTGGATG CGGCGACCGG CTTCACCGAA 4300
GCGTTCACCC ATCTGCGCAC AGGAGCACCC TGCGCTGACC GGATCGGGCT AATGAACGTT ATCTTGGCGG AAGGGATCAA CCTCGGCTTG CGCAAAATGG 4400
CGGATCGGAC AAACACCCAC ACCTTCTGGG AATTGATCCG CATTGGACGG TGGCATGTCG AGGGCGAAGC CTATGACCGG GCGCTGGCCA TGGTGGTCGA 4500
GGCACAGGCA GCGTTACCCA TGGCCCGGTT CTGGGGCATG GGCACGTCGG CTTCGAGCGA CGGACAGTTC TTCGTCGCTA CAGAGCAAGG TGAGGCCATG 4600
AACCTGGTCA ACGCGAAATA TGGCAATACC CCGGGCCTGA AAGCCTATAG CCACGTCTCC GACCAATATG CGCCGTTCGC AACCCAGGTG ATTCCTGCAA 4700
CGGCAAGCGA AGCGCCTTAC ATCCTCGATG GCCTGCTGAT GAACGATGCT GGACGCCATA TCCGCGAGCA GTTCACCGAC ACGGGCGGCT TCACCGATCA 4800
CGTCTTTGCC GCATGTGCCA TTCTCGGCTA CCGGTTCGCT CCGCGCATCC GCGACCTGCC ATCCAAACGG CTCTACGCGT TCAATCCGTC GGCCGCCCCG 4900
GCGCACCTGC GAGCGTTGAT CGGCGGAAAG GTCAACCAAG CCATGATCGA GCGCAATTGG CCCGACATCC TGCGCATCGC CGCCACCATT GCTGCCGGGA 5000
CCGTCGCGCC AAGCCAGATT CTGCGGAAAC TCGCCTCCTA TCCGCGGCAG AACGAGCTCG CGACAGCCCT GCGGGAAGTC GGTCGCGTCG AGCGCACCCT 5100
GTTCATGATC GACTGGATTC TGGATGCCGA ACTCCAACGG CGTGCCCAGA TCGGGCTCAA CAAAGGCGAA GCTCATCATG CGCTGAAGCG GGCAATCAGC 5200
TTCCACCGCC GCGGTGAAAT CCGCGACCGT TCCGCCGAAG GCCAGCATTA CCGCATCGCC GGCATGAATC TGCTCGCCGC CATCATCATC TTCTGGAACA 5300
CCATGAAGCT CGGCGAGGTC GTTGCAAACC AGAAACGCGA TGGAAAGCTG CTATCGCCCG ATCTCTTGGC CCATGTTTCG CCGCTCGGAT GGGAACACAT 5400
CAATCTCACC GGAGAATATC GCTGGCCAAA GCCTTAGCGT AGGATTCCGC CCCCTCCCGC AAACGACCCC
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| Recombination Sites |
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| Name |
Coordinates |
Gene |
Sequence |
| res |
2330-2551 |
222 |
TGTCCCGTTC GACACCTGCG GCGCGCAAGG CGTCGTGCTG CAGGTCGAGA GACTGCGAGC
CATCGGCTTT GGAGACGCGG GCATATCCGA TCAGCATGTA TCACAAACGT TGGTTTGAGG
CGGCGCTTCG GCCACGATTG CATTGACCTC TGGAAATGTA TCTCAACCAG CTTCATAAAC
AAAGCGTCTT GAACGCTATC AGATTTTGAA AAAGGAACAT GT |
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| ORFs |
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| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| APH(6)-Id (ARO:3002660) |
Tn5393c |
107-952 |
Passenger Gene |
Antibiotic Resistance |
- |
| APH(3'')-Ib (ARO:3002639) |
Tn5393c |
943-1746 |
Passenger Gene |
Antibiotic Resistance |
- |
| tnpR |
Tn5393c |
1815-2426 |
Accessory Gene |
Resolvase |
- |
| tnpA |
Tn5393c |
2552-5437 |
Transposase |
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| APH(6)-Id (ARO:3002660) |
APH(6)-Id |
Tn5393c |
846 |
107-952 |
- |
| Class: | Passenger Gene |
| Sub Class: | Antibiotic Resistance |
| Function: | antibiotic inactivation (ARO:0001004) |
| Target: | aminoglycoside antibiotic (ARO:0000016) |
| Sequence Family: | APH(6) (ARO:3000151) |
| Comment: | strB, orfI || strict match to reference sequence for ARO:3002660 (bitscore: 568) |
Protein Sequence:
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MGLMFMPPVF PAHWHVSQPV LIADTFSSLV WKVSLPDGTP AIVKGLKPIE DIADELRGAD YLVWRNGRGA VRLLGRENNL MLLEYAGERM LSHIVAEHGD
YQATEIAAEL MAKLYAASEE PLPSALLPIR DRFAALFQRA RDDQNAGCQT DYVHAAIIAD QMMSNASELR GLHGDLHHEN IMFSSRGWLV IDPVGLVGEV
GFGAANMFYD PADRDDLCLD PRRIAQMADA FSRALDVDPR RLLDQAYAYG CLSAAWNADG EEEQRDLAIA AAIKQVRQTS Y
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| APH(3'')-Ib (ARO:3002639) |
APH(3'')-Ib |
Tn5393c |
804 |
943-1746 |
- |
| Class: | Passenger Gene |
| Sub Class: | Antibiotic Resistance |
| Function: | antibiotic inactivation (ARO:0001004) |
| Target: | aminoglycoside antibiotic (ARO:0000016) |
| Sequence Family: | APH(3'') (ARO:3000127) |
| Comment: | strA, orfH || perfect match to reference sequence for ARO: 3002639 |
Protein Sequence:
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MNRTNIFFGE SHSDWLPVRG GESGDFVFRR GDGHAFAKIA PASRRGELAG ERDRLIWLKG RGVACPEVIN WQEEQEGACL VITAIPGVPA ADLSGADLLK
AWPSMGQQLG AVHSLSVDQC PFERRLSRMF GRAVDVVSRN AVNPDFLPDE DKSTPQLDLL ARVERELPVR LDQERTDMVV CHGDPCMPNF MVDPKTLQCT
GLIDLGRLGT ADRYADLALM IANAEENWAA PDEAERAFAV LFNVLGIEAP DRERLAFYLR LDPLTWG
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpR |
TnpR |
Tn5393c |
612 |
1815-2426 |
- |
| Class: | Accessory Gene |
| Sub Class: | Resolvase |
| Function: | recombinaseactivity (GO:0000150) |
| Transpoase Chemistry: | Serine |
| Sequence Family: | Serine Site-Specific Recombinase |
Protein Sequence:
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MLIGYARVSK ADGSQSLDLQ HDALRAAGVE RDNIYDDLAS GGRDDRPGLT ACLKSLRDGD VLVVWKLDRL GRSLAHLVNT VKELSDRKIG LRVLTGKGAQ
IDTTTASGRM VFGIFATLAE FERDLIRERT MAGLASARAR GRKGGRKFAL TKAQVRLAQA AMAQRDTSVS DLCKELGIER VTLYRYVGPK GELRDHGKHV
LGLT
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
Tn5393c |
2886 |
2552-5437 |
+ |
| Class: | Transposase |
| Function: | transposase activity (GO:0004803) |
| Transpoase Chemistry: | DDE |
Protein Sequence:
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MPRRVTLTDR QKDALLRLPT SQTDLLKHYT LSDEDLGHIR LRRRAHNRFG FALQLCVLRY PGRVLAPGEL IPAEVIEFIG AQLGLGADDL VDYAAREETR
HEHLAELRGL YGFRTFSGRG ASELKEWLFR EAEMAVSNED IARRFVAECR RTRTVLPATS TIERLCAAAL VDAERRIETR IASRLPMSIR EQLLALLEET
ADDRVTRFVW LRQFEPGSNS SSANRLLDRL EYLQRIDLPE DLLAGVPAHR VTRLRRQGER YYADGMRDLP EDRRLAILAV CVSEWQAMLA DAVVETHDRI
VGRLYRASER ICHAKVADEA GVVRDTLKSF AEIGGALVDA QDDGQPLGDV IASGSGWDGL KTLVAMATRL TATMADDPLN HVLDGYHRFR RYAPRMLRLL
DLRAAPVALP LLEAVTALRT GLNDAAMTSF LRPSSKWHRH LRAQRAGDAR LWEIAVLFHL RDAFRSGDVW LTRSRRYGDL KHALVPAQSI AEGGRLAVPL
RPEEWLADRQ ARLDMRLRDV GRAARAGTIP GGSIENGVLH IEKLEAAAPT GAEDLVLDLY KQIPPTRITD LLLEVDAATG FTEAFTHLRT GAPCADRIGL
MNVILAEGIN LGLRKMADRT NTHTFWELIR IGRWHVEGEA YDRALAMVVE AQAALPMARF WGMGTSASSD GQFFVATEQG EAMNLVNAKY GNTPGLKAYS
HVSDQYAPFA TQVIPATASE APYILDGLLM NDAGRHIREQ FTDTGGFTDH VFAACAILGY RFAPRIRDLP SKRLYAFNPS AAPAHLRALI GGKVNQAMIE
RNWPDILRIA ATIAAGTVAP SQILRKLASY PRQNELATAL REVGRVERTL FMIDWILDAE LQRRAQIGLN KGEAHHALKR AISFHRRGEI RDRSAEGQHY
RIAGMNLLAA IIIFWNTMKL GEVVANQKRD GKLLSPDLLA HVSPLGWEHI NLTGEYRWPK P
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| Internal Repeat Elements |
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| Name |
Associated Mobile Element |
Coordinates |
Sequence (Top Strand) |
| IRL |
Tn5393c |
1-40 |
GGGGTCGTTT GCGGGAGAGG GCGAAATCCT ACGCTAAGGC |
| IRRl |
Tn5393c |
5390-5470 |
ACCCTTGTGT AGTTAGAGTG GCCTCTTATA GCGACCGGTT TCGGAATCGC
ATCCTAAGGC GGGGGAGGGC GTTTGCTGGG G |
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| References |
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Sundin GW, Mayfield CT, Zhao Y, Gunasekera TS, Foster GL, Ullrich MS. Complete nucleotide sequence and analysis of pPSR1 (72,601 bp), a pPT23A-family plasmid from Pseudomonas syringae pv. syringae A2. Mol Genet Genomics. 2004 Jan;270(6):462-76. doi: 10.1007/s00438-003-0945-9. Epub 2003 Nov 21. PubMed ID: 14634868
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