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Recombination Sites | |
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Internal Transposable Elements | |
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Internal Repeats | |
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| Name: Tn6138 |
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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: | Sphingobium japonicum UT26 | Molecular Source: | plasmid pCHQ1 |
| Place of Origin: | Japan | Date of Isolation: | 2011 |
| | Other Geographic Information: | upland experimental field treated with gamma-HCH |
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| Map |
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| Terminal Inverted Repeats (IR) |
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| IRL (Length: 45 bp) |  | GGGGTGACTACACGAAAGTGACGTATCTGCACGCTAAGAGCGAAC |
| IRR (Length: 45 bp) | | GGGGTGACTACACGAAAGTGACGCATCCGCACGCTAAGCGCGAAC |
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| Sequence |
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--------10 --------20 --------30 --------40 --------50 --------60 --------70 --------80 --------90 -------100
GGGGTGACTA CACGAAAGTG ACGTATCTGC ACGCTAAGAG CGAACAAATC CGGTACAATG CCAGCAGAGG CTACCTGTAG GTACTCAACG GCGTGTTCAA 100
CCTATCCTTT GAGCATGTGT CGATCATTGC GGGCGCCGAT ATGGGAGTGC CGCAAGCCGG CTCACCAACG ATCGAGGTAG AGCCCTGCTC GCCAAGTATG 200
TGAGTCGGTT GCCCATCCCC GGTATGGCGA AGGATCGCCG ATGAACCAGA GCGTCGACGG CAAGGGTCGC GCAGCGATCA ACGTTCATCA AGCCCAACTT 300
TCCCCACTTC AAATCGCTGA GGGCAGCCAT GTCGGTGTCA ATGCCACCGG GTGCAAAAGA CCCAACGCTC ACACCCGTCC CGGCAAGCTC GATGGAAAGT 400
GCCCGCATGA GGGTACTCAC ATAGGCCTTC GACGCGCCGT AGACCGCTTG GAAGGGTACG GATGTTTCGC CCGCCAGGCT CGACACTGCG ATTATTGAGG 500
ATTCAAACGG CTGCTGCCGG AAGATCGCAA TCAGGCGGGC CAGCAAATCC GTGAAGCCGG CTACGTTTGT TCCAATCACC TCGGCATAGG CGTCGGCACG 600
GCTAGCATCA AACGGACCGG CGCTCGTCAG CCCGGCAGCC AAGAAAGCCG CATTGACTTT CAATTCTATA ACCTTGGCCG CAATCTTCTC CCTGCCCTCA 700
ATTTCACGTT GATCGGCCAC TATGATCTCG CACGGGACAT TAAACCGCTC GCCAATTTCG GATTGTAGCT CCCGCAAGTT GTCGAGCCTT CGCCCAACAA 800
TCAGGGGCTT GGCCTGGTAC GATGCCGCCA AACGGAGGGC TGACGCCCTG CCCAAACCGG TTGAGGCCCC TGTAACCAGC ACCCACGAGT TCTGGATCGG 900
CAGCGGTTTC ATGCGCTTTC CAGAGCCTTG TACAGGGCGG TTTTCCCGAT CTTGAGCCGA GCCGCCGCCT CACGAACAGT TAGGCCCGCT GCGATGTGCG 1000
CCCGCGCCTT GCGCAGCTTG TCGGGAGTGA CGACAGGGCG GCGACCGCCC TGACTACCGC GCTCGCGCGC GGCTCGCAGG CCAGCATGGG TGCGTTCCCG 1100
GATCAGATCG CGCTCGAATT GGGCAAGCGA GCCGAAGATG TTGAATACCA GCATCCCGCC TGACGTGGTG GTATCGATCT GCTCGGTGAG CGAGCGGAAA 1200
CCCACGCCGC GCGCCGCCAG CTCGCCGACT TTCTCGATCA GGTGGCTCAT CGAACGCCCA AGACGATCGA GTTTCCAGAC CACCAGCGTG TCGCCGGTAC 1300
GCAGATAGGT GAGCGCCTCG GCCAGGCCGG GCCGATCGGC TTTTGCTCCA GATGCATAAT CGTCGAATAT GCGATCGCAA CCGGCAGCGC TCAACGCGTC 1400
GAGCTGGAGC GCCAGCTTCT GGTCTGCGGT CGAGACGCGC GCATAGCCGA TCAGCGCCAC ATGCTGCCCG ATCGTGTCCG TTTTCCCATC ATTTTGCGAT 1500
CTTGTCCGAA TCGCCATCAC AGGTCCAGAG TTGACGGACA TATTCATCCT GGCCGCCAGA GGACCGTCTG ACGGACAAGG ACGCGGAAGG AGATAGTGCT 1600
TGGCGAGACG GCGACTGGTG AGCGCGGAAA TCTGGGCAGG GCATTATGGC GCGCCGCTCG ATGAGCGCGA GATTGCGCGG CACTATACGC TGACCGGTGA 1700
CGACCTGGAA ATTGTCGGCC GCCGTCGCGG CGATGCCACC CGGCTCGGCT ACGCGATGCT CCTACTCTAT ATGAGATGGC CTGGCCGTGC GCTGGAAGCG 1800
GGTGAAGTCC CGCCCGCTCC TGTGCTCGCC TATGTGGCGC AGCAACTCGG CGTCGCGCCC GAAGCCTTCG CGGACTATGC CCATCGGGAC CAGACCCGTC 1900
GCGAACATCT CGTTGAAATC CGACGATCGC ACGGGTTCAG GATTTTCGAC CGCAAGGCTT TCCACGAAGT TGTCGCATTC TCGATCCCGA TCGCACAGAC 2000
CATCGTCCAC CCCGGCCAGA TGGCGGGGGT CATCGTTGAC GAACTTCGGC GCCGGCAGAT CCTCCTGCCT TCTTCATCGG TTCTCGAAGC GGTACTCCGG 2100
CGTGCTCGCC AGCAGGCCGA ACAGCTTACC TATGAAGTGC TCACGAACGG CCTGCGGCCC GATACGCTGC AGGGGCTGGA CGATCTGCTG GCCCGACGAA 2200
CAGGGCAAGC CGCGACATGG CTATCCTGGC TGCGCAATGC ACCACAGTCG CCGGCAGCGC GCAACATCCT ACGCCTGATC GAACGGCTCA CTCATATCCG 2300
CGCGCTGGAT CTCGATCGCG CCCGTGCCGA CATGATCCCG GCTTTGACTT TTGACAGGCT GGCGGACGAA GGCAGCCGGA TCACACCCCA GCACCTTGGC 2400
GAACTCAATG CCCTGCGCCG CCATGCGACG CTGGCGGCGC AGGGCATCCG TCTTGAGGAA AGCCTGACCG ATGCCACCCT GACGATGTTC GACAAGCTGT 2500
TGGGCAGCAT GTCGCGTCGC GCCGAGAACC GGACCCGTGA CAAAGCCCTC AAGACGGTGC GCGAGTTGCA AGGCCATCTC CGGACGCTCA CAGGGTCTTG 2600
CCGCATTCTC ATCGAAGCGC GCACCAACGG TGTGGACTCT CTGGCGCAGA TCGAGGCGCT GGATTGGCAG CGCTTCGCCG TGGCGGTCGC GCGGGCCGAA 2700
GTACTCGGGC GACCGGAAAC CGTCGATCGC ACCGCTGAAT TGATCGAGCG GCATCGCACG GTGAAGCTCT TTGCCGGTGC CTTTCTCAAC ACCTTCGAAT 2800
TTCGCGGCGC CGGTGCGGTG CAGGGACTCC TGTCGGCGCT TACCATCATC GCGGAGCTAT ACCGGACCGG CAAACGGCGC TTGCCTGATC GCGTGCCGCT 2900
GCGCTTTGTG CCCTCCGCAT GGCGGCCGTT CGTCCTGCGG GACGGCATCG TCGATCGCGC CGCCTATGAA CTATGCGCCT TGTCCCAGCT ACGGGAGCGG 3000
TTGCGAGCGG GAGACATATG GGTCTCGGGA AGCCGCCAGT TCCGCGATTT CGATAGCTAC CTCATCCCGC CGGCCACCTT CGACGCGCTT CGCGAGAAGG 3100
GGCCGTTGCC GCTCGCCATC GAAACGGACT TCGATCGTCA TATCGAGGAA AGGCGCGCCA GGCTCGACAC GGCGATCGAA CAGGTGACGG TCCTCGCCCG 3200
ACAGGGCGAG CTGCCCCAGG TCAGGCTTGA CGAAAGCGGC CTTATCATCT CGCCGCTGAA AGCGGCAACG CCACCCGCCA CCGAGATTGC CCGTCGCGCT 3300
GCCTATGACC GACTGCCGCG CGTGAAGATC ACCGATCTCC TGCTTGAGGT CGATGCCTGG ACCGGGTTCA GCGAATGCTT CATCCATCGG CGTTCGGGCC 3400
GGGAGGCCGA CGACCGCAAT GCGCTGCTCA CCGTCATCCT TGCCGATGGC ATCAATCTCG GCCTCACACG CATGGCGGAA ACCTGCCGAG GCGCAAGCCT 3500
GCGCCAGCTC GCCCATCTCC ACGACTGGCA CATCAGCGAG GCCGCCTATG GTGAAGCGCT GGGAAGGCTG ATCGACGCCC ATCGCGCCAT GCCGCTCGCC 3600
GCGCTGTGGG GAGACGGCAC CACCTCGTCG AGCGACGGAC AGCAATTCCA TGCCGGGGGC CGTGGCGCCG CAATCGGCGA CATCAACGCG CGCAGCGGCA 3700
ACGAACCGGG CGTTGCCTTC TACACCCATG TCTCGGATCG ATATGACCCC TTCGCGACCC GGGTAATCGC GGCGACCGCC GGCGAAGCTC CCTATGTGCT 3800
GGATGGCTTG CTGTATCAGC AGACCGGCCT GACAATCGAG GAGCACTACA CCGATACAGG CGGTGCATCG GACCATGTGT TCGGCCTTAT GCCCTTCTTC 3900
GGCTACCGCT TCGCGCCGCG CCTGCGCGAC ATCAAGCAGC GTCGTTTGCA CCTCCTTCCC GGCCAGGAAG CCGGCCCCTT GCTTGCCGGC ATGACGGCCG 4000
AACCGATCGC ATTGGGTCAT GTCGCGGCGC ATTGGGATGA ACTGCTGCGG TTCGCCACAT CGATACGCAC CGGCACCGCC ACCGCTTCGG CGATGCTTCG 4100
CCGCCTGTCC GCCTATCCGC GACAGAACGG ACTGGCCCTC GCGATGCGCG AGCTGGGCCG CCTCGAACGC TCGATCTTCA TGCTCGACTG GCTGCGCGAC 4200
ATTGATCTGC GCCGGCGTAC CCAGGCGGGC CTCAACAAGG GCGAGGCCCG CAACGCGCTC GCACGCGCGC TCTTCTTCAA CCAGCTCGGC GAATTGCGTG 4300
ATCGGCGGTT CGAGAACCAG ACCTATCGCG CCTCCGGCCT CAACCTGCTC GTCGCCGCCA TCATCCTGTG GAACACCCGC TATCTCGAAG TGGCGCTGGC 4400
TGATATCGGC ACGCCCGACG AAATCGCACG TCACGTCGCG CCATTGGGCT GGGAACATAT CTCGCTCACC GGCGACTATA GCTGGAATGT TGAAGATCGG 4500
CCCGATCCGG ATGTCCTGCG GCCACTGCGC GCCATCAGTT CGTTGCTCGC CGCGTAACGT TCACCATACG TTCGCGCTTA GCGTGCGGAT GCGTCACTTT 4600
CGTGTAGTCA CCCC
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| ORFs |
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| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| sdr-family |
Tn6138 |
124-912 |
Passenger Gene |
Other |
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| tnpR |
Tn6138 |
909-1517 |
Accessory Gene |
Resolvase |
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| tnpA |
Tn6138 |
1600-4557 |
Transposase |
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| sdr-family |
Sdr-family |
Tn6138 |
789 |
124-912 |
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| Class: | Passenger Gene |
| Sub Class: | Other |
| Function: | oxidoreductase activity (GO:0016491) |
| Sequence Family: | SDR-family |
| Comment: | short-chain dehydrogenase |
Protein Sequence:
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MKPLPIQNSW VLVTGASTGL GRASALRLAA SYQAKPLIVG RRLDNLRELQ SEIGERFNVP CEIIVADQRE IEGREKIAAK VIELKVNAAF LAAGLTSAGP
FDASRADAYA EVIGTNVAGF TDLLARLIAI FRQQPFESSI IAVSSLAGET SVPFQAVYGA SKAYVSTLMR ALSIELAGTG VSVGSFAPGG IDTDMAALSD
LKWGKLGLMN VDRCATLAVD ALVHRRSFAI PGMGNRLTYL ASRALPRSLV SRLAALPYRR PQ
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpR |
TnpR |
Tn6138 |
609 |
909-1517 |
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| Class: | Accessory Gene |
| Sub Class: | Resolvase |
| Function: | recombinase activity (GO:0000150) |
| Transpoase Chemistry: | Serine |
| Sequence Family: | Serine Site-Specific Recombinase |
| Comment: | UniProt accession: D4YYA0 |
Protein Sequence:
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MAIRTRSQND GKTDTIGQHV ALIGYARVST ADQKLALQLD ALSAAGCDRI FDDYASGAKA DRPGLAEALT YLRTGDTLVV WKLDRLGRSM SHLIEKVGEL
AARGVGFRSL TEQIDTTTSG GMLVFNIFGS LAQFERDLIR ERTHAGLRAA RERGSQGGRR PVVTPDKLRK ARAHIAAGLT VREAAARLKI GKTALYKALE
SA
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| tnpA |
TnpA |
Tn6138 |
2958 |
1600-4557 |
+ |
| Class: | Transposase |
| Transpoase Chemistry: | DDE |
Protein Sequence:
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MARRRLVSAE IWAGHYGAPL DEREIARHYT LTGDDLEIVG RRRGDATRLG YAMLLLYMRW PGRALEAGEV PPAPVLAYVA QQLGVAPEAF ADYAHRDQTR
REHLVEIRRS HGFRIFDRKA FHEVVAFSIP IAQTIVHPGQ MAGVIVDELR RRQILLPSSS VLEAVLRRAR QQAEQLTYEV LTNGLRPDTL QGLDDLLARR
TGQAATWLSW LRNAPQSPAA RNILRLIERL THIRALDLDR ARADMIPALT FDRLADEGSR ITPQHLGELN ALRRHATLAA QGIRLEESLT DATLTMFDKL
LGSMSRRAEN RTRDKALKTV RELQGHLRTL TGSCRILIEA RTNGVDSLAQ IEALDWQRFA VAVARAEVLG RPETVDRTAE LIERHRTVKL FAGAFLNTFE
FRGAGAVQGL LSALTIIAEL YRTGKRRLPD RVPLRFVPSA WRPFVLRDGI VDRAAYELCA LSQLRERLRA GDIWVSGSRQ FRDFDSYLIP PATFDALREK
GPLPLAIETD FDRHIEERRA RLDTAIEQVT VLARQGELPQ VRLDESGLII SPLKAATPPA TEIARRAAYD RLPRVKITDL LLEVDAWTGF SECFIHRRSG
READDRNALL TVILADGINL GLTRMAETCR GASLRQLAHL HDWHISEAAY GEALGRLIDA HRAMPLAALW GDGTTSSSDG QQFHAGGRGA AIGDINARSG
NEPGVAFYTH VSDRYDPFAT RVIAATAGEA PYVLDGLLYQ QTGLTIEEHY TDTGGASDHV FGLMPFFGYR FAPRLRDIKQ RRLHLLPGQE AGPLLAGMTA
EPIALGHVAA HWDELLRFAT SIRTGTATAS AMLRRLSAYP RQNGLALAMR ELGRLERSIF MLDWLRDIDL RRRTQAGLNK GEARNALARA LFFNQLGELR
DRRFENQTYR ASGLNLLVAA IILWNTRYLE VALADIGTPD EIARHVAPLG WEHISLTGDY SWNVEDRPDP DVLRPLRAIS SLLAA
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| References |
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Nagata Y, Natsui S, Endo R, Ohtsubo Y, Ichikawa N, Ankai A, Oguchi A, Fukui S, Fujita N, Tsuda M. Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium. Enzyme Microb Technol. 2011 Dec 10;49(6-7):499-508. doi: 10.1016/j.enzmictec.2011.10.005. Epub 2011 Nov 7. PubMed ID: 22142724
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