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Recombination Sites | |
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Internal Transposable Elements | |
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Internal Repeats | |
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| Name: Tn6134 |
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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 | Molecular Source: | genomic DNA UT26 |
| Place of Origin: | Japan | Date of Isolation: | 2011 |
| | Other Geographic Information: | Yuji Nagata Tohoku University, Graduate School of Life Sciences |
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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) | | GGGGTGACTACACGAAAGTGACGTATCTGCACGCTAAGGGCGAAC |
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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 ACGGACAGGC ACAGCGAAGG AGATGATGCT 1600
TGGCGAGGCG GCGACTGGTG AGCCTGGAAA TCTGGGCGGG GCATTATGAC GCGCCGCTCG ATGAGCGCGA GATTGCACGT CACTATACGC TGACCAGTGA 1700
CGACCTGGAA ATTGTCGGTC GCCGTCGCGG CGATGCCACC CGGCTCGGTT TCGCGATGCT CCTGCTCACC ATGAGATGGC CTGGCCGTGC GCTGGAAGCG 1800
GGCGAAGTCC CGCCCGCCCC TGTGCTCGGT TATGTGGCCC GCCAACTCGG CGTCGCGCCC GACGCCTTTG CGGACTATGC TCGTCGGGAT CAGACCCGCC 1900
GCGAGCATCT TGTCGAAATC CGACGATCGC ACGGGTTCAG GATTTTCGAT CGCGACGCAT TCCGCGAAGT CGTCGCCTTC TCGATCCCTA TCGCACAGAC 2000
CATCATCCAC CCCGGCCAGA TGGCAGGCGT CATCGTCGAC GAACTCCGGC GTCGGCAGAT CCTCCTACCT TCTTCTTCGA TTCTAGAAGC GGTGCTGCGG 2100
CGGGCTCGCC AGCAAGCCGA ACAGCTTACC TATGAAGTGC TCACAAACGG TCTGCGGCCC GACACCCTTC AGGACCTGGA CGATTTGCTG GCCCGACGAA 2200
CGGGGCAAGC CGCGACATGG CTATCCTGGC TTCGCAATGC GTCACAATCG CCGGCAGCGC GCAACATTCT GCGCCTGATC GAACGGCTCG CCTATGTCCG 2300
CGCACTGGGC CTCGATCGCG GGCGGGCTGA CATGATTCCG GCTTCGACTT TTGACAGGCT CGCGGACGAG GGCAGCCGCA TCACGCCCCA GCATCTTGGC 2400
GAACTCAATG CCCTGCGCCG ACATGCGACG CTGGCGGCAA CCGGCATCCG CCTTGAGGAA GACCTGACCG ACGCAACCCT GACGATGTTC GACAAGCTGT 2500
TGGGCAGCAT GGTGCGCCGC GCCGAAAACC GGACCCGCGA CAAAGCCCTC AAGACGGTGC GCGAGCTGCA GGGTCATCTC CGGACGCTCA CAGGGTCTTG 2600
CCGCATCCTC ATCGACGCGC GAACCAACGG CGTGGACTCG CTGGCGCAGA TCGAGGCGCT GGACTGGCAG CGCTTCGCCG TGTCGGTCGA GCAAGCCGAA 2700
GTGCTCAGCC GACCGGAAAC CGTCGATCGC ACCGCTGAAT TGATTGAGCG GCATCGCACG GTAAAGCTCT TTGCCGGCGC CTTTCTCAAC ACCTTCGAAT 2800
TTCGCGGTGC CGGTGCGGTG CAGGGACTTC TGTCGGCGCT GGCCATTATC GCGGAGCTAT ACCGGACCGG CAAACGGCGC TTGCCTGATC GCGTGCCGCT 2900
GCGCTTTGTG CCGTCCGCAT GGCGGCCGTT CATCCTGCGC GATGGCATCG TCGACCGCGC CGCCTATGAA CTATGCGCTC TGTCGCAGCT ACGTGAGCGG 3000
CTGCGAGCGG GAGACATATG GGTCGCGGGC AGCCGCCAGT TTCGCGATTT CGACAGCTAC CTCATCCCAC CGGCCACCTA TGCGGCGCTT CGCGAGAAGG 3100
GACCACTGCC GCTCGCCATC GAAACGGATT TCGAGCGCCA TATTGAGGAA AGGCGCACCA GGCTCGACAC GGCCATCGAA CAGGTAACGG TCCTCGCGCG 3200
ACAAGGCGAG CTGCCCCAGG TCAGGCTTGA CGAAAACGGC CTCATCATCT CGCCGCTGAA GGCGGCAACG CCGCCCGCTA CCGAAATTGC CCGTCGCGCA 3300
GCCTATGATC GCCTGCCACG GGTGAAGATC ACCGACCTGC TGCTTGAGGT CGATGCTTGG ACCGGGTTCA GCGAATGCTT CATCCACCGA CGTTCGGGCC 3400
GGGAGGCCGA CGATCGCAAT GCGCTTCTCA CCGTCATCCT CGCCGATGGC ATCAATCTCG GCCTCACGCG CATGGCGGAA ACCTGCCGGG GCGCAAGTCT 3500
GCGCCAGCTT GCTCACTTGC ATGACTGGCA CATCAGCGAG GCCGCCTATG GCGAGGCGCT GGGAAGGCTG ATCAACGCCC ATCGCACCAT GCCGCTCGCC 3600
GCGCTGTGGG GAGACGGCAC CACCTCGTCG AGCGACGGAC AGCAGTTTCA TGCCGGCGGT CGTGGGGCCG CGATCGGTGA CATCAACGCG CGCAGCGGCA 3700
ACGAACCGGG CGTCGCCTTC TACACCCATG TCTCGGATCG ATATGATCCC TTTGCGAGCC GGGTGATCGC GGCGACCGCA GGCGAAGCGC CCTATGTCCT 3800
GGATGGCTTG CTGTATCACC AGACCGGCAT GACGATCGAG GAGCACTACA CCGATACGGG TGGAGCATCG GACCATGTGT TCGGTCTCAT GCCCTTCTTC 3900
GGCTACCGCT TCGCGCCGCG CTTGCGCGAC ATTAAGGAGC GTCGTTTGCA CCTCCTTCCC GGCCAGGAAT CCGGCCCCTT GCTCGCCGGC ATGACGACCG 4000
AACCGATCGC ATTGGGCCAT GTCGCGGCGC ATTGGGACGA ACTGCTACGG TTCGCCACGT CGATCCGCAC CGGCACCGTC ACTGCTTCGG CGATGCTGCG 4100
CCGGCTATCC GGCTATCCGC GACAGAACGG ACTGGCCCTC GCGCTGCGCG AGCTTGGCCG CCTCGAACGC TCGATCTTCA TGCTCGACTG GCTGCGCGAC 4200
ATCGACCTGC GCCGGCGCAC CCAGGCGGGC CTCAACAAGG GCGAAGCCCG CAACGCGCTC GCCCGCGCGC TCTTCTTTAA CCAGCTCGGC GAATTGCGTG 4300
ATCGGCGGTT CGAAAACCAG ACTTATCGCG CCTCCGGCCT CAACCTGCTC GTCGCCGCCA TCATCCTGTG GAACACTCGC TATCTCGAAA TGGCGCTGGC 4400
TGACATCGGC ACGCCCGACG AGATCGCGCG CCACGTCGCG CCATTGGGCT GGGAGCATAT CTCGCTGACG GGGGACTATA GCTGGAATGT CGAAGATCGG 4500
CCCGATCCGG ATGCCTTGCG GCCGCTGCGC GCCGTCAGCT CCCTGCTCGC CGCGTGAAGT TCGCTATCCG TTCGCCCTTA GCGTGCAGAT ACGTCACTTT 4600
CGTGTAGTCA CCCC
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| ORFs |
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| Gene Name |
Associated TE |
Coordinates |
Class |
Sub Class |
Orientation |
| sdr-family |
Tn6134 |
124-912 |
Passenger Gene |
Other |
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| tnpR |
Tn6134 |
909-1517 |
Accessory Gene |
Resolvase |
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| tnpA |
Tn6134 |
1600-4557 |
Transposase |
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| Gene Name |
Protein Name |
Associated TE |
Gene Length |
Coordinates |
Strand |
| sdr-family |
Sdr-family |
Tn6134 |
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 |
Tn6134 |
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 |
Tn6134 |
2958 |
1600-4557 |
+ |
| Class: | Transposase |
| Function: | transposase activity (GO:0004803) |
| Transpoase Chemistry: | DDE |
| Comment: | uniProt accession: D4YY99 (D4YY99_SPHJU) |
Protein Sequence:
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MARRRLVSLE IWAGHYDAPL DEREIARHYT LTSDDLEIVG RRRGDATRLG FAMLLLTMRW PGRALEAGEV PPAPVLGYVA RQLGVAPDAF ADYARRDQTR
REHLVEIRRS HGFRIFDRDA FREVVAFSIP IAQTIIHPGQ MAGVIVDELR RRQILLPSSS ILEAVLRRAR QQAEQLTYEV LTNGLRPDTL QDLDDLLARR
TGQAATWLSW LRNASQSPAA RNILRLIERL AYVRALGLDR GRADMIPAST FDRLADEGSR ITPQHLGELN ALRRHATLAA TGIRLEEDLT DATLTMFDKL
LGSMVRRAEN RTRDKALKTV RELQGHLRTL TGSCRILIDA RTNGVDSLAQ IEALDWQRFA VSVEQAEVLS RPETVDRTAE LIERHRTVKL FAGAFLNTFE
FRGAGAVQGL LSALAIIAEL YRTGKRRLPD RVPLRFVPSA WRPFILRDGI VDRAAYELCA LSQLRERLRA GDIWVAGSRQ FRDFDSYLIP PATYAALREK
GPLPLAIETD FERHIEERRT RLDTAIEQVT VLARQGELPQ VRLDENGLII SPLKAATPPA TEIARRAAYD RLPRVKITDL LLEVDAWTGF SECFIHRRSG
READDRNALL TVILADGINL GLTRMAETCR GASLRQLAHL HDWHISEAAY GEALGRLINA HRTMPLAALW GDGTTSSSDG QQFHAGGRGA AIGDINARSG
NEPGVAFYTH VSDRYDPFAS RVIAATAGEA PYVLDGLLYH QTGMTIEEHY TDTGGASDHV FGLMPFFGYR FAPRLRDIKE RRLHLLPGQE SGPLLAGMTT
EPIALGHVAA HWDELLRFAT SIRTGTVTAS AMLRRLSGYP RQNGLALALR ELGRLERSIF MLDWLRDIDL RRRTQAGLNK GEARNALARA LFFNQLGELR
DRRFENQTYR ASGLNLLVAA IILWNTRYLE MALADIGTPD EIARHVAPLG WEHISLTGDY SWNVEDRPDP DALRPLRAVS 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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