Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100672
Name   oriT_pD10-A in_silico
Organism   Escherichia coli strain D10
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP010158 (28700..28989 [+], 290 nt)
oriT length   290 nt
IRs (inverted repeats)      225..232, 235..242 n  (GCAAAAAC..GTTTTTGC)
Location of nic site      251..252
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 290 nt

>oriT_pD10-A
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   744 GenBank   WP_077897617
Name   TraI_pD10-A insolico UniProt ID   _
Length   952 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 952 a.a.        Molecular weight: 104516.80 Da        Isoelectric Point: 6.4857

>WP_077897617.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMVEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMTFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLIIDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAVSVKAGEESVAQVSGVREQAMLTQTIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGAYFHERRSLNNFHRDRVITFEQIAE

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3496..29551

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RG43_RS27015 (RG43_25485) 2862..3089 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
RG43_RS27020 (RG43_25490) 3089..3487 + 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
RG43_RS27025 (RG43_25495) 3496..5649 - 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
RG43_RS29325 (RG43_25500) 5902..6633 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
RG43_RS29330 (RG43_25505) 6658..7179 - 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
RG43_RS27035 (RG43_25510) 7212..10028 - 2817 WP_073507088 conjugal transfer mating-pair stabilization protein TraG traG
RG43_RS27040 (RG43_25515) 10025..11398 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
RG43_RS27045 (RG43_25520) 11398..11760 - 363 WP_073507089 P-type conjugative transfer protein TrbJ -
RG43_RS27050 (RG43_25525) 11690..12235 - 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
RG43_RS27055 (RG43_25530) 12222..12506 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
RG43_RS27060 (RG43_25535) 12587..12901 + 315 WP_000415567 hypothetical protein -
RG43_RS27065 (RG43_25540) 12903..13250 - 348 WP_001287913 conjugal transfer protein TrbA -
RG43_RS27070 (RG43_25545) 13266..14009 - 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
RG43_RS27075 (RG43_25550) 14002..14259 - 258 WP_000864318 conjugal transfer protein TrbE -
RG43_RS27080 (RG43_25555) 14286..16094 - 1809 WP_000821847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
RG43_RS27085 (RG43_25560) 16091..16729 - 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
RG43_RS27090 (RG43_25565) 16738..17730 - 993 WP_000830187 conjugal transfer pilus assembly protein TraU traU
RG43_RS27095 (RG43_25570) 17727..18359 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
RG43_RS27100 (RG43_25575) 18356..18742 - 387 WP_000097319 type-F conjugative transfer system protein TrbI -
RG43_RS27105 (RG43_25580) 18739..21366 - 2628 WP_001064247 type IV secretion system protein TraC virb4
RG43_RS27110 (RG43_25585) 21526..21747 - 222 WP_001278689 conjugal transfer protein TraR -
RG43_RS27115 (RG43_25590) 21882..22397 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
RG43_RS27120 (RG43_25595) 22394..22645 - 252 WP_001038342 conjugal transfer protein TrbG -
RG43_RS27125 (RG43_25600) 22657..22854 - 198 WP_001324648 conjugal transfer protein TrbD -
RG43_RS27130 (RG43_25605) 22841..23431 - 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
RG43_RS27135 (RG43_25610) 23421..24848 - 1428 WP_000146692 F-type conjugal transfer pilus assembly protein TraB traB
RG43_RS27140 (RG43_25615) 24848..25576 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
RG43_RS27145 (RG43_25620) 25563..26129 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
RG43_RS27150 (RG43_25625) 26151..26462 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
RG43_RS27155 (RG43_25630) 26477..26842 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
RG43_RS27160 (RG43_25635) 26875..27270 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
RG43_RS27165 (RG43_25640) 27369..28058 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
RG43_RS27170 (RG43_25645) 28245..28628 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
RG43_RS27175 (RG43_25650) 28949..29551 + 603 WP_000243709 transglycosylase SLT domain-containing protein virB1
RG43_RS27180 (RG43_25655) 29848..30669 - 822 WP_001234469 DUF932 domain-containing protein -
RG43_RS27185 (RG43_25660) 30791..31077 - 287 Protein_36 hypothetical protein -
RG43_RS30195 (RG43_25665) 31102..31248 - 147 WP_349356976 single-stranded DNA-binding protein -
RG43_RS29950 31230..31403 + 174 Protein_38 hypothetical protein -
RG43_RS29955 31401..31631 - 231 WP_001426396 hypothetical protein -
RG43_RS27200 (RG43_25675) 31851..31976 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
RG43_RS29960 31918..32067 - 150 Protein_41 plasmid maintenance protein Mok -
RG43_RS29540 (RG43_25680) 32089..32277 + 189 WP_001299721 hypothetical protein -
RG43_RS27210 (RG43_25685) 32246..33008 - 763 Protein_43 plasmid SOS inhibition protein A -
RG43_RS27215 (RG43_25690) 33005..33439 - 435 WP_000845895 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   1132 GenBank   NZ_CP010158
Plasmid name   pD10-A Incompatibility group   IncFIB
Plasmid size   128612 bp Coordinate of oriT [Strand]   28700..28989 [+]
Host baterium   Escherichia coli strain D10

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -