Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121089
Name   oriT_pSh8213-1 in_silico
Organism   Staphylococcus hominis strain Sh8213
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP142856 (39401..39436 [+], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      4..10, 14..20  (GCGAACG..CGTTCGC)
Location of nic site      29..30
Conserved sequence flanking the
  nic site    		  GTGCGCCCTT
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pSh8213-1
CACGCGAACGGAACGTTCGCATAAGTGCGCCCTTAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13316 GenBank   WP_030061449
Name   MobA_MobL_VXJ98_RS11870_pSh8213-1 insolico UniProt ID   A0A848EWD6
Length   665 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 665 a.a.        Molecular weight: 78725.60 Da        Isoelectric Point: 5.1613

>WP_030061449.1 MULTISPECIES: MobA/MobL family protein [Staphylococcus]
MAMYHFQNKFVSKANGQSATAKAAYNSASRIKDFKENEFKDYSNKQCDYSEILLPNNADDKFKDREYLWN
KVNDVENRKNSQVAREIIIGLPNEFDPNSNIELAKEFAESLSNEGMIVDLNIHKINDENPHAHLLCTLRG
LDKNNEFEPKRKGNDYIRDWNTKDKHNEWRKRWETVQNKHLEMNGFSVRVSADSYKKQNIDLEPTKKEGW
KARKFEDETGKKSSISKHNESIKKRNQQKINKMFDEVDDMKSHKLNAFSYMDKSDSTTLKDMAKDLKIYV
TPINMYEENERLYDLKQKTALITDDEDRLNKIENIEDRQKKLESINEVFEKQAGIFFDKNYPEQALNYSD
DEKIFITRTILNDRDVLPANHELEDIVKEKRIKEAQISLNTVIGNRDISIESIEKESNFFADKLSNILDK
NNLSFDDVLENKHEGIEDSLKIDYYTSKLEVLRNAENTLEDYYDVQIKELFTDDEDYKAFNEVTDIKEKQ
QLIDFKTYHGTENTLEMLETGNFIPKYSDEDRKYITEQVKLLQEKEFKPNKNQHDKFVFGAIQKKLLNEY
DFDYSDNNDLKHLYQESNEVGDETSKDNIEEFYEGNDILVDKETYNNYNRKQQAYGLVNAGLDSMIFNFN
EIFRERMPKYINNQYKGKNHSKQRHELKNKRGMHL

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-216)

Nicking enzyme C-terminal middle helical domain (NES_C_h)

(265-359)


  Protein structure


Source ID Structure
AlphaFold DB A0A848EWD6


T4CP

ID   15605 GenBank   WP_030061486
Name   t4cp2_VXJ98_RS11755_pSh8213-1 insolico UniProt ID   _
Length   548 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 548 a.a.        Molecular weight: 62899.75 Da        Isoelectric Point: 5.9714

>WP_030061486.1 MULTISPECIES: VirD4-like conjugal transfer protein, CD1115 family [Staphylococcaceae]
MTTLLGELESKATSINKKNLVIQDFDTKCPNRNIFVVGGPGSFKSAGYVIPNVIVKNQQSIVVTDPSGEV
YEKTANIKRMQGYDVRVVNFKNFLASDRQNFFDYIDKDSDCSIVAELIIKSAGDSKMNKDVWYKSSVGLL
NSLLLYAKYEFEPEKRTIGNIIKFIQNNKPNHDDEGSVELDNRFNELPKDHPARESYEFGFAVSEGRTRA
SIILTFVADLRNYIDNEIRSYTSDSDFDLRDVGLRKTIIYVMLPVLGNTVQSLSSLFFSQMFQQLYRLGD
ENGARLPVPVDFLLDEWPNIGAIPDYEETLATCRKYGISITTIVQSISQAVDKYNKDKANAIIGNHAVIL
CLGNVNNDTAKYIKEELGNATVEFETSSEGSSSGKDSRSKSSNKNVSYTGRALLNEDEISNMQQDKAILI
TKNRNPKIIKKLAYFKMFPNLTETYIAPQNEYKRKKNQSMIDKHNRLREEWDKKQEKIKQQKLEEYKEEQ
RQKELEEEQQAQEEQQNEEVKESKSKNEEQQEDKKDEQQKINDSKKAFYEKLKQKQAK

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(3-462)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5307..16910

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
VXJ98_RS11675 (VXJ98_11675) 377..610 + 234 WP_000602212 hypothetical protein -
VXJ98_RS11680 (VXJ98_11680) 873..1913 + 1041 WP_000073390 hypothetical protein -
VXJ98_RS11685 (VXJ98_11685) 1916..2245 + 330 WP_030061459 plasmid segregation protein ParR -
VXJ98_RS11690 (VXJ98_11690) 2249..2509 - 261 WP_001008214 helix-turn-helix domain-containing protein -
VXJ98_RS11695 (VXJ98_11695) 2892..3851 + 960 WP_030061463 replication initiator protein A -
VXJ98_RS11700 (VXJ98_11700) 3955..4143 - 189 WP_030061465 hypothetical protein -
VXJ98_RS11705 (VXJ98_11705) 4316..5290 + 975 WP_030061467 conjugative transfer protein TrsA -
VXJ98_RS11710 (VXJ98_11710) 5307..5624 + 318 WP_030061469 CagC family type IV secretion system protein virB2
VXJ98_RS11715 (VXJ98_11715) 5683..6090 + 408 WP_030061471 hypothetical protein trsC
VXJ98_RS11720 (VXJ98_11720) 6077..6760 + 684 WP_030061473 TrsD/TraD family conjugative transfer protein trsD
VXJ98_RS11725 (VXJ98_11725) 6781..8793 + 2013 WP_030061475 VirB4 family type IV secretion system protein virb4
VXJ98_RS11730 (VXJ98_11730) 8805..10085 + 1281 WP_030061477 hypothetical protein trsF
VXJ98_RS11735 (VXJ98_11735) 10103..11179 + 1077 WP_031921304 CHAP domain-containing protein trsG
VXJ98_RS11740 (VXJ98_11740) 11189..11674 + 486 WP_000735570 TrsH/TraH family protein -
VXJ98_RS11745 (VXJ98_11745) 11690..13792 + 2103 WP_030061483 DNA topoisomerase III -
VXJ98_RS11750 (VXJ98_11750) 13808..14272 + 465 WP_000715271 hypothetical protein trsJ
VXJ98_RS11755 (VXJ98_11755) 14269..15915 + 1647 WP_030061486 VirD4-like conjugal transfer protein, CD1115 family -
VXJ98_RS11760 (VXJ98_11760) 15993..16910 + 918 WP_030061488 conjugal transfer protein TrbL family protein trsL
VXJ98_RS11765 (VXJ98_11765) 16927..17322 + 396 WP_000608969 single-stranded DNA-binding protein -
VXJ98_RS11770 (VXJ98_11770) 17379..18110 + 732 WP_000869299 hypothetical protein -
VXJ98_RS11775 (VXJ98_11775) 18147..18770 + 624 WP_030061493 hypothetical protein -
VXJ98_RS11780 (VXJ98_11780) 18786..19400 + 615 WP_030061494 hypothetical protein -
VXJ98_RS11785 (VXJ98_11785) 19469..19735 + 267 WP_030061495 hypothetical protein -
VXJ98_RS11790 (VXJ98_11790) 19821..20993 + 1173 WP_032495458 IS256-like element ISEnfa4 family transposase -
VXJ98_RS11795 (VXJ98_11795) 21038..21508 + 471 WP_032495642 MerR family transcriptional regulator -

Host bacterium

ID   21517 GenBank   NZ_CP142856
Plasmid name   pSh8213-1 Incompatibility group   -
Plasmid size   39524 bp Coordinate of oriT [Strand]   39401..39436 [+]
Host baterium   Staphylococcus hominis strain Sh8213

Cargo genes

Drug resistance gene   cfr, aac(6')-aph(2'')
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA21