Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115233
Name   oriT_pCf.1_2 in_silico
Organism   Citrobacter freundii strain Cf.1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OK649970 (203537..203791 [-], 255 nt)
oriT length   255 nt
IRs (inverted repeats)      153..158, 160..165  (AAAAGT..ACTTTT)
 122..130, 135..143  (TTAAGGCTT..AAGCCTTAA)
 49..55, 60..66  (GAATTTT..AAAATTC)
Location of nic site      78..79
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 255 nt

>oriT_pCf.1_2
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9734 GenBank   WP_258238005
Name   mobH_NX086_RS01075_pCf.1_2 insolico UniProt ID   _
Length   1021 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1021 a.a.        Molecular weight: 114759.56 Da        Isoelectric Point: 4.6282

>WP_258238005.1 MobH family relaxase [Citrobacter freundii]
MIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPTGIQTFNEQSILSLYREKLHSISMMLAISD
SDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGGLLSHSLEVAILSLKNAHHSELRPIGYQDE
EVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWTPSSQSLLDWARENDVVEYEIHWRKRIHNQ
HNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYTDGNDFLSKCVRTADFYSTGTDLNVLRDPI
MGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGEVYLNENAFLDFVLNDFELHKYNFPQGEAG
KTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFRNGIGKLEFYNLLKLRWIGLIFDSYKIPDS
VPGLFSVNANKDFIYIDEQKKVTEYRRPVPGRDVITKITDTVETAVLKVNDLGRSSASIDVDIHSKKNEG
SSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESEDESAKDTESHVLVNQLHELLLSAPLSNDY
IVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGSLDGMWIVRDIDDLRLVQLGDNCAGFQLTY
HEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLELPPPRVNAVEEHSGDVEYHGTDSASATGP
LKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVGSCATSSSVHNEKLLSEPSELPELNREQNA
DPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAAATSVMASEEPALPPVLEESNGEHAPTDAK
GHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPASPVSGHNLNSKVFASTESDQNGEFSLISEG
DVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTLYLTQSCVEKFGSQLEAQDLFNKLPQYLVN
SGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(79-275)


  Protein structure



No available structure.




T4CP

ID   11353 GenBank   WP_001284073
Name   traD_NX086_RS01080_pCf.1_2 insolico UniProt ID   _
Length   694 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 694 a.a.        Molecular weight: 78123.91 Da        Isoelectric Point: 8.0177

>WP_001284073.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANDTLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(406-609)

AAA-like domain (AAA_10)

(199-249)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2396..11636

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NX086_RS00005 1..876 + 876 WP_000594611 RepB family plasmid replication initiator protein -
NX086_RS00010 2025..2378 + 354 WP_000423602 hypothetical protein -
NX086_RS00015 2396..2746 + 351 WP_001447770 type IV conjugative transfer system protein TraL traL
NX086_RS00020 2758..3546 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
NX086_RS00025 3546..4817 + 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
NX086_RS00030 4819..5280 + 462 WP_000521242 plasmid transfer protein HtdO -
NX086_RS00035 5270..6625 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
NX086_RS00040 6633..7115 + 483 WP_058685169 hypothetical protein -
NX086_RS00045 7234..7986 + 753 WP_182911723 protein-disulfide isomerase HtdT -
NX086_RS00050 7996..8946 + 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
NX086_RS00055 8955..11636 + 2682 WP_000387412 TraC family protein virb4
NX086_RS00065 15417..15578 + 162 WP_001371949 hypothetical protein -

Host bacterium

ID   15668 GenBank   NZ_OK649970
Plasmid name   pCf.1_2 Incompatibility group   IncHI2A
Plasmid size   261511 bp Coordinate of oriT [Strand]   203537..203791 [-]
Host baterium   Citrobacter freundii strain Cf.1

Cargo genes

Drug resistance gene   blaTEM-1B, aac(3)-IId, mph(A), tet(D), dfrA12, aadA2, aph(3')-Ia, qepA1, qnrS1, floR, sul2, mcr-9
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE, rcnR/yohL, ncrC, pcoE, pcoS
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -