Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121127
Name   oriT_pF3221-NDM in_silico
Organism   Citrobacter freundii strain F3221
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137202 (223846..224100 [+], 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_pF3221-NDM
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13337 GenBank   WP_012477394
Name   mobH_R5Q27_RS27195_pF3221-NDM insolico UniProt ID   A0A2Z2E7B6
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118067.47 Da        Isoelectric Point: 4.6347

>WP_012477394.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDVITKITDT
VETAVLKVNDLGRSSASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVG
SCATSSSVHNEKLLSEPSELPELNREQNADPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFASTESDQNGEFSLISEGDVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure


Source ID Structure
AlphaFold DB A0A2Z2E7B6


T4CP

ID   15626 GenBank   WP_284237523
Name   traD_R5Q27_RS27190_pF3221-NDM 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: 78139.95 Da        Isoelectric Point: 8.0177

>WP_284237523.1 conjugative transfer system coupling protein TraD [Citrobacter freundii]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANDTLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQILIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

  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: 137825..147065

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R5Q27_RS26725 (R5Q27_26725) 135116..135277 - 162 WP_001371949 hypothetical protein -
R5Q27_RS26730 (R5Q27_26730) 137825..140506 - 2682 WP_000387412 TraC family protein virb4
R5Q27_RS26735 (R5Q27_26735) 140515..141465 - 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
R5Q27_RS26740 (R5Q27_26740) 141475..142227 - 753 WP_182911723 protein-disulfide isomerase HtdT -
R5Q27_RS26745 (R5Q27_26745) 142346..142828 - 483 WP_000377632 hypothetical protein -
R5Q27_RS26750 (R5Q27_26750) 142836..144191 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
R5Q27_RS26755 (R5Q27_26755) 144181..144642 - 462 WP_000521242 plasmid transfer protein HtdO -
R5Q27_RS26760 (R5Q27_26760) 144644..145915 - 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
R5Q27_RS26765 (R5Q27_26765) 145915..146703 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
R5Q27_RS26770 (R5Q27_26770) 146715..147065 - 351 WP_001447770 type IV conjugative transfer system protein TraL traL
R5Q27_RS26775 (R5Q27_26775) 147083..147436 - 354 WP_000423602 hypothetical protein -
R5Q27_RS26780 (R5Q27_26780) 148585..149460 - 876 WP_000594611 RepB family plasmid replication initiator protein -
R5Q27_RS26785 (R5Q27_26785) 149937..150989 + 1053 WP_001065778 hypothetical protein -
R5Q27_RS26790 (R5Q27_26790) 151009..151209 + 201 WP_000594930 hypothetical protein -
R5Q27_RS26795 (R5Q27_26795) 151206..151922 + 717 WP_000838219 zinc finger-like domain-containing protein -

Host bacterium

ID   21555 GenBank   NZ_CP137202
Plasmid name   pF3221-NDM Incompatibility group   IncHI2A
Plasmid size   333190 bp Coordinate of oriT [Strand]   223846..224100 [+]
Host baterium   Citrobacter freundii strain F3221

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, sul1, qacE, ARR-3, catB3, blaOXA-1, blaNDM-1, blaNDM-18
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -