Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113929
Name   oriT_pD36-1 in_silico
Organism   Citrobacter freundii strain D36-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MF083142 (170096..170349 [+], 254 nt)
oriT length   254 nt
IRs (inverted repeats)      152..157, 159..164  (AAAAGT..ACTTTT)
 121..129, 134..142  (TTAAGGCTT..AAGCCTTAA)
 50..55, 59..64  (AATTTT..AAAATT)
Location of nic site      77..78
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 254 nt

>oriT_pD36-1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8943 GenBank   WP_000980119
Name   mobH_HTN67_RS00850_pD36-1 insolico UniProt ID   A0A0H3VVI8
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118035.42 Da        Isoelectric Point: 4.6054

>WP_000980119.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDT
VETAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVG
SCATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure


Source ID Structure
AlphaFold DB A0A0H3VVI8


T4CP

ID   10387 GenBank   WP_087879520
Name   traD_HTN67_RS00845_pD36-1 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: 78200.00 Da        Isoelectric Point: 8.0177

>WP_087879520.1 conjugative transfer system coupling protein TraD [Citrobacter freundii]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANETLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAVASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKFH

  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: 89216..98423

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTN67_RS00420 89216..91897 - 2682 WP_000387412 TraC family protein virb4
HTN67_RS00425 91906..92856 - 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
HTN67_RS00430 92866..93618 - 753 WP_182911723 protein-disulfide isomerase HtdT -
HTN67_RS00435 93737..94219 - 483 WP_000377632 hypothetical protein -
HTN67_RS00440 94227..95582 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
HTN67_RS00445 95572..96033 - 462 WP_000521242 plasmid transfer protein HtdO -
HTN67_RS00450 96035..97306 - 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
HTN67_RS00455 97306..98094 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
HTN67_RS00460 98106..98456 - 351 WP_001447770 type IV conjugative transfer system protein TraL -
HTN67_RS00465 98474..98827 - 354 WP_000423602 hypothetical protein -
HTN67_RS00470 99976..100851 - 876 WP_000594611 RepB family plasmid replication initiator protein -
HTN67_RS00475 101328..102380 + 1053 WP_001065778 hypothetical protein -
HTN67_RS00480 102400..102600 + 201 WP_000594930 hypothetical protein -
HTN67_RS00485 102597..103313 + 717 WP_000838219 zinc finger-like domain-containing protein -

Host bacterium

ID   14364 GenBank   NZ_MF083142
Plasmid name   pD36-1 Incompatibility group   IncHI2A
Plasmid size   188310 bp Coordinate of oriT [Strand]   170096..170349 [+]
Host baterium   Citrobacter freundii strain D36-1

Cargo genes

Drug resistance gene   mcr-1.1
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -