Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120499
Name   oriT_p56415CZ_MCR_9 in_silico
Organism   Citrobacter freundii strain 56415CZ
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP085727 (172167..172421 [+], 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_p56415CZ_MCR_9
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12908 GenBank   WP_012477394
Name   mobH_LJU42_RS24770_p56415CZ_MCR_9 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   15159 GenBank   WP_001284073
Name   traD_LJU42_RS24765_p56415CZ_MCR_9 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: 77611..86851

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LJU42_RS24260 (LJU42_24260) 74901..75062 - 162 WP_001371949 hypothetical protein -
LJU42_RS24265 (LJU42_24265) 77611..80292 - 2682 WP_000387412 TraC family protein virb4
LJU42_RS24270 (LJU42_24270) 80301..81251 - 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
LJU42_RS24275 (LJU42_24275) 81261..82013 - 753 WP_182911723 protein-disulfide isomerase HtdT -
LJU42_RS24280 (LJU42_24280) 82132..82614 - 483 WP_000377632 hypothetical protein -
LJU42_RS24285 (LJU42_24285) 82622..83977 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
LJU42_RS24290 (LJU42_24290) 83967..84428 - 462 WP_000521242 plasmid transfer protein HtdO -
LJU42_RS24295 (LJU42_24295) 84430..85701 - 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
LJU42_RS24300 (LJU42_24300) 85701..86489 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
LJU42_RS24305 (LJU42_24305) 86501..86851 - 351 WP_001447770 type IV conjugative transfer system protein TraL traL
LJU42_RS24310 (LJU42_24310) 86869..87222 - 354 WP_000423602 hypothetical protein -
LJU42_RS24315 (LJU42_24315) 88367..89242 - 876 WP_000594611 RepB family plasmid replication initiator protein -
LJU42_RS24320 (LJU42_24320) 89719..90771 + 1053 WP_001065778 hypothetical protein -
LJU42_RS24325 (LJU42_24325) 90791..90991 + 201 WP_000594930 hypothetical protein -
LJU42_RS24330 (LJU42_24330) 90988..91704 + 717 WP_000838219 zinc finger-like domain-containing protein -

Host bacterium

ID   20928 GenBank   NZ_CP085727
Plasmid name   p56415CZ_MCR_9 Incompatibility group   IncHI2A
Plasmid size   265587 bp Coordinate of oriT [Strand]   172167..172421 [+]
Host baterium   Citrobacter freundii strain 56415CZ

Cargo genes

Drug resistance gene   aph(3')-Ia, mcr-9, catA2, sul1, qacE, ant(3'')-Ia, cmlA1, aadA2, dfrA19
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW, arsH, arsR, arsB, arsC, rcnR/yohL, ncrC, pcoE, pcoS, merR, merT, merP, merC, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -