Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120589
Name   oriT_p48846_IncHI2 in_silico
Organism   Citrobacter freundii strain CF48846
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP070539 (199709..199963 [+], 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_p48846_IncHI2
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12968 GenBank   WP_001011153
Name   mobH_JW295_RS01515_p48846_IncHI2 insolico UniProt ID   A0A7M1I0G5
Length   1048 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1048 a.a.        Molecular weight: 117835.11 Da        Isoelectric Point: 4.6347

>WP_001011153.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPTGI
QTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGGLL
SHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWTPS
SQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYTDG
NDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGEVY
LNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFRNG
IGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDVITKITDTVE
TAVLKVNDLGRSSASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESEDE
SAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGSLD
GMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLELP
PPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVGSC
ATSSSVHNEKLLSEPSELPELNREQNADPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEATAT
SVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPASPV
SGHNLNSKVFASTESDQNGEFSLISEGDVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTLYL
TQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(106-302)


  Protein structure


Source ID Structure
AlphaFold DB A0A7M1I0G5


T4CP

ID   15228 GenBank   WP_001284073
Name   traD_JW295_RS01510_p48846_IncHI2 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: 102973..112213

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JW295_RS00985 (JW295_00985) 100263..100424 - 162 WP_001371949 hypothetical protein -
JW295_RS00990 (JW295_00990) 102973..105654 - 2682 WP_000387412 TraC family protein virb4
JW295_RS00995 (JW295_00995) 105663..106613 - 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
JW295_RS01000 (JW295_01000) 106623..107375 - 753 WP_182911723 protein-disulfide isomerase HtdT -
JW295_RS01005 (JW295_01005) 107494..107976 - 483 WP_000377632 hypothetical protein -
JW295_RS01010 (JW295_01010) 107984..109339 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
JW295_RS01015 (JW295_01015) 109329..109790 - 462 WP_000521242 plasmid transfer protein HtdO -
JW295_RS01020 (JW295_01020) 109792..111063 - 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
JW295_RS01025 (JW295_01025) 111063..111851 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
JW295_RS01030 (JW295_01030) 111863..112213 - 351 WP_001447770 type IV conjugative transfer system protein TraL traL
JW295_RS01035 (JW295_01035) 112231..112584 - 354 WP_000423602 hypothetical protein -
JW295_RS01040 (JW295_01040) 113733..114608 - 876 WP_000594611 RepB family plasmid replication initiator protein -
JW295_RS01045 (JW295_01045) 115085..116137 + 1053 WP_001065778 hypothetical protein -
JW295_RS01050 (JW295_01050) 116157..116357 + 201 WP_000594930 hypothetical protein -
JW295_RS01055 (JW295_01055) 116354..117070 + 717 WP_000838219 zinc finger-like domain-containing protein -

Host bacterium

ID   21018 GenBank   NZ_CP070539
Plasmid name   p48846_IncHI2 Incompatibility group   IncHI2A
Plasmid size   256303 bp Coordinate of oriT [Strand]   199709..199963 [+]
Host baterium   Citrobacter freundii strain CF48846

Cargo genes

Drug resistance gene   qacE, ARR-3, catB3, blaOXA-1, aac(6')-Ib-cr, tet(B), sul1, qnrA1
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terW, merR, merT, merP, merC, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -