Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120437
Name   oriT_p3-L2724hy-NDM-1 in_silico
Organism   Citrobacter portucalensis strain L2724hy
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP136604 (49476..50093 [+], 618 nt)
oriT length   618 nt
IRs (inverted repeats)      589..594, 608..613  (TCCATG..CATGGA)
 592..597, 602..607  (ATGCCC..GGGCAT)
 520..527, 530..537  (CCTCCCGT..ACGGGAGG)
 455..460, 464..469  (ATTCGC..GCGAAT)
 197..202, 208..213  (TTCAAT..ATTGAA)
 85..90, 96..101  (TGCTTT..AAAGCA)
Location of nic site      315..316
Conserved sequence flanking the
  nic site    		  TCCTGCATCG
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 618 nt

>oriT_p3-L2724hy-NDM-1
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGTATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12872 GenBank   WP_004199101
Name   mobP1_RY846_RS27075_p3-L2724hy-NDM-1 insolico UniProt ID   A0A515HL38
Length   386 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 386 a.a.        Molecular weight: 44388.82 Da        Isoelectric Point: 10.6017

>WP_004199101.1 MULTISPECIES: MobP1 family relaxase [Enterobacterales]
MGVYVDKEFRVKRKSSEAGRKSAFAHKVKNGGKNYQRNVQERINRKGASKEVVVKISGGAITRQGVRNSI
DYMSRESELPVMSESGQVWKGDEIQEAKEHMIDRANDPQNVFDDKGKENKKVTQNIVFSPPVSAKVKPED
LLESVRKTMNKKYPNHRFVLGYHNDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKMKGYD
VKATHKQQHGLNQSIKDAHKTAPKRQKGVYEVVDVGYDHYQNDKTKPKQHFIKLKTLNKGVEKTYWGADF
GELTTRENVKKGDLVKLKKLGQKEVKIPALDKNGVQHGWKTAHRNEWQLENLGVKGIDRISSSSKELVLN
SAEMIKKQQLQMRNFSQIKQSMIQSEQKVKIGIRLG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(90-240)


  Protein structure


Source ID Structure
AlphaFold DB A0A515HL38


T4CP

ID   15122 GenBank   WP_000053822
Name   t4cp2_RY846_RS27005_p3-L2724hy-NDM-1 insolico UniProt ID   _
Length   611 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 611 a.a.        Molecular weight: 69204.04 Da        Isoelectric Point: 7.4342

>WP_000053822.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacterales]
MSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREKLLGNKVYLLDPFNSKTHQFNPLF
YIDLKEESGAKDLLKLIEILFPSYGLTGAEAHFNNLAGQYWTGLAKLLHFFINYDPSWLGEFGLKPVFSI
GSVVDLYSNIDRELILSKREDLEGTKGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDMSLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGVEGAKTLMSAHPCRIIYAVSEEDDAKKIS
EKLGYITTKSTGSSKTSGRSTSKSSSESEAQRALVLPQELGTLDFKEEFIILKGENPVKAEKALYFLDPY
FMDRLMMVSPKLTELTASLNKTKKVLGVKGLKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(102-572)

  Protein structure



No available structure.



ID   15123 GenBank   WP_015060057
Name   t4cp2_RY846_RS27050_p3-L2724hy-NDM-1 insolico UniProt ID   _
Length   917 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 917 a.a.        Molecular weight: 104788.72 Da        Isoelectric Point: 6.2666

>WP_015060057.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacterales]
MSTVFKGLTRPALIRGLGVPLYPFLGMCVICVLLGVWIHEAMYALILPGWYAIKRVTKIDERFFDLLYLR
MQIKGNPLANKRFNAVHYAGSSYDAVDISKVDNFMKLKDQSSLEELIPYSSHITDNLIVTRNHDLLATWQ
IDGAYFECVDEADLALLTDQLNTLIRSFDGKPVTFYTHRIRVRKEVRPVFDSKIPFVNRVMNDYYESLSA
AEYFENKLYLTVCYKPFSAEDKVTHFLSRKKGNKNIFEEPINDMNEICGRLSTYLSRFHSRRLGLYEENN
IVYSEQLTLFQKLLSGRWQKVRVTNSPFYTYLGGKDLFFGNDAGQITASDHARYFRCIEIKDYFQETDAG
IFDALMYLPVEYVQTSSLTPIDKQSAIKALDDQIDKLEMTDDAAKSLLADLKVGLDMVSSGYISFGKSHQ
TLIVYADSPERLVKDTNIVTTTLEDLGLIVTYSTLSLGAAYFAQLPGNYTLRPRLSSISSLNFAEMESFH
NFFTGKEKGNTWGNNLITLGGSGNDIYNLNYHMTTEHQNYFGKNPTLGHTEILGTSNVGKTVVMMTKAFA
AQQFGTPESFPPERKLKKLTTVFFDKDRAAEPGIRSMGGAYFRVKEGEPTGWNPAALPPTKRNISFMKDL
VRLLCTLNSEPLDDYQNRLISDAVERLMQRSNRSYPISKLRPLILEPDDTETRRHGLKARLNAWVQGGEF
GWVFDNPDDTFDVDNLDVFGIDGTEFLDNKVLSSAASFYLIYRVTMLADGRRLLIYMDEFWQWINNEAFR
DFVYNKLKTARKLDMVLVVATQSPDELIKSPIAAAVREQCATHIYLANPKAKRSEYVDELEVRELYFDKI
KAIDPLSRQFLVVKNPQRKGESDDFAAFARLDLGKAAYYLPVLSASKPQLELFDEIWKEGMKPEEWLDTY
LERANLI

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(272-474)

Type IV secretory pathway, VirB3-like protein (VirB3)

(2-83)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36786..46895

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RY846_RS26980 (RY846_26980) 31909..33171 - 1263 WP_000517490 ATP-binding protein -
RY846_RS26985 (RY846_26985) 33254..33748 - 495 WP_001215543 thermonuclease family protein -
RY846_RS26990 (RY846_26990) 33745..34071 - 327 WP_004208538 hypothetical protein -
RY846_RS26995 (RY846_26995) 34157..34471 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
RY846_RS27000 (RY846_27000) 34559..34951 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
RY846_RS27005 (RY846_27005) 34948..36783 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
RY846_RS27010 (RY846_27010) 36786..37820 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
RY846_RS27015 (RY846_27015) 37817..38014 - 198 WP_000629109 DNA-binding protein -
RY846_RS27020 (RY846_27020) 38016..39230 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
RY846_RS27025 (RY846_27025) 39227..40156 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
RY846_RS27030 (RY846_27030) 40162..40890 - 729 WP_004199085 virB8 family protein virB8
RY846_RS27035 (RY846_27035) 41085..42140 - 1056 WP_000235886 type IV secretion system protein virB6
RY846_RS27040 (RY846_27040) 42152..42409 - 258 WP_000759841 EexN family lipoprotein -
RY846_RS27045 (RY846_27045) 42419..43189 - 771 WP_000716326 type IV secretion system protein -
RY846_RS27050 (RY846_27050) 43199..45952 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
RY846_RS27055 (RY846_27055) 45977..46267 - 291 WP_000916156 TrbC/VirB2 family protein virB2
RY846_RS27060 (RY846_27060) 46251..46895 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
RY846_RS27065 (RY846_27065) 46941..47177 - 237 WP_001348696 hypothetical protein -
RY846_RS27070 (RY846_27070) 47128..47637 - 510 WP_000455437 transcription termination/antitermination NusG family protein -
RY846_RS27075 (RY846_27075) 47990..49150 - 1161 WP_004199101 MobP1 family relaxase -
RY846_RS27080 (RY846_27080) 49153..49698 - 546 WP_001348698 DNA distortion polypeptide 1 -
RY846_RS27085 (RY846_27085) 50039..50296 - 258 WP_004199355 hypothetical protein -
RY846_RS27090 (RY846_27090) 50293..50457 - 165 WP_000004083 hypothetical protein -
RY846_RS27095 (RY846_27095) 50532..50870 - 339 WP_001099725 hypothetical protein -
RY846_RS27100 (RY846_27100) 50964..51206 - 243 WP_000008707 hypothetical protein -
RY846_RS27105 (RY846_27105) 51196..51465 - 270 WP_001006717 hypothetical protein -

Host bacterium

ID   20866 GenBank   NZ_CP136604
Plasmid name   p3-L2724hy-NDM-1 Incompatibility group   IncX3
Plasmid size   54000 bp Coordinate of oriT [Strand]   49476..50093 [+]
Host baterium   Citrobacter portucalensis strain L2724hy

Cargo genes

Drug resistance gene   blaSHV-12, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -