Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113899
Name   oriT_pEn_NDM in_silico
Organism   Enterobacter cloacae strain En_MCR4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH061381 (40968..41585 [+], 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_pEn_NDM
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8924 GenBank   WP_004199101
Name   mobP1_HTR39_RS00255_pEn_NDM 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   10364 GenBank   WP_000053822
Name   t4cp2_HTR39_RS00185_pEn_NDM 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   10365 GenBank   WP_015060057
Name   t4cp2_HTR39_RS00230_pEn_NDM 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: 28278..38387

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTR39_RS00160 23401..24663 - 1263 WP_000517490 ATP-binding protein -
HTR39_RS00165 24746..25240 - 495 WP_001215543 thermonuclease family protein -
HTR39_RS00170 25237..25563 - 327 WP_004208538 hypothetical protein -
HTR39_RS00175 25649..25963 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTR39_RS00180 26051..26443 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTR39_RS00185 26440..28275 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTR39_RS00190 28278..29312 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTR39_RS00195 29309..29506 - 198 WP_000629109 DNA-binding protein -
HTR39_RS00200 29508..30722 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTR39_RS00205 30719..31648 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTR39_RS00210 31654..32382 - 729 WP_004199085 virB8 family protein virB8
HTR39_RS00215 32577..33632 - 1056 WP_000235886 type IV secretion system protein virB6
HTR39_RS00220 33644..33901 - 258 WP_000759841 EexN family lipoprotein -
HTR39_RS00225 33911..34681 - 771 WP_000716326 type IV secretion system protein -
HTR39_RS00230 34691..37444 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
HTR39_RS00235 37469..37759 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTR39_RS00240 37743..38387 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTR39_RS00245 38433..38669 - 237 WP_001348696 hypothetical protein -
HTR39_RS00250 38620..39270 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTR39_RS00255 39482..40642 - 1161 WP_004199101 MobP1 family relaxase -
HTR39_RS00260 40645..41190 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTR39_RS00265 41531..41788 - 258 WP_004199355 hypothetical protein -
HTR39_RS00270 41785..41937 - 153 WP_162542717 hypothetical protein -
HTR39_RS00275 42024..42362 - 339 WP_001099725 hypothetical protein -
HTR39_RS00280 42456..42698 - 243 WP_000008707 hypothetical protein -
HTR39_RS00285 42688..42969 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   14334 GenBank   NZ_MH061381
Plasmid name   pEn_NDM Incompatibility group   IncX3
Plasmid size   45739 bp Coordinate of oriT [Strand]   40968..41585 [+]
Host baterium   Enterobacter cloacae strain En_MCR4

Cargo genes

Drug resistance gene   blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -