Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103561
Name   oriT_pHD7296-NDM in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain HD7296
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_ON209140 (42218..42835 [+], 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_pHD7296-NDM
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2665 GenBank   WP_004199101
Name   Relaxase_OZD79_RS00260_pHD7296-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   2483 GenBank   WP_000053822
Name   t4cp2_OZD79_RS00190_pHD7296-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   2484 GenBank   WP_015060057
Name   t4cp2_OZD79_RS00235_pHD7296-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: 29528..39637

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OZD79_RS00165 24651..25913 - 1263 WP_000517490 ATP-binding protein -
OZD79_RS00170 25996..26490 - 495 WP_001215543 thermonuclease family protein -
OZD79_RS00175 26487..26813 - 327 WP_004208538 hypothetical protein -
OZD79_RS00180 26899..27213 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
OZD79_RS00185 27301..27693 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
OZD79_RS00190 27690..29525 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
OZD79_RS00195 29528..30562 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
OZD79_RS00200 30559..30756 - 198 WP_000629109 DNA-binding protein -
OZD79_RS00205 30758..31972 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
OZD79_RS00210 31969..32898 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
OZD79_RS00215 32904..33632 - 729 WP_004199085 type IV secretion system protein virB8
OZD79_RS00220 33827..34882 - 1056 WP_000235886 type IV secretion system protein virB6
OZD79_RS00225 34894..35151 - 258 WP_000759841 EexN family lipoprotein -
OZD79_RS00230 35161..35931 - 771 WP_000716326 type IV secretion system protein -
OZD79_RS00235 35941..38694 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
OZD79_RS00240 38719..39009 - 291 WP_000916156 TrbC/VirB2 family protein virB2
OZD79_RS00245 38993..39637 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
OZD79_RS00250 39683..39919 - 237 WP_001348696 hypothetical protein -
OZD79_RS00255 39870..40520 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
OZD79_RS00260 40732..41892 - 1161 WP_004199101 MobP1 family relaxase -
OZD79_RS00265 41895..42440 - 546 WP_001348698 DNA distortion polypeptide 1 -
OZD79_RS00270 42781..43038 - 258 WP_004199355 hypothetical protein -
OZD79_RS00275 43035..43187 - 153 WP_162542717 hypothetical protein -
OZD79_RS00280 43274..43612 - 339 WP_001099725 hypothetical protein -
OZD79_RS00285 43706..43948 - 243 WP_000008707 hypothetical protein -
OZD79_RS00290 43938..44219 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   4004 GenBank   NZ_ON209140
Plasmid name   pHD7296-NDM Incompatibility group   IncX3
Plasmid size   46989 bp Coordinate of oriT [Strand]   42218..42835 [+]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain HD7296

Cargo genes

Drug resistance gene   blaNDM-5
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -