Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103533
Name   oriT_pHD7807-NDM in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain HD7807
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_ON209128 (43350..43967 [+], 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_pHD7807-NDM
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2644 GenBank   WP_004199101
Name   Relaxase_OZD76_RS00265_pHD7807-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   2454 GenBank   WP_000053822
Name   t4cp2_OZD76_RS00180_pHD7807-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   2455 GenBank   WP_241836040
Name   t4cp2_OZD76_RS00225_pHD7807-NDM insolico UniProt ID   _
Length   813 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 813 a.a.        Molecular weight: 92993.66 Da        Isoelectric Point: 5.5248

>WP_241836040.1 conjugal transfer protein [Enterobacter hormaechei]
MKLKDQSSLEELIPYSSHITDNLIVTRNHDLLATWQIDGAYFECVDEADLALLTDQLNTLIRSFDGKPVT
FYTHRIRVRKEVRPVFDSKIPFVNRVMNDYYESLSAAEYFENKLYLTVCYKPFSAEDKVTHFLSRKKGNK
NIFEEPINDMNEICGRLSTYLSRFHSRRLGLYEENNIVYSEQLTLFQKLLSGRWQKVRVTNSPFYTYLGG
KDLFFGNDAGQITASDHARYFRCIEIKDYFQETDAGIFDALMYLPVEYVQTSSLTPIDKQSAIKALDDQI
DKLEMTDDAAKSLLADLKVGLDMVSSGYISFGKSHQTLIVYADSPERLVKDTNIVTTTLEDLGLIVTYST
LSLGAAYFAQLPGNYTLRPRLSSISSLNFAEMESFHNFFTGKEKGNTWGNNLITLGGSGNDIYNLNYHMT
TEHQNYFGKNPTLGHTEILGTSNVGKTVVMMTKAFAAQQFGTPESFPPERKLKKLTTVFFDKDRAAEPGI
RSMGGAYFRVKEGEPTGWNPAALPPTKRNISFMKDLVRLLCTLNSEPLDDYQNRLISDAVERLMQRSNRS
YPISKLRPLILEPDDTETRRHGLKARLNAWVQGGEFGWVFDNPDDTFDVDNLDVFGIDGTEFLDNKVLSS
AASFYLIYRVTMLADGRRLLIYMDEFWQWINNEAFRDFVYNKLKTARKLDMVLVVATQSPDELIKSPIAA
AVREQCATHIYLANPKAKRSEYVDELEVRELYFDKIKAIDPLSRQFLVVKNPQRKGESDDFAAFARLDLG
KAAYYLPVLSASKPQLELFDEIWKEGMKPEEWLDTYLERANLI

  Protein domains


Predicted by InterproScan.

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

(168-370)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 28700..40769

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OZD76_RS00155 23823..25085 - 1263 WP_000517490 ATP-binding protein -
OZD76_RS00160 25168..25662 - 495 WP_001215543 thermonuclease family protein -
OZD76_RS00165 25659..25985 - 327 WP_004208538 hypothetical protein -
OZD76_RS00170 26071..26385 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
OZD76_RS00175 26473..26865 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
OZD76_RS00180 26862..28697 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
OZD76_RS00185 28700..29734 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
OZD76_RS00190 29731..29928 - 198 WP_000629109 DNA-binding protein -
OZD76_RS00195 29930..31144 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
OZD76_RS00200 31141..32070 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
OZD76_RS00205 32076..32804 - 729 WP_004199085 type IV secretion system protein virB8
OZD76_RS00210 32999..34054 - 1056 WP_000235886 type IV secretion system protein virB6
OZD76_RS00215 34066..34323 - 258 WP_000759841 EexN family lipoprotein -
OZD76_RS00220 34333..35103 - 771 WP_000716326 type IV secretion system protein -
OZD76_RS00225 35113..37554 - 2442 WP_241836040 conjugal transfer protein virb4
OZD76_RS00230 37655..38437 - 783 WP_001317493 IS21-like element IS100kyp family helper ATPase IstB -
OZD76_RS00235 38434..39456 - 1023 WP_000255946 IS21-like element IS100 family transposase -
OZD76_RS00240 39470..39826 - 357 WP_265185415 VirB3 family type IV secretion system protein virB3
OZD76_RS00245 39851..40141 - 291 WP_000916156 TrbC/VirB2 family protein virB2
OZD76_RS00250 40125..40769 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
OZD76_RS00255 40815..41051 - 237 WP_001348696 hypothetical protein -
OZD76_RS00260 41002..41652 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
OZD76_RS00265 41864..43024 - 1161 WP_004199101 MobP1 family relaxase -
OZD76_RS00270 43027..43572 - 546 WP_001348698 DNA distortion polypeptide 1 -
OZD76_RS00275 43913..44170 - 258 WP_004199355 hypothetical protein -
OZD76_RS00280 44167..44319 - 153 WP_162542717 hypothetical protein -
OZD76_RS00285 44406..44744 - 339 WP_001099725 hypothetical protein -
OZD76_RS00290 44838..45080 - 243 WP_000008707 hypothetical protein -
OZD76_RS00295 45070..45351 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   3976 GenBank   NZ_ON209128
Plasmid name   pHD7807-NDM Incompatibility group   IncX3
Plasmid size   48121 bp Coordinate of oriT [Strand]   43350..43967 [+]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain HD7807

Cargo genes

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