Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103563
Name   oriT_pHD8763-NDM in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain HD8763
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_ON209135 (40633..41250 [+], 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_pHD8763-NDM
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2667 GenBank   WP_004199101
Name   Relaxase_OZD75_RS00250_pHD8763-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   2487 GenBank   WP_000053822
Name   t4cp2_OZD75_RS00180_pHD8763-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   2488 GenBank   WP_015060057
Name   t4cp2_OZD75_RS00225_pHD8763-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: 27943..38052

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OZD75_RS00155 23066..24328 - 1263 WP_000517490 ATP-binding protein -
OZD75_RS00160 24411..24905 - 495 WP_001215543 thermonuclease family protein -
OZD75_RS00165 24902..25228 - 327 WP_004208538 hypothetical protein -
OZD75_RS00170 25314..25628 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
OZD75_RS00175 25716..26108 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
OZD75_RS00180 26105..27940 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
OZD75_RS00185 27943..28977 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
OZD75_RS00190 28974..29171 - 198 WP_000629109 DNA-binding protein -
OZD75_RS00195 29173..30387 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
OZD75_RS00200 30384..31313 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
OZD75_RS00205 31319..32047 - 729 WP_004199085 type IV secretion system protein virB8
OZD75_RS00210 32242..33297 - 1056 WP_000235886 type IV secretion system protein virB6
OZD75_RS00215 33309..33566 - 258 WP_000759841 EexN family lipoprotein -
OZD75_RS00220 33576..34346 - 771 WP_000716326 type IV secretion system protein -
OZD75_RS00225 34356..37109 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
OZD75_RS00230 37134..37424 - 291 WP_000916156 TrbC/VirB2 family protein virB2
OZD75_RS00235 37408..38052 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
OZD75_RS00240 38098..38334 - 237 WP_001348696 hypothetical protein -
OZD75_RS00245 38285..38935 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
OZD75_RS00250 39147..40307 - 1161 WP_004199101 MobP1 family relaxase -
OZD75_RS00255 40310..40855 - 546 WP_001348698 DNA distortion polypeptide 1 -
OZD75_RS00260 41196..41453 - 258 WP_004199355 hypothetical protein -
OZD75_RS00265 41450..41602 - 153 WP_162542717 hypothetical protein -
OZD75_RS00270 41689..42027 - 339 WP_001099725 hypothetical protein -
OZD75_RS00275 42121..42363 - 243 WP_000008707 hypothetical protein -
OZD75_RS00280 42353..42634 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   4006 GenBank   NZ_ON209135
Plasmid name   pHD8763-NDM Incompatibility group   IncX3
Plasmid size   45404 bp Coordinate of oriT [Strand]   40633..41250 [+]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain HD8763

Cargo genes

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