Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117294
Name   oriT_pACESH0366-NDM in_silico
Organism   Klebsiella quasipneumoniae subsp. similipneumoniae strain ACESH00366hy
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP138836 (4596..5213 [-], 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_pACESH0366-NDM
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11021 GenBank   WP_004199101
Name   mobP1_SHK10_RS26885_pACESH0366-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   12875 GenBank   WP_015060057
Name   t4cp2_SHK10_RS26905_pACESH0366-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.



ID   12876 GenBank   WP_000053822
Name   t4cp2_SHK10_RS26950_pACESH0366-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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 7794..17903

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SHK10_RS26855 3224..3493 + 270 WP_001006717 hypothetical protein -
SHK10_RS26860 3483..3725 + 243 WP_000008707 hypothetical protein -
SHK10_RS26865 3819..4157 + 339 WP_001099725 hypothetical protein -
SHK10_RS26870 4232..4396 + 165 WP_000004083 hypothetical protein -
SHK10_RS26875 4393..4650 + 258 WP_004199355 hypothetical protein -
SHK10_RS26880 4991..5536 + 546 WP_001348698 DNA distortion polypeptide 1 -
SHK10_RS26885 5539..6699 + 1161 WP_004199101 MobP1 family relaxase -
SHK10_RS26890 7052..7561 + 510 WP_000455437 transcription termination/antitermination NusG family protein -
SHK10_RS26895 7794..8438 + 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
SHK10_RS26900 8422..8712 + 291 WP_000916156 TrbC/VirB2 family protein virB2
SHK10_RS26905 8737..11490 + 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
SHK10_RS26910 11500..12270 + 771 WP_000716326 type IV secretion system protein -
SHK10_RS26915 12280..12537 + 258 WP_000759841 EexN family lipoprotein -
SHK10_RS26920 12549..13604 + 1056 WP_000235886 type IV secretion system protein virB6
SHK10_RS26925 13799..14527 + 729 WP_004199085 virB8 family protein virB8
SHK10_RS26930 14533..15462 + 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
SHK10_RS26935 15459..16673 + 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
SHK10_RS26940 16675..16872 + 198 WP_000629109 DNA-binding protein -
SHK10_RS26945 16869..17903 + 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
SHK10_RS26950 17906..19741 + 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
SHK10_RS26955 19738..20130 + 393 WP_000738524 cag pathogenicity island Cag12 family protein -
SHK10_RS26960 20218..20532 + 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
SHK10_RS26965 20618..20944 + 327 WP_004208538 hypothetical protein -
SHK10_RS26970 20941..21435 + 495 WP_001215543 thermonuclease family protein -
SHK10_RS26975 21518..22780 + 1263 WP_000517490 ATP-binding protein -

Host bacterium

ID   17727 GenBank   NZ_CP138836
Plasmid name   pACESH0366-NDM Incompatibility group   IncX3
Plasmid size   53624 bp Coordinate of oriT [Strand]   4596..5213 [-]
Host baterium   Klebsiella quasipneumoniae subsp. similipneumoniae strain ACESH00366hy

Cargo genes

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