Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102986
Name   oriT_p45-IncX3 in_silico
Organism   Klebsiella pneumoniae strain ST512
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT362706 (58432..59049 [+], 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_p45-IncX3
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2240 GenBank   WP_004199101
Name   Relaxase_HTF84_RS00300_p45-IncX3 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   1931 GenBank   WP_000053822
Name   t4cp2_HTF84_RS00230_p45-IncX3 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   1932 GenBank   WP_000108726
Name   t4cp2_HTF84_RS00275_p45-IncX3 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: 104822.73 Da        Isoelectric Point: 6.2666

>WP_000108726.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacterales]
MSTVFKGLTRPALIRGLGVPLYPFLGMCVICVLLGVWIHEAMYALILPGWYAIKRVTKIDERFFDLLYLR
MQIKGNPLANKRFNAVHYAGSSYDAVDISKVDNFMKLKDQSSLEELIPYSSHITDNLIVTRNHDLLATWQ
IDGAYFECVDEADLALLTDQLNTLIRSFDGKPVTFYTHRIRVRKEVRPVFDSKIPFVNRVMNDYYESLSA
AEYFENKLYLTVCYKPFSAEDKVTHFLSRKKGNKNIFEEPINDMNEICGRLSTYLSRFHSRRLGLYEENN
IVYSEQLTLFQKLLSGRWQKVRVTNSPFYTYLGGKDLFFGNDAGQITASDHARYFRCIEIKDYFQETDAG
IFDALMYLPVEYVQTSSFTPIDKQSAIKALDDQIDKLEMTDDAAKSLLADLKVGLDMVSSGYISFGKSHQ
TLIVYADSPERLVKDTNIVTTTLEDLGLIVTYSTLSLGAAYFAQLPGNYTLRPRLSSISSLNFAEMESFH
NFFTGKEKGNTWGNNLITLGGSGNDIYNLNYHMTTEHQNYFGKNPTLGHTEILGTSNVGKTVVMMTKAFA
AQQFGTPESFPPERKLKKLTTVFFDKDRAAEPGIRSMGGAYFRVKEGEPTGWNPAALPPTKRNISFMKDL
VRLLCTLNSEPLDDYQNRLISDAVERLMQRSNRSYPISKLRPLILEPDDTETRRHGLKARLNAWVQGGEF
GWVFDNPDDTFDVDNLDVFGIDGTEFLDNKVLSSAASFYLIYRVTMLADGRRLLIYMDEFWQWINNEAFR
DFVYNKLKTARKLDMVLVVATQSPDELIKSPIAAAVREQCATHIYLANPKAKRSEYVDELEVRELYFDKI
KAIDPLSRQFLVVKNPQRKGESDDFAAFARLDLGKAAYYLPVLSASKPQLELFDEIWKEGMKPEEWLDTY
LERANLI

  Protein domains


Predicted by InterproScan.

Type IV secretory pathway, VirB3-like protein (VirB3)

(2-83)

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

(272-474)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 45743..55852

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTF84_RS00205 40866..42128 - 1263 WP_000517490 ATP-binding protein -
HTF84_RS00210 42211..42705 - 495 WP_001215543 thermonuclease family protein -
HTF84_RS00215 42702..43028 - 327 WP_004208538 hypothetical protein -
HTF84_RS00220 43114..43428 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTF84_RS00225 43516..43908 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTF84_RS00230 43905..45740 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTF84_RS00235 45743..46777 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTF84_RS00240 46774..46971 - 198 WP_000629109 DNA-binding protein -
HTF84_RS00245 46973..48187 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTF84_RS00250 48184..49113 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTF84_RS00255 49119..49847 - 729 WP_004199085 type IV secretion system protein virB8
HTF84_RS00260 50042..51097 - 1056 WP_000235886 type IV secretion system protein virB6
HTF84_RS00265 51109..51366 - 258 WP_000759841 EexN family lipoprotein -
HTF84_RS00270 51376..52146 - 771 WP_000716326 type IV secretion system protein -
HTF84_RS00275 52156..54909 - 2754 WP_000108726 VirB3 family type IV secretion system protein virb4
HTF84_RS00280 54934..55224 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTF84_RS00285 55208..55852 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTF84_RS00290 55898..56134 - 237 WP_001348696 hypothetical protein -
HTF84_RS00295 56085..56594 - 510 WP_000455437 transcription termination/antitermination NusG family protein -
HTF84_RS00300 56946..58106 - 1161 WP_004199101 MobP1 family relaxase -
HTF84_RS00305 58109..58654 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTF84_RS00310 58995..59252 - 258 WP_004199355 hypothetical protein -
HTF84_RS00315 59249..59401 - 153 WP_162542717 hypothetical protein -
HTF84_RS00320 59488..59826 - 339 WP_001099725 hypothetical protein -
HTF84_RS00325 59920..60162 - 243 WP_000008707 hypothetical protein -
HTF84_RS00330 60152..60433 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   3429 GenBank   NZ_KT362706
Plasmid name   p45-IncX3 Incompatibility group   IncX3
Plasmid size   63203 bp Coordinate of oriT [Strand]   58432..59049 [+]
Host baterium   Klebsiella pneumoniae strain ST512

Cargo genes

Drug resistance gene   blaSHV-182, blaKPC-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -