Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108117
Name   oriT_pCS-WR3 in_silico
Organism   Cronobacter sakazakii strain NMI5563_17
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT759838 (38934..39551 [+], 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_pCS-WR3
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5444 GenBank   WP_004199101
Name   mobP1_KBP74_RS00250_pCS-WR3 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   5786 GenBank   WP_000053822
Name   t4cp2_KBP74_RS00180_pCS-WR3 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   5787 GenBank   WP_000108726
Name   t4cp2_KBP74_RS00225_pCS-WR3 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: 26244..36353

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KBP74_RS00155 21367..22629 - 1263 WP_000517490 ATP-binding protein -
KBP74_RS00160 22712..23206 - 495 WP_001215543 thermonuclease family protein -
KBP74_RS00165 23203..23529 - 327 WP_004208538 hypothetical protein -
KBP74_RS00170 23615..23929 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
KBP74_RS00175 24017..24409 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
KBP74_RS00180 24406..26241 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
KBP74_RS00185 26244..27278 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
KBP74_RS00190 27275..27472 - 198 WP_000629109 DNA-binding protein -
KBP74_RS00195 27474..28688 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
KBP74_RS00200 28685..29614 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
KBP74_RS00205 29620..30348 - 729 WP_004199085 type IV secretion system protein virB8
KBP74_RS00210 30543..31598 - 1056 WP_000235886 type IV secretion system protein virB6
KBP74_RS00215 31610..31867 - 258 WP_000759841 EexN family lipoprotein -
KBP74_RS00220 31877..32647 - 771 WP_000716326 type IV secretion system protein -
KBP74_RS00225 32657..35410 - 2754 WP_000108726 VirB3 family type IV secretion system protein virb4
KBP74_RS00230 35435..35725 - 291 WP_000916156 TrbC/VirB2 family protein virB2
KBP74_RS00235 35709..36353 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
KBP74_RS00240 36399..36635 - 237 WP_001348696 hypothetical protein -
KBP74_RS00245 36586..37236 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
KBP74_RS00250 37448..38608 - 1161 WP_004199101 MobP1 family relaxase -
KBP74_RS00255 38611..39156 - 546 WP_001348698 DNA distortion polypeptide 1 -
KBP74_RS00265 39497..39754 - 258 WP_004199355 hypothetical protein -
KBP74_RS00270 39751..39903 - 153 WP_162542717 hypothetical protein -
KBP74_RS00275 39990..40328 - 339 WP_101529254 hypothetical protein -
KBP74_RS00280 40422..40664 - 243 WP_000008707 hypothetical protein -
KBP74_RS00285 40654..40935 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   8552 GenBank   NZ_MT759838
Plasmid name   pCS-WR3 Incompatibility group   IncX3
Plasmid size   43705 bp Coordinate of oriT [Strand]   38934..39551 [+]
Host baterium   Cronobacter sakazakii strain NMI5563_17

Cargo genes

Drug resistance gene   blaSHV-12, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -