Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101772
Name   oriT_pA8sk2_4 in_silico
Organism   Klebsiella pneumoniae strain CPE7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACYGQ010000009 (48172..48789 [+], 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_pA8sk2_4
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1489 GenBank   WP_004199101
Name   mobP1_IYY95_RS29120_pA8sk2_4 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   1165 GenBank   WP_000053822
Name   t4cp2_IYY95_RS29050_pA8sk2_4 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   1166 GenBank   WP_000108726
Name   t4cp2_IYY95_RS29095_pA8sk2_4 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: 35482..45591

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IYY95_RS29025 30605..31867 - 1263 WP_000517490 ATP-binding protein -
IYY95_RS29030 31950..32444 - 495 WP_001215543 thermonuclease family protein -
IYY95_RS29035 32441..32767 - 327 WP_004208538 hypothetical protein -
IYY95_RS29040 32853..33167 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
IYY95_RS29045 33255..33647 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
IYY95_RS29050 33644..35479 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
IYY95_RS29055 35482..36516 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
IYY95_RS29060 36513..36710 - 198 WP_000629109 DNA-binding protein -
IYY95_RS29065 36712..37926 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
IYY95_RS29070 37923..38852 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
IYY95_RS29075 38858..39586 - 729 WP_004199085 type IV secretion system protein virB8
IYY95_RS29080 39781..40836 - 1056 WP_000235886 type IV secretion system protein virB6
IYY95_RS29085 40848..41105 - 258 WP_000759841 EexN family lipoprotein -
IYY95_RS29090 41115..41885 - 771 WP_000716326 type IV secretion system protein -
IYY95_RS29095 41895..44648 - 2754 WP_000108726 VirB3 family type IV secretion system protein virb4
IYY95_RS29100 44673..44963 - 291 WP_000916156 TrbC/VirB2 family protein virB2
IYY95_RS29105 44947..45591 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
IYY95_RS29110 45637..45873 - 237 WP_001348696 hypothetical protein -
IYY95_RS29115 45824..46333 - 510 WP_000455437 transcription termination/antitermination NusG family protein -
IYY95_RS29120 46686..47846 - 1161 WP_004199101 MobP1 family relaxase -
IYY95_RS29125 47849..48394 - 546 WP_001348698 DNA distortion polypeptide 1 -
IYY95_RS29135 48735..48992 - 258 WP_004199355 hypothetical protein -
IYY95_RS29140 48989..49153 - 165 WP_000004083 hypothetical protein -
IYY95_RS29145 49228..49566 - 339 WP_001099725 hypothetical protein -
IYY95_RS29150 49660..49902 - 243 WP_000008707 hypothetical protein -
IYY95_RS29155 49892..50161 - 270 WP_001006717 hypothetical protein -

Host bacterium

ID   2216 GenBank   NZ_JACYGQ010000009
Plasmid name   pA8sk2_4 Incompatibility group   IncX3
Plasmid size   51392 bp Coordinate of oriT [Strand]   48172..48789 [+]
Host baterium   Klebsiella pneumoniae strain CPE7

Cargo genes

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