Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119513
Name   oriT_pNDM-CR33 in_silico
Organism   Klebsiella aerogenes strain CR33
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK450349 (4913..5530 [-], 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_pNDM-CR33
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTAAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12328 GenBank   WP_004199101
Name   mobP1_HTV60_RS00055_pNDM-CR33 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   14476 GenBank   WP_015060057
Name   t4cp2_HTV60_RS00080_pNDM-CR33 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   14477 GenBank   WP_000053822
Name   t4cp2_HTV60_RS00125_pNDM-CR33 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: 8111..18220

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTV60_RS00025 3529..3810 + 282 WP_001348701 hypothetical protein -
HTV60_RS00030 3800..4042 + 243 WP_000008707 hypothetical protein -
HTV60_RS00035 4136..4474 + 339 WP_001099725 hypothetical protein -
HTV60_RS00040 4561..4713 + 153 WP_162542717 hypothetical protein -
HTV60_RS00045 4710..4967 + 258 WP_004199355 hypothetical protein -
HTV60_RS00050 5308..5853 + 546 WP_001348698 DNA distortion polypeptide 1 -
HTV60_RS00055 5856..7016 + 1161 WP_004199101 MobP1 family relaxase -
HTV60_RS00060 7228..7878 + 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTV60_RS00065 7829..8065 + 237 WP_001348696 hypothetical protein -
HTV60_RS00070 8111..8755 + 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTV60_RS00075 8739..9029 + 291 WP_000916156 TrbC/VirB2 family protein virB2
HTV60_RS00080 9054..11807 + 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
HTV60_RS00085 11817..12587 + 771 WP_000716326 type IV secretion system protein -
HTV60_RS00090 12597..12854 + 258 WP_000759841 EexN family lipoprotein -
HTV60_RS00095 12866..13921 + 1056 WP_000235886 type IV secretion system protein virB6
HTV60_RS00100 14116..14844 + 729 WP_004199085 virB8 family protein virB8
HTV60_RS00105 14850..15779 + 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTV60_RS00110 15776..16990 + 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTV60_RS00115 16992..17189 + 198 WP_000629109 DNA-binding protein -
HTV60_RS00120 17186..18220 + 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTV60_RS00125 18223..20058 + 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTV60_RS00130 20055..20447 + 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTV60_RS00135 20535..20849 + 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTV60_RS00140 20935..21261 + 327 WP_004208538 hypothetical protein -
HTV60_RS00145 21258..21752 + 495 WP_001215543 thermonuclease family protein -
HTV60_RS00150 21835..23097 + 1263 WP_000517490 ATP-binding protein -

Host bacterium

ID   19943 GenBank   NZ_MK450349
Plasmid name   pNDM-CR33 Incompatibility group   IncX3
Plasmid size   43252 bp Coordinate of oriT [Strand]   4913..5530 [-]
Host baterium   Klebsiella aerogenes strain CR33

Cargo genes

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