Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103244
Name   oriT_pAD-19R in_silico
Organism   Escherichia coli strain AD-19R
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX833071 (41390..42007 [+], 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_pAD-19R
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2426 GenBank   WP_004199101
Name   Relaxase_HTK51_RS00250_pAD-19R 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   2189 GenBank   WP_000053822
Name   t4cp2_HTK51_RS00180_pAD-19R 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   2190 GenBank   WP_015060057
Name   t4cp2_HTK51_RS00225_pAD-19R 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 28700..38809

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTK51_RS00155 23823..25085 - 1263 WP_000517490 ATP-binding protein -
HTK51_RS00160 25168..25662 - 495 WP_001215543 thermonuclease family protein -
HTK51_RS00165 25659..25985 - 327 WP_004208538 hypothetical protein -
HTK51_RS00170 26071..26385 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTK51_RS00175 26473..26865 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTK51_RS00180 26862..28697 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTK51_RS00185 28700..29734 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTK51_RS00190 29731..29928 - 198 WP_000629109 DNA-binding protein -
HTK51_RS00195 29930..31144 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTK51_RS00200 31141..32070 - 930 WP_072667011 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTK51_RS00205 32076..32804 - 729 WP_004199085 type IV secretion system protein virB8
HTK51_RS00210 32999..34054 - 1056 WP_000235886 type IV secretion system protein virB6
HTK51_RS00215 34066..34323 - 258 WP_000759841 EexN family lipoprotein -
HTK51_RS00220 34333..35103 - 771 WP_000716326 type IV secretion system protein -
HTK51_RS00225 35113..37866 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
HTK51_RS00230 37891..38181 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTK51_RS00235 38165..38809 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTK51_RS00240 38855..39091 - 237 WP_001348696 hypothetical protein -
HTK51_RS00245 39042..39551 - 510 WP_000455437 transcription termination/antitermination NusG family protein -
HTK51_RS00250 39904..41064 - 1161 WP_004199101 MobP1 family relaxase -
HTK51_RS00255 41067..41612 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTK51_RS00260 41953..42210 - 258 WP_004199355 hypothetical protein -
HTK51_RS00265 42207..42359 - 153 WP_162542717 hypothetical protein -
HTK51_RS00270 42446..42784 - 339 WP_001099725 hypothetical protein -
HTK51_RS00275 42878..43120 - 243 WP_000008707 hypothetical protein -
HTK51_RS00280 43110..43391 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   3687 GenBank   NZ_KX833071
Plasmid name   pAD-19R Incompatibility group   IncX3
Plasmid size   46161 bp Coordinate of oriT [Strand]   41390..42007 [+]
Host baterium   Escherichia coli strain AD-19R

Cargo genes

Drug resistance gene   blaNDM-17
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -