Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113993
Name   oriT_pABC302-NDM-4 in_silico
Organism   Enterobacter cloacae strain ABC302
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK372388 (44631..45248 [+], 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_pABC302-NDM-4
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8988 GenBank   WP_004199101
Name   mobP1_HTV50_RS00265_pABC302-NDM-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   10423 GenBank   WP_000053822
Name   t4cp2_HTV50_RS00195_pABC302-NDM-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   10424 GenBank   WP_015060057
Name   t4cp2_HTV50_RS00240_pABC302-NDM-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: 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: 31941..42050

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTV50_RS00170 27064..28326 - 1263 WP_000517490 ATP-binding protein -
HTV50_RS00175 28409..28903 - 495 WP_001215543 thermonuclease family protein -
HTV50_RS00180 28900..29226 - 327 WP_004208538 hypothetical protein -
HTV50_RS00185 29312..29626 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTV50_RS00190 29714..30106 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTV50_RS00195 30103..31938 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTV50_RS00200 31941..32975 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTV50_RS00205 32972..33169 - 198 WP_000629109 DNA-binding protein -
HTV50_RS00210 33171..34385 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTV50_RS00215 34382..35311 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTV50_RS00220 35317..36045 - 729 WP_004199085 virB8 family protein virB8
HTV50_RS00225 36240..37295 - 1056 WP_000235886 type IV secretion system protein virB6
HTV50_RS00230 37307..37564 - 258 WP_000759841 EexN family lipoprotein -
HTV50_RS00235 37574..38344 - 771 WP_000716326 type IV secretion system protein -
HTV50_RS00240 38354..41107 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
HTV50_RS00245 41132..41422 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTV50_RS00250 41406..42050 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTV50_RS00255 42096..42332 - 237 WP_001348696 hypothetical protein -
HTV50_RS00260 42283..42933 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTV50_RS00265 43145..44305 - 1161 WP_004199101 MobP1 family relaxase -
HTV50_RS00270 44308..44853 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTV50_RS00275 45194..45451 - 258 WP_004199355 hypothetical protein -
HTV50_RS00280 45448..45600 - 153 WP_162542717 hypothetical protein -
HTV50_RS00285 45687..46025 - 339 WP_001099725 hypothetical protein -
HTV50_RS00290 46119..46361 - 243 WP_000008707 hypothetical protein -
HTV50_RS00295 46351..46632 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   14428 GenBank   NZ_MK372388
Plasmid name   pABC302-NDM-4 Incompatibility group   IncX3
Plasmid size   49402 bp Coordinate of oriT [Strand]   44631..45248 [+]
Host baterium   Enterobacter cloacae strain ABC302

Cargo genes

Drug resistance gene   blaNDM-4
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -