Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113909
Name   oriT_IncX-3 in_silico
Organism   Serratia marcescens strain 427862
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU934011 (46954..47571 [+], 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_IncX-3
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8931 GenBank   WP_004199101
Name   mobP1_HTH78_RS00255_IncX-3 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   10372 GenBank   WP_000053822
Name   t4cp2_HTH78_RS00185_IncX-3 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   10373 GenBank   WP_000108726
Name   t4cp2_HTH78_RS00230_IncX-3 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: 34264..44373

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH78_RS00160 29387..30649 - 1263 WP_000517490 ATP-binding protein -
HTH78_RS00165 30732..31226 - 495 WP_001215543 thermonuclease family protein -
HTH78_RS00170 31223..31549 - 327 WP_004208538 hypothetical protein -
HTH78_RS00175 31635..31949 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTH78_RS00180 32037..32429 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTH78_RS00185 32426..34261 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTH78_RS00190 34264..35298 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTH78_RS00195 35295..35492 - 198 WP_000629109 DNA-binding protein -
HTH78_RS00200 35494..36708 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTH78_RS00205 36705..37634 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTH78_RS00210 37640..38368 - 729 WP_004199085 virB8 family protein virB8
HTH78_RS00215 38563..39618 - 1056 WP_000235886 type IV secretion system protein virB6
HTH78_RS00220 39630..39887 - 258 WP_000759841 EexN family lipoprotein -
HTH78_RS00225 39897..40667 - 771 WP_000716326 type IV secretion system protein -
HTH78_RS00230 40677..43430 - 2754 WP_000108726 VirB3 family type IV secretion system protein virb4
HTH78_RS00235 43455..43745 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTH78_RS00240 43729..44373 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTH78_RS00245 44419..44655 - 237 WP_001348696 hypothetical protein -
HTH78_RS00250 44606..45256 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTH78_RS00255 45468..46628 - 1161 WP_004199101 MobP1 family relaxase -
HTH78_RS00260 46631..47176 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTH78_RS00265 47517..47774 - 258 WP_004199355 hypothetical protein -
HTH78_RS00270 47771..47923 - 153 WP_162542717 hypothetical protein -
HTH78_RS00275 48010..48348 - 339 WP_001099725 hypothetical protein -
HTH78_RS00280 48442..48684 - 243 WP_000008707 hypothetical protein -
HTH78_RS00285 48674..48955 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   14344 GenBank   NZ_KU934011
Plasmid name   IncX-3 Incompatibility group   IncX3
Plasmid size   53292 bp Coordinate of oriT [Strand]   46954..47571 [+]
Host baterium   Serratia marcescens strain 427862

Cargo genes

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