Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107803
Name   oriT_pABC140-NDM-1 in_silico
Organism   Morganella morganii strain ABC140
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK372385 (47820..48437 [+], 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_pABC140-NDM-1
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5240 GenBank   WP_004199101
Name   mobP1_HTV47_RS00280_pABC140-NDM-1 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   5484 GenBank   WP_000053822
Name   t4cp2_HTV47_RS00210_pABC140-NDM-1 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   5485 GenBank   WP_015060057
Name   t4cp2_HTV47_RS00255_pABC140-NDM-1 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: 35130..45239

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTV47_RS00185 30253..31515 - 1263 WP_000517490 ATP-binding protein -
HTV47_RS00190 31598..32092 - 495 WP_001215543 thermonuclease family protein -
HTV47_RS00195 32089..32415 - 327 WP_004208538 hypothetical protein -
HTV47_RS00200 32501..32815 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTV47_RS00205 32903..33295 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTV47_RS00210 33292..35127 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTV47_RS00215 35130..36164 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTV47_RS00220 36161..36358 - 198 WP_000629109 DNA-binding protein -
HTV47_RS00225 36360..37574 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTV47_RS00230 37571..38500 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTV47_RS00235 38506..39234 - 729 WP_004199085 type IV secretion system protein virB8
HTV47_RS00240 39429..40484 - 1056 WP_000235886 type IV secretion system protein virB6
HTV47_RS00245 40496..40753 - 258 WP_000759841 EexN family lipoprotein -
HTV47_RS00250 40763..41533 - 771 WP_000716326 type IV secretion system protein -
HTV47_RS00255 41543..44296 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
HTV47_RS00260 44321..44611 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTV47_RS00265 44595..45239 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTV47_RS00270 45285..45521 - 237 WP_001348696 hypothetical protein -
HTV47_RS00275 45472..46122 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTV47_RS00280 46334..47494 - 1161 WP_004199101 MobP1 family relaxase -
HTV47_RS00285 47497..48042 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTV47_RS00290 48383..48640 - 258 WP_004199355 hypothetical protein -
HTV47_RS00295 48637..48789 - 153 WP_162542717 hypothetical protein -
HTV47_RS00300 48876..49214 - 339 WP_001099725 hypothetical protein -
HTV47_RS00305 49308..49550 - 243 WP_000008707 hypothetical protein -
HTV47_RS00310 49540..49821 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   8238 GenBank   NZ_MK372385
Plasmid name   pABC140-NDM-1 Incompatibility group   IncX3
Plasmid size   52591 bp Coordinate of oriT [Strand]   47820..48437 [+]
Host baterium   Morganella morganii strain ABC140

Cargo genes

Drug resistance gene   blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -