Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111053
Name   oriT_pABC80-NDM-1 in_silico
Organism   Citrobacter freundii strain ABC80
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK372383 (48252..48869 [+], 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_pABC80-NDM-1
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7268 GenBank   WP_004199101
Name   mobP1_HTV46_RS00290_pABC80-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   8273 GenBank   WP_000053822
Name   t4cp2_HTV46_RS00220_pABC80-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   8274 GenBank   WP_015060057
Name   t4cp2_HTV46_RS00265_pABC80-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: 35562..45671

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTV46_RS00195 30685..31947 - 1263 WP_000517490 ATP-binding protein -
HTV46_RS00200 32030..32524 - 495 WP_001215543 thermonuclease family protein -
HTV46_RS00205 32521..32847 - 327 WP_004208538 hypothetical protein -
HTV46_RS00210 32933..33247 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTV46_RS00215 33335..33727 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTV46_RS00220 33724..35559 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTV46_RS00225 35562..36596 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTV46_RS00230 36593..36790 - 198 WP_000629109 DNA-binding protein -
HTV46_RS00235 36792..38006 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTV46_RS00240 38003..38932 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTV46_RS00245 38938..39666 - 729 WP_004199085 type IV secretion system protein virB8
HTV46_RS00250 39861..40916 - 1056 WP_000235886 type IV secretion system protein virB6
HTV46_RS00255 40928..41185 - 258 WP_000759841 EexN family lipoprotein -
HTV46_RS00260 41195..41965 - 771 WP_000716326 type IV secretion system protein -
HTV46_RS00265 41975..44728 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
HTV46_RS00270 44753..45043 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTV46_RS00275 45027..45671 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTV46_RS00280 45717..45953 - 237 WP_001348696 hypothetical protein -
HTV46_RS00285 45904..46554 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTV46_RS00290 46766..47926 - 1161 WP_004199101 MobP1 family relaxase -
HTV46_RS00295 47929..48474 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTV46_RS00300 48815..49072 - 258 WP_004199355 hypothetical protein -
HTV46_RS00305 49069..49221 - 153 WP_162542717 hypothetical protein -
HTV46_RS00310 49308..49646 - 339 WP_001099725 hypothetical protein -
HTV46_RS00315 49740..49982 - 243 WP_000008707 hypothetical protein -
HTV46_RS00320 49972..50253 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   11488 GenBank   NZ_MK372383
Plasmid name   pABC80-NDM-1 Incompatibility group   IncX3
Plasmid size   53023 bp Coordinate of oriT [Strand]   48252..48869 [+]
Host baterium   Citrobacter freundii strain ABC80

Cargo genes

Drug resistance gene   blaSHV-12, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -