Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104924
Name   oriT_pNDM1_SCLZS47 in_silico
Organism   Citrobacter freundii strain SCLZS47
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP092495 (52213..52830 [+], 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_pNDM1_SCLZS47
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3468 GenBank   WP_004199101
Name   mobP1_MJ253_RS25910_pNDM1_SCLZS47 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   3412 GenBank   WP_000053822
Name   t4cp2_MJ253_RS25840_pNDM1_SCLZS47 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   3413 GenBank   WP_015060057
Name   t4cp2_MJ253_RS25885_pNDM1_SCLZS47 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: 39523..49632

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MJ253_RS25815 (MJ253_25815) 34646..35908 - 1263 WP_000517490 ATP-binding protein -
MJ253_RS25820 (MJ253_25820) 35991..36485 - 495 WP_001215543 thermonuclease family protein -
MJ253_RS25825 (MJ253_25825) 36482..36808 - 327 WP_004208538 hypothetical protein -
MJ253_RS25830 (MJ253_25830) 36894..37208 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
MJ253_RS25835 (MJ253_25835) 37296..37688 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
MJ253_RS25840 (MJ253_25840) 37685..39520 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
MJ253_RS25845 (MJ253_25845) 39523..40557 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
MJ253_RS25850 (MJ253_25850) 40554..40751 - 198 WP_000629109 DNA-binding protein -
MJ253_RS25855 (MJ253_25855) 40753..41967 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
MJ253_RS25860 (MJ253_25860) 41964..42893 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
MJ253_RS25865 (MJ253_25865) 42899..43627 - 729 WP_004199085 type IV secretion system protein virB8
MJ253_RS25870 (MJ253_25870) 43822..44877 - 1056 WP_000235886 type IV secretion system protein virB6
MJ253_RS25875 (MJ253_25875) 44889..45146 - 258 WP_000759841 EexN family lipoprotein -
MJ253_RS25880 (MJ253_25880) 45156..45926 - 771 WP_000716326 type IV secretion system protein -
MJ253_RS25885 (MJ253_25885) 45936..48689 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
MJ253_RS25890 (MJ253_25890) 48714..49004 - 291 WP_000916156 TrbC/VirB2 family protein virB2
MJ253_RS25895 (MJ253_25895) 48988..49632 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
MJ253_RS25900 (MJ253_25900) 49678..49914 - 237 WP_001348696 hypothetical protein -
MJ253_RS25905 (MJ253_25905) 49865..50374 - 510 WP_000455437 transcription termination/antitermination NusG family protein -
MJ253_RS25910 (MJ253_25910) 50727..51887 - 1161 WP_004199101 MobP1 family relaxase -
MJ253_RS25915 (MJ253_25915) 51890..52435 - 546 WP_001348698 DNA distortion polypeptide 1 -
MJ253_RS25920 (MJ253_25920) 52776..53033 - 258 WP_004199355 hypothetical protein -
MJ253_RS25925 (MJ253_25925) 53030..53194 - 165 WP_000004083 hypothetical protein -
MJ253_RS25930 (MJ253_25930) 53269..53607 - 339 WP_001099725 hypothetical protein -
MJ253_RS25935 (MJ253_25935) 53701..53943 - 243 WP_000008707 hypothetical protein -
MJ253_RS25940 (MJ253_25940) 53933..54202 - 270 WP_001006717 hypothetical protein -

Host bacterium

ID   5362 GenBank   NZ_CP092495
Plasmid name   pNDM1_SCLZS47 Incompatibility group   IncX3
Plasmid size   56984 bp Coordinate of oriT [Strand]   52213..52830 [+]
Host baterium   Citrobacter freundii strain SCLZS47

Cargo genes

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