Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103042
Name   oriT_pNDM5-NJ-IncX3 in_silico
Organism   Escherichia coli strain MCR1_NJ
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX447767 (34749..35366 [+], 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_pNDM5-NJ-IncX3
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2274 GenBank   WP_004199101
Name   Relaxase_HTI38_RS00225_pNDM5-NJ-IncX3 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   1975 GenBank   WP_000053822
Name   t4cp2_HTI38_RS00155_pNDM5-NJ-IncX3 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   1976 GenBank   WP_015060057
Name   t4cp2_HTI38_RS00200_pNDM5-NJ-IncX3 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: 22059..32168

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTI38_RS00130 17182..18444 - 1263 WP_000517490 ATP-binding protein -
HTI38_RS00135 18527..19021 - 495 WP_001215543 thermonuclease family protein -
HTI38_RS00140 19018..19344 - 327 WP_004208538 hypothetical protein -
HTI38_RS00145 19430..19744 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTI38_RS00150 19832..20224 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTI38_RS00155 20221..22056 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTI38_RS00160 22059..23093 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTI38_RS00165 23090..23287 - 198 WP_000629109 DNA-binding protein -
HTI38_RS00170 23289..24503 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTI38_RS00175 24500..25429 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTI38_RS00180 25435..26163 - 729 WP_004199085 type IV secretion system protein virB8
HTI38_RS00185 26358..27413 - 1056 WP_000235886 type IV secretion system protein virB6
HTI38_RS00190 27425..27682 - 258 WP_000759841 EexN family lipoprotein -
HTI38_RS00195 27692..28462 - 771 WP_000716326 type IV secretion system protein -
HTI38_RS00200 28472..31225 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
HTI38_RS00205 31250..31540 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTI38_RS00210 31524..32168 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTI38_RS00215 32214..32450 - 237 WP_001348696 hypothetical protein -
HTI38_RS00220 32401..33051 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTI38_RS00225 33263..34423 - 1161 WP_004199101 MobP1 family relaxase -
HTI38_RS00230 34426..34971 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTI38_RS00235 35312..35569 - 258 WP_004199355 hypothetical protein -
HTI38_RS00240 35566..35718 - 153 WP_162542717 hypothetical protein -
HTI38_RS00245 35805..36143 - 339 WP_001099725 hypothetical protein -
HTI38_RS00250 36237..36479 - 243 WP_000008707 hypothetical protein -
HTI38_RS00255 36469..36750 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   3485 GenBank   NZ_KX447767
Plasmid name   pNDM5-NJ-IncX3 Incompatibility group   IncX3
Plasmid size   39520 bp Coordinate of oriT [Strand]   34749..35366 [+]
Host baterium   Escherichia coli strain MCR1_NJ

Cargo genes

Drug resistance gene   blaNDM-5
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -