Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120616
Name   oriT_pNDM1_140542 in_silico
Organism   Citrobacter freundii strain 140542
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP103366 (48267..48884 [+], 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_140542
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12985 GenBank   WP_004199101
Name   mobP1_NYE91_RS25350_pNDM1_140542 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   15246 GenBank   WP_000053822
Name   t4cp2_NYE91_RS25280_pNDM1_140542 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   15247 GenBank   WP_015060057
Name   t4cp2_NYE91_RS25325_pNDM1_140542 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: 35577..45686

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NYE91_RS25255 (NYE91_25230) 30700..31962 - 1263 WP_000517490 ATP-binding protein -
NYE91_RS25260 (NYE91_25235) 32045..32539 - 495 WP_001215543 thermonuclease family protein -
NYE91_RS25265 (NYE91_25240) 32536..32862 - 327 WP_004208538 hypothetical protein -
NYE91_RS25270 (NYE91_25245) 32948..33262 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
NYE91_RS25275 (NYE91_25250) 33350..33742 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
NYE91_RS25280 (NYE91_25255) 33739..35574 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
NYE91_RS25285 (NYE91_25260) 35577..36611 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
NYE91_RS25290 (NYE91_25265) 36608..36805 - 198 WP_000629109 DNA-binding protein -
NYE91_RS25295 (NYE91_25270) 36807..38021 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
NYE91_RS25300 (NYE91_25275) 38018..38947 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
NYE91_RS25305 (NYE91_25280) 38953..39681 - 729 WP_004199085 virB8 family protein virB8
NYE91_RS25310 (NYE91_25285) 39876..40931 - 1056 WP_000235886 type IV secretion system protein virB6
NYE91_RS25315 (NYE91_25290) 40943..41200 - 258 WP_000759841 EexN family lipoprotein -
NYE91_RS25320 (NYE91_25295) 41210..41980 - 771 WP_000716326 type IV secretion system protein -
NYE91_RS25325 (NYE91_25300) 41990..44743 - 2754 WP_015060057 VirB3 family type IV secretion system protein virb4
NYE91_RS25330 (NYE91_25305) 44768..45058 - 291 WP_000916156 TrbC/VirB2 family protein virB2
NYE91_RS25335 (NYE91_25310) 45042..45686 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
NYE91_RS25340 (NYE91_25315) 45732..45968 - 237 WP_001348696 hypothetical protein -
NYE91_RS25345 (NYE91_25320) 45919..46428 - 510 WP_000455437 transcription termination/antitermination NusG family protein -
NYE91_RS25350 (NYE91_25325) 46781..47941 - 1161 WP_004199101 MobP1 family relaxase -
NYE91_RS25355 (NYE91_25330) 47944..48489 - 546 WP_001348698 DNA distortion polypeptide 1 -
NYE91_RS25360 (NYE91_25335) 48830..49087 - 258 WP_004199355 hypothetical protein -
NYE91_RS25365 (NYE91_25340) 49084..49248 - 165 WP_000004083 hypothetical protein -
NYE91_RS25370 (NYE91_25345) 49323..49661 - 339 WP_001099725 hypothetical protein -
NYE91_RS25375 (NYE91_25350) 49755..49997 - 243 WP_000008707 hypothetical protein -
NYE91_RS25380 (NYE91_25355) 49987..50256 - 270 WP_001006717 hypothetical protein -

Host bacterium

ID   21045 GenBank   NZ_CP103366
Plasmid name   pNDM1_140542 Incompatibility group   IncX3
Plasmid size   53038 bp Coordinate of oriT [Strand]   48267..48884 [+]
Host baterium   Citrobacter freundii strain 140542

Cargo genes

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