Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114152
Name   oriT_psg_ww281 in_silico
Organism   Salmonella enterica subsp. enterica serovar Brancaster strain sg_ww281
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP037995 (3166..3781 [+], 616 nt)
oriT length   616 nt
IRs (inverted repeats)      599..604, 609..614  (ATGCCC..GGGCAT)
 526..532, 538..544  (CCTCCCG..CGGGAGG)
 462..467, 471..476  (GTTCGC..GCGAAC)
 52..58, 62..68  (CATTATC..GATAATG)
 40..45, 54..59  (TGATAA..TTATCA)
Location of nic site      322..323
Conserved sequence flanking the
  nic site    		  TCCTGCATCG
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 616 nt

>oriT_psg_ww281
TCTTACTTCTTTGCGTAGCTGTTAAATACAGCGTTGTTTTGATAAAATCATCATTATCATCGATAATGCTTTCTTCAATTTTTTTATCCTTACTCTTTAATAAAGCACTTGCTAATAACTTCATACCTTTTGCAACTGTCAAATTTGGTTCATCAGGGTAAATGCTTTTAAGGCATACTAACAAATAATCATGGTCTTCATCTTCAACTCTAAACTGAATTTTTTTCATCATAACTCCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGCTGAAAAATAACGTCGAATGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAATCTGGCGCCGCTCATAAATTGTGCTTGAGCATCAACAAAAATGCAAAAAGGCTGATGTTGTCATGGCTGAACATACGTACGTCTGCGACCGGAAACCCGATCAATGCGGTAAGGACAGTGCCGTCAGGTTCGCTCCGCGAACGGTCTGGCAGGAAGCGCAAGCGCAGTCCCGCGCAATATATCAGAAAGCACCTCCCGAAATACGGGAGGGCTTCGGCTATTCAGCTAAGGTTGCTCTGTTCAGGTTGCTGAGTGTAGCCTTCCATGCCCTGACGGGCATCA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   10533 GenBank   WP_000053826
Name   t4cp2_DBZ83_RS23975_psg_ww281 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: 69231.07 Da        Isoelectric Point: 8.0208

>WP_000053826.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWAFIILVMCLIAYYTGSVAIYFFNHKTPLYIWKHYDSLLLWRVIIDSSIKSEVRFTALPS
LLSGALASLAAPAFIIWKLNQKDAPLFGDAKFASDSDLKKSKLLKWEKENDTDILVGRYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNMLVKKHSIIALDPKQELWKITSKVREQILGNKVYLLDPFNTKTHKCNPLF
YVDLKSESGAKDLLKLVEILFPSFGLTGAEAHFNNLAGQYWTGLAKLLHFFINFAPEWIEELRVKPVFSI
GTVVDLYSNIDREQVLSNRETFEELAQGNETALFHLKDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQMRREDITVYVGVNAEDMILAYDFLNLFFNLVVEVTLRENPDFDPTLKHDCLLFL
DEFPSIGYMPIIKKGSGYIAGYKLKLLTIYQNISQLNEIYGTEGAKTLLSAHPCRVIYAVSEEDDAKKIS
EKLGYITARSKGSSKTSGKATSRSNSENEAQRALVLPQELGTLDFSEEMIILKGEHPVKAEKALYYLDNY
FMERLMLVSPKLTALTASINRSNKIFGVKGIKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(102-581)

  Protein structure



No available structure.



ID   10534 GenBank   WP_254447134
Name   t4cp2_DBZ83_RS24015_psg_ww281 insolico UniProt ID   _
Length   603 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 603 a.a.        Molecular weight: 68064.51 Da        Isoelectric Point: 5.4293

>WP_254447134.1 hypothetical protein [Salmonella enterica]
MFFGNDAGQITASQNARYFRSIEIKDYFQETDAGIFDALMYLPVEYVFTSSFTSMDKQAAVKALDDQIDK
LELTDDAAKSLLADLRVGLDMVSSGYNSFGKCHQTLIVFADTPERLVKDTNIVTTTLEDLGLIVTYSTLS
LGAAFFSQLPGNYNLRPRLSMLSSLNFAEMESFHNFFHGKATGNTWGNSLMALRGSGNDVYHLNYHMTTE
NINFFGKNPTLGHCEILGTSNVGKTVLMMIMSYAAQQFGTPESFPENRKVRKLTTVFFDKDRAGEVGIRA
MGGAYFRVKGGEPTGWNPAALPPTKRNIAFVKDIIRLICKLNGNTVDDYQHSLISSAVDRLMQREDRSFP
ISKLIPLIMEPDDTETKRHGLKARLRAWKQGGEYGWLLDNASDSFDVAHLDVFGIDGTEFLDDKVVAPVA
SFYLIYRVTMLADGRRLLIYMDEFWQWINNDAFKDFVYNKLKTGRKLDMVLVPATQSPDELIKSPIAAAV
REQCATHIYLANPKAKRNEYVDELQVRDLYFDKIKAIDPLSRQFLVVKNPQRQGERDDFAAFAKLDLGKA
AYYLPILSASAEQLELFDEIWSEGMAPEEWIDTYLERANRGVK

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(3-158)

TraG P-loop domain (P-loop_TraG)

(373-501)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 38947..48207

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DBZ83_RS24455 34027..34113 - 87 Protein_45 micrococcal nuclease -
DBZ83_RS24590 34134..34223 + 90 WP_114142201 Tn3 family transposase -
DBZ83_RS23955 (DBZ83_24025) 34260..35168 + 909 WP_000174819 C45 family peptidase -
DBZ83_RS23960 (DBZ83_24030) 35322..36137 - 816 WP_000018321 aminoglycoside O-phosphotransferase APH(3')-Ia -
DBZ83_RS24460 36380..36712 - 333 WP_000699980 hypothetical protein -
DBZ83_RS23970 (DBZ83_24040) 36715..37110 - 396 WP_000733627 cag pathogenicity island Cag12 family protein -
DBZ83_RS23975 (DBZ83_24045) 37107..38942 - 1836 WP_000053826 type IV secretory system conjugative DNA transfer family protein -
DBZ83_RS23980 (DBZ83_24050) 38947..39984 - 1038 WP_000217791 P-type DNA transfer ATPase VirB11 virB11
DBZ83_RS23985 (DBZ83_24055) 40002..41216 - 1215 WP_001295061 VirB10/TraB/TrbI family type IV secretion system protein virB10
DBZ83_RS23990 (DBZ83_24060) 41213..42142 - 930 WP_000776689 TrbG/VirB9 family P-type conjugative transfer protein virB9
DBZ83_RS23995 (DBZ83_24065) 42148..42870 - 723 WP_000394570 type IV secretion system protein virB8
DBZ83_RS24000 (DBZ83_24070) 43060..43979 - 920 Protein_56 type IV secretion system protein -
DBZ83_RS24005 (DBZ83_24075) 44126..44386 - 261 WP_001228869 EexN family lipoprotein -
DBZ83_RS24010 (DBZ83_24080) 44396..45133 - 738 WP_000737859 type IV secretion system protein -
DBZ83_RS24015 (DBZ83_24085) 45135..47893 - 2759 Protein_59 VirB3 family type IV secretion system protein -
DBZ83_RS24020 (DBZ83_24090) 47917..48207 - 291 WP_000921916 TrbC/VirB2 family protein virB2

Host bacterium

ID   14587 GenBank   NZ_CP037995
Plasmid name   psg_ww281 Incompatibility group   IncX1
Plasmid size   48223 bp Coordinate of oriT [Strand]   3166..3781 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Brancaster strain sg_ww281

Cargo genes

Drug resistance gene   blaTEM-176, qnrS1, tet(A), floR, dfrA14, aph(3')-Ia
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -