Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104672
Name   oriT_pR16.0676_34k in_silico
Organism   Salmonella enterica subsp. enterica serovar Anatum strain R16.0676
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP029801 (22983..23083 [+], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      32..38, 43..49  (TTACGAT..ATCGTAA)
 21..26, 38..43  (TTTTCA..TGAAAA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_pR16.0676_34k
AATTAGAATAATTTGTTTTGTTTTCAAGCATTTACGATGAAAATCGTAATTGCGTATGGTGTATAGCCATTAAGGGATACCATAACACGCCTTTTTTAAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3344 GenBank   WP_049286431
Name   mobF_DNA64_RS23870_pR16.0676_34k insolico UniProt ID   A0A3G4RLH4
Length   969 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 969 a.a.        Molecular weight: 108469.56 Da        Isoelectric Point: 9.7925

>WP_049286431.1 MULTISPECIES: MobF family relaxase [Enterobacteriaceae]
MLNITTITRQRVDKVVDYYADGADDYYAKDGNAMQWQGAGAEELGLTGEVEQKRFAKLLDGKVTDDISVM
RKTANSESKERLGYDLTFSAPKGVTLQALVNGDKRIIEAHDRAVTKAIEEAERLALGRFTVNKKTHVENT
NKLIVGKFRHETSRELDPDLHTHAFVMNLTKTSDGKWRSLTNDGIVNSLTLLGNVYKSELARELELAGYN
LRYDRNGTFDLAHFSQEQIAQFSQRSQQIEAELAKNGLSRETASHEQKNAAALKTRKSKGEVDRDVLYEG
WKNRAKELQIDFDSREWKGAANDDIARNTQPAALEKPIEYQADKVMTFAIRSLTERQSVITERELMDVAM
KHGYGRLTLDDIRAARERAITTGNLIKEEATYAAATTNKKQQNVAMTREQWVTELVKAGRNKDEARKLVD
KGITNGRLVQQKPRFTTQLAQQRERNILKMEREGRGKIQTPYTREFSEGWLASRTLKPEQLKAVMGIIHT
PNQFISVHGFAGTGKSYMTKSAADFLKEQGVHVTSLAPYGSQVKALQAEGLESRTLQSFLRASDKKIGPG
SVVFIDEAGVIPARQMEETMRVIRDAGARAVFLGDTKQTKAVEAGKPFEQLIKAGMETAYMKDIQRQKDP
ELLKAALNAAEGKIKASLTHVTSIVEEKNHDQRYRRIVGDYVTMPPTDRANALIITGTNDSRKKINAYIQ
AELGLKGQGINYPLLNRLDTTQAQRQHSKYYEKGAVIIPERDYSNGLKRGAVYTVLDTGPGNKLTVSDGS
GDTIAFSPARFSKLSVYSVEKTELAVGDQVRITRNDAHLDLANGDRFKVKGVQSGEVLLENEKGRLVKID
ANKPMYLGLAYASTVHSAQGLTCDKVFINMDTRSLTTAKDVYYVAVTRAKHEAVIYTDDEKKLDKAASRE
GFKTAALELEQLKRYAKEQQHDAREKGRDKTEPTQEKDNAKRKGKGHDKNNDERAFTSL

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(475-649)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(850-896)

TrwC relaxase (TrwC)

(14-287)


  Protein structure


Source ID Structure
AlphaFold DB A0A3G4RLH4


T4CP

ID   3284 GenBank   WP_021536815
Name   t4cp2_DNA64_RS23875_pR16.0676_34k insolico UniProt ID   _
Length   525 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 525 a.a.        Molecular weight: 58961.81 Da        Isoelectric Point: 9.3727

>WP_021536815.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MNEADKGKICLGALLFTPLVTWFIAAKALYGFTPKDARERLVLLIQQTFDLWPLWGALLVGEIIAIIGLI
IFFKFNHQIFKGAPFKKIYRGTRLVSQRALASITKEREPQITIADIPIPTKAEGTHISIAGATGVGKSTI
FAEMMKCCLMRGKMQRVASNKDRMIILDPDGDFLSRFYKKGDKILNPYDARTEGWVFFNEIKSDFDFERF
GVSIVPTAKDSQTEEWNGYGRLLFTEVSRKVFNTSRNPTMEEVFYWTNEVPLEELEEYVRGTKAQALFAG
SGRAVGSARFVLSNKLAAHLKMPAGNFSIREWLEDPKGGNLYITWTDEMREALKSLISCWTDSIFSIVLG
MSKSNSRKIWTFIDELESLDYLPSLRDALTKGRKKGLRVVTGYQSYSQVISIYGSDVAETLLSNHRTSVV
MAAGRLGERTLEFVSKSLGEIEGEREKTGISRRFGQLGTKNTNDDHKRERAVTPTEIATLDDLTGYIAFP
GNLPVAKFETHHVNYTRSNPVPGVVLRESTAFAGM

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(111-499)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 4751..22541

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DNA64_RS23730 (DNA64_23730) 394..1278 - 885 WP_063448731 replication protein RepA -
DNA64_RS23735 (DNA64_23735) 1311..1895 - 585 WP_021544366 recombinase family protein -
DNA64_RS23745 (DNA64_23745) 2347..2592 + 246 WP_021536799 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
DNA64_RS23750 (DNA64_23750) 2604..2861 + 258 WP_016240387 hypothetical protein -
DNA64_RS23755 (DNA64_23755) 2851..3177 + 327 WP_016240388 endoribonuclease MazF -
DNA64_RS23760 (DNA64_23760) 3186..3623 + 438 WP_042041938 hypothetical protein -
DNA64_RS23765 (DNA64_23765) 3648..3884 - 237 WP_042041953 Hha/YmoA family nucleoid-associated regulatory protein -
DNA64_RS23770 (DNA64_23770) 4050..4775 - 726 WP_224132007 restriction endonuclease -
DNA64_RS23775 (DNA64_23775) 4751..5065 - 315 WP_110962185 hypothetical protein tfc15
DNA64_RS23780 (DNA64_23780) 5068..5385 - 318 WP_059324879 TrbM/KikA/MpfK family conjugal transfer protein -
DNA64_RS23785 (DNA64_23785) 5390..5827 - 438 WP_023187074 hypothetical protein -
DNA64_RS23790 (DNA64_23790) 5839..6075 - 237 WP_021536804 H-NS histone family protein -
DNA64_RS23795 (DNA64_23795) 6138..6878 + 741 WP_059324881 lytic transglycosylase domain-containing protein virB1
DNA64_RS23800 (DNA64_23800) 6901..7218 + 318 WP_001267114 hypothetical protein -
DNA64_RS23805 (DNA64_23805) 7202..7492 + 291 WP_023223518 TrbC/VirB2 family protein virB2
DNA64_RS23810 (DNA64_23810) 7544..7858 + 315 WP_001053888 VirB3 family type IV secretion system protein virB3
DNA64_RS23815 (DNA64_23815) 8215..10488 + 2274 WP_224132005 VirB4 family type IV secretion/conjugal transfer ATPase -
DNA64_RS23820 (DNA64_23820) 10498..11205 + 708 WP_023187073 type IV secretion system protein virB5
DNA64_RS23825 (DNA64_23825) 11209..11445 + 237 WP_000733633 EexN family lipoprotein -
DNA64_RS23830 (DNA64_23830) 11464..12507 + 1044 WP_021536808 type IV secretion system protein virB6
DNA64_RS24860 12602..12772 + 171 WP_021536809 hypothetical protein -
DNA64_RS23835 (DNA64_23835) 12775..13491 + 717 WP_000914645 type IV secretion system protein virB8
DNA64_RS23840 (DNA64_23840) 13494..14381 + 888 WP_000744355 TrbG/VirB9 family P-type conjugative transfer protein virB9
DNA64_RS23845 (DNA64_23845) 14378..15532 + 1155 WP_001224296 type IV secretion system protein VirB10 virB10
DNA64_RS23850 (DNA64_23850) 15525..16556 + 1032 WP_000138004 P-type DNA transfer ATPase VirB11 virB11
DNA64_RS23855 (DNA64_23855) 16519..17073 + 555 WP_000616063 phospholipase D family protein -
DNA64_RS23860 (DNA64_23860) 17074..17568 + 495 WP_052765801 GNAT family protein -
DNA64_RS23865 (DNA64_23865) 17580..17774 + 195 WP_110962186 hypothetical protein -
DNA64_RS23870 (DNA64_23870) 18052..20961 - 2910 WP_049286431 MobF family relaxase -
DNA64_RS23875 (DNA64_23875) 20964..22541 - 1578 WP_021536815 type IV secretion system DNA-binding domain-containing protein virb4
DNA64_RS23880 (DNA64_23880) 22534..22881 - 348 WP_001139329 hypothetical protein -
DNA64_RS23885 (DNA64_23885) 23368..23802 + 435 WP_045348531 hypothetical protein -
DNA64_RS23890 (DNA64_23890) 23815..24525 + 711 WP_000686338 StbB family protein -
DNA64_RS23895 (DNA64_23895) 24527..24895 + 369 WP_049286430 plasmid stabilization protein StbC -
DNA64_RS23900 (DNA64_23900) 25109..25879 + 771 WP_042113825 SprT-like domain-containing protein -
DNA64_RS23905 (DNA64_23905) 25920..26108 - 189 WP_049286429 hypothetical protein -
DNA64_RS23910 (DNA64_23910) 26113..26370 - 258 WP_110962187 hypothetical protein -
DNA64_RS24740 26443..26598 - 156 WP_021536821 hypothetical protein -
DNA64_RS23915 (DNA64_23915) 26702..26884 - 183 WP_042113821 hypothetical protein -
DNA64_RS23920 (DNA64_23920) 26941..27183 - 243 WP_049286427 hypothetical protein -
DNA64_RS23925 (DNA64_23925) 27245..27532 - 288 WP_001098466 hypothetical protein -

Host bacterium

ID   5111 GenBank   NZ_CP029801
Plasmid name   pR16.0676_34k Incompatibility group   -
Plasmid size   34063 bp Coordinate of oriT [Strand]   22983..23083 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Anatum strain R16.0676

Cargo genes

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