Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116366
Name   oriT_pK2521-2 in_silico
Organism   Citrobacter koseri strain K2521
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP136829 (79..179 [-], 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_pK2521-2
AATTAGAATAATTTGTTTTGTTTTCAAGCATTTACGATGAAAATCGTAATTGCGTATGGTGTATAGCCGTTAAGGGATAACATACCACGCCTTTTTTAAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10456 GenBank   WP_000932317
Name   mobF_R1917_RS23590_pK2521-2 insolico UniProt ID   A0A626R2M1
Length   969 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 969 a.a.        Molecular weight: 108425.51 Da        Isoelectric Point: 9.7925

>WP_000932317.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLNITTITRQRVDKVVDYYADGADDYYAKDGNAMQWQGAGAEELGLTGEVEQKRFAKLLDGKVTDDISVM
RKTANSESKERLGYDLTFSAPKGVTLQALVNGDKRIIEAHDRAVTKAIEEAERLALGRFTVNKKTHVENT
NKLIVGKFRHETSRELDPDLHTHAFVMNLTKTSDGKWRSLTNDGIVNSLTLLGNVYKSELARELELAGYN
LRYDRNGTFDLAHFSQEQIAQFSQRSQQIEAELAKNGLSRETASHEQKNAAALKTRKSKGEVDRDVLYEG
WKNRAKELQIDFDSREWKGAANDDIARNTQPAALEKPIEYQADKVMTFAIRSLTERQSVITERELMDVAM
KHGYGRLTLDDIRAARERAITSGNLIKEEATYAAATTNKKQQNVAMTREQWVTELVKAGRNKDEARKLVD
KGITNGRLVQQKPRFTTQLAQQRERNILKMEREGRGKIQTPYTREFSEGWLASRTLKPEQLKAVMGIIHT
PNQFISVHGFAGTGKSYMTKSAADFLKEQGVHVTSLAPYGSQVKALQAEGLESRTLQSFLRASDKKIGPG
SVVFIDEAGVIPARQMEETMRVIRDAGARAVFLGDTKQTKAVEAGKPFEQLIKAGMETAYMKDIQRQKDP
ELLKAALNAAEGKIKASLTHVTSIVEEKNHDQRYRRIVGDYVAMPPTDRANALIITGTNDSRKKINAYIQ
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 A0A626R2M1


T4CP

ID   12209 GenBank   WP_001001035
Name   t4cp2_R1917_RS23585_pK2521-2 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: 59019.93 Da        Isoelectric Point: 9.5507

>WP_001001035.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MNEADKGKICLGALLFTPLVTWFIAAKTLYGFTPKDARERLVLLIQQTFDLWPLWGALLVGEIIAIIGLI
IFFKFNHQIFKGAPFKKIYRGTRLVSQRALASLTKEREPQITIADIPIPTKAEGTHISIAGATGVGKSTI
FAEMMKGCLMRGKMQRVASKKDRMIILDPDGDFLSRFYKKGDKILNPYDARTEGWVFFNEIKSDFDFERF
GVSIVPTAKDSQTEEWNGYGRLLFTEVSRKVFNTSRNPTMEEVFYWTNEVPLEELEEYVRGTKAQALFAG
SGRAVGSARFVLSNKLAAHLKMPAGNFSIREWLEDPKGGNLYITWTDEMREALKSLISCWTDSIFSIVLG
MSKSNTRKIWTYIDELESLDYLPSLRDALTKGRKKGLRVVTGYQSYSQVISIYGSDVAETLLSNHRTSVV
MAAGRLGERTLEFVSKSLGEIEGEREKTGISRRFGQMGTKNINDDHKRERAVTPTEIATLDDLTGYIAFP
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: 621..18410

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R1917_RS23580 (R1917_23580) 281..628 + 348 WP_001139329 hypothetical protein -
R1917_RS23585 (R1917_23585) 621..2198 + 1578 WP_001001035 type IV secretion system DNA-binding domain-containing protein virb4
R1917_RS23590 (R1917_23590) 2201..5110 + 2910 WP_000932317 MobF family relaxase -
R1917_RS23595 (R1917_23595) 5388..5582 - 195 WP_000529710 hypothetical protein -
R1917_RS23600 (R1917_23600) 5594..6088 - 495 WP_050868853 GNAT family N-acetyltransferase -
R1917_RS23605 (R1917_23605) 6089..6643 - 555 WP_000616063 phospholipase D family protein -
R1917_RS23610 (R1917_23610) 6606..7637 - 1032 WP_000138004 P-type DNA transfer ATPase VirB11 virB11
R1917_RS23615 (R1917_23615) 7630..8784 - 1155 WP_001224296 type IV secretion system protein VirB10 virB10
R1917_RS23620 (R1917_23620) 8781..9668 - 888 WP_000744355 TrbG/VirB9 family P-type conjugative transfer protein virB9
R1917_RS23625 (R1917_23625) 9671..10387 - 717 WP_000914645 virB8 family protein virB8
R1917_RS23630 (R1917_23630) 10390..10560 - 171 WP_021536809 hypothetical protein -
R1917_RS23635 (R1917_23635) 10655..11698 - 1044 WP_021536808 type IV secretion system protein virB6
R1917_RS23640 (R1917_23640) 11717..11953 - 237 WP_000733633 EexN family lipoprotein -
R1917_RS23645 (R1917_23645) 11957..12664 - 708 WP_108714636 type IV secretion system protein virB5
R1917_RS23650 (R1917_23650) 12674..14947 - 2274 WP_225386901 VirB4 family type IV secretion/conjugal transfer ATPase virb4
R1917_RS23655 (R1917_23655) 15304..15618 - 315 WP_001053888 type IV secretion system protein VirB3 virB3
R1917_RS23660 (R1917_23660) 15668..15958 - 291 WP_114266869 TrbC/VirB2 family protein virB2
R1917_RS23665 (R1917_23665) 15942..16259 - 318 WP_001267114 hypothetical protein -
R1917_RS23670 (R1917_23670) 16282..17022 - 741 WP_000815895 lytic transglycosylase domain-containing protein virB1
R1917_RS23675 (R1917_23675) 17085..17321 + 237 WP_000089855 H-NS family nucleoid-associated regulatory protein -
R1917_RS23680 (R1917_23680) 17333..17770 + 438 WP_108714638 hypothetical protein -
R1917_RS23685 (R1917_23685) 17869..18093 + 225 WP_317361516 TrbM/KikA/MpfK family conjugal transfer protein -
R1917_RS23690 (R1917_23690) 18096..18410 + 315 WP_023223516 hypothetical protein tfc15
R1917_RS23695 (R1917_23695) 18386..19111 + 726 WP_225386900 restriction endonuclease -
R1917_RS23700 (R1917_23700) 19277..19513 + 237 WP_042041953 Hha/YmoA family nucleoid-associated regulatory protein -
R1917_RS23705 (R1917_23705) 19539..19976 - 438 WP_060628251 hypothetical protein -
R1917_RS23710 (R1917_23710) 19985..20311 - 327 WP_016240388 endoribonuclease MazF -
R1917_RS23715 (R1917_23715) 20301..20558 - 258 WP_108714640 hypothetical protein -
R1917_RS23720 (R1917_23720) 20570..20815 - 246 WP_021536799 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
R1917_RS23725 (R1917_23725) 21267..21851 + 585 WP_021536796 recombinase family protein -
R1917_RS23730 (R1917_23730) 21884..22768 + 885 WP_023187082 replication protein RepA -

Host bacterium

ID   16799 GenBank   NZ_CP136829
Plasmid name   pK2521-2 Incompatibility group   -
Plasmid size   34990 bp Coordinate of oriT [Strand]   79..179 [-]
Host baterium   Citrobacter koseri strain K2521

Cargo genes

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