Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120495
Name   oriT_pRHBSTW-00302_4 in_silico
Organism   Citrobacter freundii strain RHBSTW-00302
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP056638 (40755..40855 [-], 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_pRHBSTW-00302_4
AATTAGAATAATTTGTTTTGTTTTCAAGCATTTACGATGAAAATCGTAATTGCGTATGGTGTATAGCCGTTAAGGGATACCATACCACGCCTTTTTTAAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12905 GenBank   WP_023187071
Name   mobF_HV147_RS27145_pRHBSTW-00302_4 insolico UniProt ID   _
Length   969 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 969 a.a.        Molecular weight: 108499.54 Da        Isoelectric Point: 9.7610

>WP_023187071.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLNITTITRQRVDKVVDYYADGADDYYAKDGNAMQWQGAGAEELGLTGEVEQKRFAKLLDGKVTDDISVM
RKTANSESKERLGYDLTFSAPKGVTLQALVNGDKRIIEAHDRAVTKAIEEAERLALGRFTVNKKTHVENT
NKLIVGKFRHETSRELDPDLHTHAFVMNLTKTSDGKWRSLTNDGIVNSLTLLGNVYKSELARELELAGYN
LRYDRNGTFDLAHFSQEQIAQFSQRSQQIEAELAKNGLSRETASHEQKNAAALKTRKSKGEVDRDVLYEG
WKNRAKELQIDFDSREWKGAANDDIARNTQPAALEKPIEYQADKVMTFAIRSLTERQSVITERELMDVAM
KHGYGRLTLDDIRAARERAITSGNLIKEEATYAAATTNKKQQNVAMTREQWVTELVKAGRNKDEARKLVD
KGITNGRLVQQKPRFTTQLAQQRERNILKMEREGRGKIQTPYTREFSEGWLASRTLKPEQLKAVMGIIHT
PNQFISVHGFAGTGKSYMTKSAADFLKEQGVHVTSLAPYGSQVKALQAEGLESRTLQSFLRASDKKIGPG
SVVFIDEAGVIPARQMEETMRVIRDAGARAVFLGDTKQTKAVEAGKPFEQLIKAGMETAYMKDIQRQKDP
ELLKAALNAAEGKIKASLTHVTSIVEEKNHDQRYRRIVGDYVAMPPTDRANALIITGTNDSRKKINEYIQ
AELGLKGQGINYPLLNRLDTTQAQRQHSKYYEKGAVIIPERDYSNGLKRGAVYTVLDTGPGNKLTVSDGS
GDTIAFSPARFSKLSVYSVEKTELAVGDQVRITRNDAHLDLANGDRFKVKGVQSGEVLLENEKGRLVKID
ANKPMYLGLAYASTVHSAQGLTCDKVFINMDTRSLTTAKDVYYVAVTRAKHEAVIYTDDEKKLDKAASRE
GFKTAALELEQLKRYAKEQQHDAREKGRDKTEPTQEKDNSKRKGKGHDKNNDERAFTSL

  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



No available structure.




T4CP

ID   15156 GenBank   WP_021536815
Name   t4cp2_HV147_RS27140_pRHBSTW-00302_4 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: 41297..59085

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HV147_RS27115 (HV147_27115) 37877..38704 - 828 WP_213721551 TnsA endonuclease C-terminal domain-containing protein -
HV147_RS27120 (HV147_27120) 38954..39322 - 369 WP_015345231 plasmid stabilization protein StbC -
HV147_RS27125 (HV147_27125) 39324..40034 - 711 WP_021544361 StbB family protein -
HV147_RS27130 (HV147_27130) 40047..40481 - 435 WP_023223528 hypothetical protein -
HV147_RS27135 (HV147_27135) 40957..41304 + 348 WP_001139329 hypothetical protein -
HV147_RS27140 (HV147_27140) 41297..42874 + 1578 WP_021536815 type IV secretion system DNA-binding domain-containing protein virb4
HV147_RS27145 (HV147_27145) 42877..45786 + 2910 WP_023187071 MobF family relaxase -
HV147_RS27150 (HV147_27150) 46064..46258 - 195 WP_000529710 hypothetical protein -
HV147_RS27155 (HV147_27155) 46270..46752 - 483 WP_021536813 GNAT family N-acetyltransferase -
HV147_RS27160 (HV147_27160) 46764..47318 - 555 WP_130532805 phospholipase D family protein -
HV147_RS27165 (HV147_27165) 47281..48312 - 1032 WP_000138004 P-type DNA transfer ATPase VirB11 virB11
HV147_RS27170 (HV147_27170) 48305..49459 - 1155 WP_115737954 type IV secretion system protein VirB10 virB10
HV147_RS27175 (HV147_27175) 49456..50343 - 888 WP_000744355 TrbG/VirB9 family P-type conjugative transfer protein virB9
HV147_RS27180 (HV147_27180) 50346..51062 - 717 WP_181562247 virB8 family protein virB8
HV147_RS27185 (HV147_27185) 51065..51235 - 171 WP_021536809 hypothetical protein -
HV147_RS27190 (HV147_27190) 51330..52373 - 1044 WP_172691888 type IV secretion system protein virB6
HV147_RS27195 (HV147_27195) 52392..52628 - 237 WP_000733633 EexN family lipoprotein -
HV147_RS27200 (HV147_27200) 52632..53339 - 708 WP_172691893 type IV secretion system protein virB5
HV147_RS27205 (HV147_27205) 53349..55622 - 2274 WP_239557407 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HV147_RS27210 (HV147_27210) 55979..56293 - 315 WP_001053888 type IV secretion system protein VirB3 virB3
HV147_RS27215 (HV147_27215) 56343..56633 - 291 WP_172691895 TrbC/VirB2 family protein virB2
HV147_RS27220 (HV147_27220) 56617..56934 - 318 WP_050008675 hypothetical protein -
HV147_RS27225 (HV147_27225) 56957..57697 - 741 WP_000815895 lytic transglycosylase domain-containing protein virB1
HV147_RS27230 (HV147_27230) 57760..57996 + 237 WP_021536804 H-NS family nucleoid-associated regulatory protein -
HV147_RS27235 (HV147_27235) 58008..58445 + 438 WP_127676309 hypothetical protein -
HV147_RS27240 (HV147_27240) 58451..58768 + 318 WP_127676310 TrbM/KikA/MpfK family conjugal transfer protein -
HV147_RS27245 (HV147_27245) 58771..59085 + 315 WP_000851068 hypothetical protein tfc15
HV147_RS27250 (HV147_27250) 59061..59786 + 726 WP_227639337 restriction endonuclease -
HV147_RS27255 59952..60188 + 237 WP_127676315 Hha/YmoA family nucleoid-associated regulatory protein -
HV147_RS27260 (HV147_27260) 60213..60650 - 438 WP_127676311 hypothetical protein -
HV147_RS27265 (HV147_27265) 60659..60985 - 327 WP_000817647 endoribonuclease MazF -
HV147_RS27270 (HV147_27270) 60975..61232 - 258 WP_127676312 hypothetical protein -
HV147_RS27275 (HV147_27275) 61244..61489 - 246 WP_021536799 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
HV147_RS27280 (HV147_27280) 61941..62525 + 585 WP_021544366 recombinase family protein -
HV147_RS27285 (HV147_27285) 62558..63442 + 885 WP_021544367 replication protein RepA -

Host bacterium

ID   20924 GenBank   NZ_CP056638
Plasmid name   pRHBSTW-00302_4 Incompatibility group   -
Plasmid size   104193 bp Coordinate of oriT [Strand]   40755..40855 [-]
Host baterium   Citrobacter freundii strain RHBSTW-00302

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -