Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120460
Name   oriT_p705SK3_1 in_silico
Organism   Citrobacter freundii strain 705SK3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP022152 (146155..146439 [+], 285 nt)
oriT length   285 nt
IRs (inverted repeats)      184..189, 191..196  (AAAAGT..ACTTTT)
Location of nic site      109..110
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 285 nt

>oriT_p705SK3_1
GGTTATTGCTACTTAATGCCGATAACGACTCAGGCTTTGAGGTTTTTTTATACGGTTCACATTTCGTTAGCAAGGTCAGGGTTTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTATGGGTAATGGCTGAAAGGTTAGTTTTAAGGTTCAAAGCGGCAGTATTAAAATTCCAAAAGTTACTTTTCATCCTTCAGAATCCAGACCTTAATTTCATGTAGAAGATTCGTACAATTGTATTGGCGCAAGGACAATCCGCACATGTCAGAATCAGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12884 GenBank   WP_007372219
Name   mobH_CES93_RS27450_p705SK3_1 insolico UniProt ID   J5UNX4
Length   900 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 900 a.a.        Molecular weight: 102218.41 Da        Isoelectric Point: 5.6551

>WP_007372219.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MLRHIKNILNTFLPDNKKATTDLFGDEIDMSVDEEIGKLISSRDNMRYPASEIGFPAQVPGEYVLRHYQK
PLVMAIKRELDIRDSEFNQLILPMLINFANFVHLFPASENHHHRAATGLLRHSLEVCFQCIRRSKNIEFD
SMAVPVHKSNRALAWRLAVAAGGLLHDLGKPFTDFEVWNEDGKIHWPPGHEPIHVWAKENNVKRYYLVWK
PGRHRQHTSSTSNMLLMIMPKEMHVYLLNGGNDIFNELTRALNASAQLNAEKISGQDVKNKILTTIKAAD
SASVNYDMRQYAGDAIRASQSGVPAVQRVVDAMRHRLKKGDWIPNKPGSPVWVTTYGVFIVWGVAVKDII
ETVRNSGAVIPQTQNSLADLMLSYHLCRPNVHQDDDTAYWRIAPHILNDKSSRESKDPKVALSCILLISP
EVLFVDTVDPLPCSSRIRIEGKWVEYLTGRPNQPKLVESEPYIGQKPVPSTGIPNEVDRSVLQGGTIIAD
EQESPLESIFGNRQVTPENAHELLHKLNLLSDEDYNRVKERNTSTKNQKDCLDDTNSPTTELAGSGESKG
LKDNQPKPVSENNEPKRRLSLKETLASAQTEIEFSVPSSLIKEPNHKTLNETLEFHSIINSYNSNEPTSS
DALDQTQPSPTRQALKEIQLHQDAVDTGIQSGEVIDDYSIYEDYDSMWQDDVKADNDFGYSAHADTSANI
PANVKFYDKFSQLYVSGLEAAKEFLVKYVTDHSDDLFIESGHLIIAIDKDFDERNYALLQDSNWLWQRFM
EAPAQYYFHRTQKCLYLRKELNNDIDLLMDGKFNDLLYSALTDVSDKDYNITDLCNEMISKGMLKRTYSG
EPVIAVSVALKRRIADELGIDITQLQKIMLMHFDFYSKTGVDYILPNSERMHNQMVDKDE

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(54-380)


  Protein structure


Source ID Structure
AlphaFold DB J5UNX4


T4CP

ID   15133 GenBank   WP_007372220
Name   traD_CES93_RS27455_p705SK3_1 insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 73279.47 Da        Isoelectric Point: 7.9696

>WP_007372220.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSEWKYNLRWRTNFEGLETLGWTAGIAATIGVNTLFNMPSLPCYLSVAVQAAYGIRSLPAAWDIYTHKRR
LKRKPKPLVMDMKSFIEQMIREPDSYLICRGFEWGQNEGQLASELIKRDIKKFVAKPSKNFMGLGWIHAL
GKKNEWIGISEELLSLHTLITGTTGSGKTTYFKLLILQAALKKQPLILIDPKNDEELAEWMKFCLELVDR
STKYNYVSLAHPEKSARISPITNYTQAGEVANRITSVIQRADSTSDPFVSFGIMSLTTVVELMKICEIKP
TLRNIKSQLSADISSLASLLIMAITKFGHKTLGESDFDIILQAKIDRYSSKIKGPKEIAEICADIYRNDI
KGNKGKGDTSIEAGIDMFGHQREHFQKMILNVMPILSQLTQGFMSELLSPDSADEDELNDTRPISNIQDI
ITTGGMLYLGLNSLADAETGSAVGSIFLSDITSVSSTVYNFLKPGGQDLASVMVLIDEAAEVINDQVIKM
LNKTRGAGFRLFISSQSTSDFEARLGSEAKMKQVITNTNHFTALRTPDPDAQEAVMKRVPPTKFKYIMRG
HGSSAGADPEQITGSVGERLMEEEGELFQSQLLGWLPNLECMAINQANKIVKGKVPVILMPRNESELSDV
RTIAKKYLSIYERQQKVRGEKSRISAEG

  Protein domains


Predicted by InterproScan.

AAA-like domain (AAA_10)

(155-247)

TraM recognition site of TraD and TraG (TraG-D_C)

(472-558)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 167036..193402

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CES93_RS27395 (CES93_27400) 162207..163541 - 1335 WP_009653617 restriction endonuclease subunit S -
CES93_RS27400 (CES93_27405) 163538..165565 - 2028 WP_009653620 class I SAM-dependent DNA methyltransferase -
CES93_RS27405 (CES93_27410) 165724..166803 + 1080 WP_007372212 restriction endonuclease -
CES93_RS27410 (CES93_27415) 167036..168364 + 1329 WP_007372213 hypothetical protein virB9
CES93_RS29290 168423..169115 + 693 WP_016241592 hypothetical protein -
CES93_RS27420 (CES93_27425) 169151..169723 - 573 WP_016241591 phospholipase D family protein -
CES93_RS27425 (CES93_27430) 169985..170320 + 336 WP_007372215 TraA family conjugative transfer protein -
CES93_RS27430 (CES93_27435) 170369..170656 - 288 WP_007372216 DUF1294 domain-containing protein -
CES93_RS27435 (CES93_27440) 170832..172307 + 1476 WP_007372217 UvrD-helicase domain-containing protein -
CES93_RS27440 (CES93_27445) 172347..173246 - 900 WP_016241590 DsbA family protein -
CES93_RS27445 (CES93_27450) 173269..173838 - 570 WP_016241589 hypothetical protein -
CES93_RS27450 (CES93_27455) 173988..176690 + 2703 WP_007372219 MobH family relaxase -
CES93_RS27455 (CES93_27460) 176683..178659 + 1977 WP_007372220 conjugative transfer system coupling protein TraD virb4
CES93_RS27460 (CES93_27465) 178662..179048 + 387 WP_009654243 hypothetical protein -
CES93_RS27465 (CES93_27470) 179033..179683 + 651 WP_007372221 DUF4400 domain-containing protein tfc7
CES93_RS27470 (CES93_27475) 179768..180061 + 294 WP_007372222 hypothetical protein -
CES93_RS27475 (CES93_27480) 180058..180876 + 819 WP_007372223 thioredoxin domain-containing protein -
CES93_RS27480 (CES93_27485) 180926..181210 + 285 WP_007372224 type IV conjugative transfer system protein TraL traL
CES93_RS27485 (CES93_27490) 181207..181833 + 627 WP_007372225 TraE/TraK family type IV conjugative transfer system protein traE
CES93_RS27490 (CES93_27495) 181993..183111 + 1119 WP_016241588 type-F conjugative transfer system secretin TraK traK
CES93_RS27495 (CES93_27500) 183116..184513 + 1398 WP_007372227 TraB/VirB10 family protein traB
CES93_RS27500 (CES93_27505) 184510..185076 + 567 WP_016241587 type IV conjugative transfer system lipoprotein TraV traV
CES93_RS27505 (CES93_27510) 185170..186768 + 1599 WP_007372228 YadA-like family protein -
CES93_RS27510 (CES93_27515) 186949..187713 + 765 WP_007372229 DsbC family protein -
CES93_RS27515 (CES93_27520) 187741..190227 + 2487 WP_007372230 type IV secretion system protein TraC virb4
CES93_RS27520 (CES93_27525) 190224..190496 + 273 WP_007372231 hypothetical protein -
CES93_RS27525 (CES93_27530) 190507..191031 + 525 WP_007372232 signal peptidase I -
CES93_RS27530 (CES93_27535) 191025..192338 + 1314 WP_232482716 TrbC family F-type conjugative pilus assembly protein traW
CES93_RS27535 (CES93_27540) 192335..193402 + 1068 WP_007372234 TraU family protein traU
CES93_RS27540 (CES93_27545) 193451..194197 - 747 WP_009653890 AcaB family transcriptional regulator -
CES93_RS27545 (CES93_27550) 194635..195246 + 612 WP_009653893 hypothetical protein -
CES93_RS27550 (CES93_27555) 195309..195809 + 501 WP_016241582 hypothetical protein -
CES93_RS28825 196176..196940 + 765 WP_016241581 single-stranded DNA-binding protein -

Region 2: 212931..225896

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CES93_RS27620 (CES93_27625) 208025..208225 - 201 WP_032640629 hypothetical protein -
CES93_RS27625 (CES93_27630) 208438..209463 + 1026 WP_040118421 IS630 family transposase -
CES93_RS27630 (CES93_27635) 210076..211101 - 1026 WP_040118421 IS630 family transposase -
CES93_RS27635 (CES93_27640) 211181..211441 + 261 WP_016241576 hypothetical protein -
CES93_RS27640 (CES93_27645) 211466..211855 + 390 WP_016241575 hypothetical protein -
CES93_RS27645 (CES93_27650) 211877..212398 + 522 WP_007372245 hypothetical protein -
CES93_RS27650 (CES93_27655) 212615..212953 + 339 WP_024196083 hypothetical protein -
CES93_RS27655 (CES93_27660) 212931..214031 + 1101 WP_088732518 conjugal transfer protein TraF traF
CES93_RS27660 (CES93_27665) 214028..215470 + 1443 WP_009653894 conjugal transfer protein TraH traH
CES93_RS29430 215485..216033 + 549 WP_326929652 conjugal transfer protein TraG N-terminal domain-containing protein traG
CES93_RS29295 215963..216982 + 1020 WP_326929653 conjugal transfer protein TraG N-terminal domain-containing protein traG
CES93_RS29300 217340..217483 - 144 WP_232482717 hypothetical protein -
CES93_RS29305 217639..218151 + 513 WP_232482718 hypothetical protein -
CES93_RS29310 218148..218366 + 219 WP_232482719 hypothetical protein -
CES93_RS29315 218363..219013 + 651 WP_232482720 hypothetical protein -
CES93_RS27675 (CES93_27680) 219449..222106 + 2658 WP_007372250 conjugal transfer mating pair stabilization protein TraN traN
CES93_RS27680 (CES93_27685) 222151..222921 - 771 WP_007372251 hypothetical protein -
CES93_RS27685 (CES93_27690) 223049..223465 - 417 WP_326929654 FlhC family transcriptional regulator -
CES93_RS27695 (CES93_27700) 224813..225343 - 531 WP_016241572 hypothetical protein -
CES93_RS27700 (CES93_27705) 225336..225896 - 561 WP_016241571 transglycosylase SLT domain-containing protein virB1
CES93_RS27705 (CES93_27710) 225926..226456 - 531 WP_016241570 hypothetical protein -
CES93_RS27710 (CES93_27715) 226471..227493 - 1023 WP_007372253 ParM/StbA family protein -
CES93_RS27715 (CES93_27720) 228020..229167 + 1148 WP_087121881 IS3 family transposase -
CES93_RS27720 (CES93_27725) 229909..230340 + 432 WP_016241569 conjugative transfer protein MobI(A/C) -

Host bacterium

ID   20889 GenBank   NZ_CP022152
Plasmid name   p705SK3_1 Incompatibility group   -
Plasmid size   296175 bp Coordinate of oriT [Strand]   146155..146439 [+]
Host baterium   Citrobacter freundii strain 705SK3

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC, arsB, arsA, arsD, arsR, yqjH, fecD, fecE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7