Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106364
Name   oriT_pCF3863_tetX in_silico
Organism   Citrobacter freundii strain 3863
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP059850 (39928..40028 [+], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 20..26, 38..44  (TAAATCA..TGATTTA)
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_pCF3863_tetX
TATTTATTTTTTTATTTTTTAAATCAGTGTGATAGTGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4264 GenBank   WP_011407157
Name   mobF_H4O05_RS23955_pCF3863_tetX insolico UniProt ID   A0A740S2B6
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120179.41 Da        Isoelectric Point: 6.5766

>WP_011407157.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB A0A740S2B6


Auxiliary protein

ID   1895 GenBank   WP_000706094
Name   WP_000706094_pCF3863_tetX insolico UniProt ID   B6UZ32
Length   96 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 96 a.a.        Molecular weight: 10829.54 Da        Isoelectric Point: 8.5040

>WP_000706094.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MKIVADRLSDVNRKLDYLFDRASDADFGPLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIA
EPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B6UZ32


T4CP

ID   4286 GenBank   WP_000342688
Name   t4cp2_H4O05_RS23960_pCF3863_tetX insolico UniProt ID   _
Length   509 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57762.87 Da        Isoelectric Point: 9.6551

>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI

  Protein domains


Predicted by InterproScan.

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

(113-489)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 13674..39361

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H4O05_RS23785 (H4O05_23700) 8882..9718 - 837 WP_001050931 RepB family plasmid replication initiator protein -
H4O05_RS23790 (H4O05_23705) 10952..11203 + 252 WP_000121743 plasmid stabilization protein -
H4O05_RS23795 (H4O05_23710) 11193..11474 + 282 WP_000220560 type II toxin-antitoxin system RelE/ParE family toxin -
H4O05_RS23800 (H4O05_23715) 11549..12246 + 698 WP_095033700 IS1-like element IS1B family transposase -
H4O05_RS23805 (H4O05_23720) 12392..12649 + 258 WP_105278499 hypothetical protein -
H4O05_RS23810 (H4O05_23725) 12686..13654 - 969 WP_077783444 IS5 family transposase -
H4O05_RS23815 (H4O05_23730) 13671..13964 + 294 Protein_17 peptidoglycan DD-metalloendopeptidase family protein -
H4O05_RS23820 (H4O05_23735) 13998..14093 - 96 Protein_18 DUF2933 domain-containing protein -
H4O05_RS23825 (H4O05_23740) 14158..14862 + 705 WP_001067855 IS6-like element IS26 family transposase -
H4O05_RS23830 (H4O05_23750) 15707..16552 + 846 WP_164538741 macrolide hydrolase EstT -
H4O05_RS23835 (H4O05_23755) 16542..17699 + 1158 WP_094309310 tetracycline-inactivating monooxygenase Tet(X4) -
H4O05_RS23840 (H4O05_23760) 18038..19480 + 1443 Protein_22 IS91-like element ISVsa3 family transposase -
H4O05_RS23845 (H4O05_23765) 19842..20546 + 705 WP_001067855 IS6-like element IS26 family transposase -
H4O05_RS23850 (H4O05_23770) 20608..20805 - 198 WP_000844102 hypothetical protein -
H4O05_RS23855 (H4O05_23775) 20810..21247 - 438 WP_020325134 restriction endonuclease -
H4O05_RS23860 (H4O05_23780) 21507..21818 - 312 WP_001452736 hypothetical protein -
H4O05_RS23865 (H4O05_23785) 21854..22168 - 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
H4O05_RS23870 (H4O05_23790) 22131..22508 - 378 WP_000504251 hypothetical protein -
H4O05_RS23875 (H4O05_23795) 22524..22895 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
H4O05_RS23880 (H4O05_23800) 22938..23672 + 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
H4O05_RS23885 (H4O05_23805) 23681..23962 + 282 WP_000440698 transcriptional repressor KorA -
H4O05_RS23890 (H4O05_23810) 23972..24265 + 294 WP_000209137 TrbC/VirB2 family protein virB2
H4O05_RS23895 (H4O05_23815) 24315..24632 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
H4O05_RS23900 (H4O05_23820) 24632..27232 + 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
H4O05_RS23905 (H4O05_23825) 27250..27963 + 714 WP_000749362 type IV secretion system protein virB5
H4O05_RS23910 (H4O05_23830) 27971..28198 + 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
H4O05_RS23915 (H4O05_23835) 28214..29254 + 1041 WP_000886022 type IV secretion system protein virB6
H4O05_RS23920 (H4O05_23840) 29337..29483 + 147 WP_001257173 conjugal transfer protein TraN -
H4O05_RS23925 (H4O05_23845) 29473..30171 + 699 WP_000646594 type IV secretion system protein virB8
H4O05_RS23930 (H4O05_23850) 30182..31066 + 885 WP_185229345 TrbG/VirB9 family P-type conjugative transfer protein virB9
H4O05_RS23935 (H4O05_23855) 31066..32226 + 1161 WP_000101711 type IV secretion system protein VirB10 virB10
H4O05_RS23940 (H4O05_23860) 32268..33263 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
H4O05_RS23945 (H4O05_23865) 33263..33796 + 534 WP_000731968 phospholipase D family protein -
H4O05_RS23950 (H4O05_23870) 33970..34596 - 627 WP_000434930 DUF6710 family protein -
H4O05_RS23955 (H4O05_23875) 34596..37832 - 3237 WP_011407157 MobF family relaxase -
H4O05_RS23960 (H4O05_23880) 37832..39361 - 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
H4O05_RS23965 (H4O05_23885) 39363..39653 - 291 WP_000706094 hypothetical protein -
H4O05_RS23970 40292..40711 + 420 WP_000802909 plasmid stabilization protein StbA -
H4O05_RS23975 (H4O05_23895) 40720..41436 + 717 WP_000861577 StbB family protein -
H4O05_RS23980 (H4O05_23900) 41438..41806 + 369 WP_000414913 plasmid stabilization protein StbC -
H4O05_RS23985 (H4O05_23905) 41988..42332 + 345 WP_000999874 hypothetical protein -
H4O05_RS23990 (H4O05_23910) 42443..42763 - 321 WP_000211833 protein CcgAII -
H4O05_RS23995 (H4O05_23915) 42818..42997 - 180 WP_000214483 protein CcgAI -
H4O05_RS24000 (H4O05_23920) 43829..44338 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   6801 GenBank   NZ_CP059850
Plasmid name   pCF3863_tetX Incompatibility group   IncN
Plasmid size   51531 bp Coordinate of oriT [Strand]   39928..40028 [+]
Host baterium   Citrobacter freundii strain 3863

Cargo genes

Drug resistance gene   tet(X4)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -