Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116007
Name   oriT_pIsolateL_B in_silico
Organism   Citrobacter freundii strain isolateL
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP135452 (72417..72517 [+], 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_pIsolateL_B
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10233 GenBank   WP_012561166
Name   mobF_RRL10_RS26125_pIsolateL_B insolico UniProt ID   D7RU03
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
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 D7RU03


Auxiliary protein

ID   6022 GenBank   WP_000706094
Name   WP_000706094_pIsolateL_B 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   11956 GenBank   WP_000342688
Name   t4cp2_RRL10_RS26130_pIsolateL_B 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: 21819..32144

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RRL10_RS25865 (RRL10_25865) 17664..19097 - 1434 WP_001288432 DNA cytosine methyltransferase -
RRL10_RS25870 (RRL10_25870) 19196..19468 + 273 Protein_21 IS1 family transposase -
RRL10_RS25875 (RRL10_25875) 19479..19685 - 207 WP_001749967 hypothetical protein -
RRL10_RS25880 (RRL10_25880) 19690..20337 - 648 WP_015344958 restriction endonuclease -
RRL10_RS25885 (RRL10_25885) 20387..20698 - 312 WP_001452736 hypothetical protein -
RRL10_RS25890 (RRL10_25890) 20734..21048 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
RRL10_RS25895 (RRL10_25895) 21045..21389 - 345 WP_001749964 hypothetical protein -
RRL10_RS25900 (RRL10_25900) 21405..21776 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
RRL10_RS25905 (RRL10_25905) 21819..22553 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
RRL10_RS25910 (RRL10_25910) 22562..22843 + 282 WP_000440698 transcriptional repressor KorA -
RRL10_RS25915 (RRL10_25915) 22853..23146 + 294 WP_001749962 hypothetical protein virB2
RRL10_RS25920 (RRL10_25920) 23196..23513 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
RRL10_RS25925 (RRL10_25925) 23513..26113 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
RRL10_RS25930 (RRL10_25930) 26131..26844 + 714 WP_001749960 type IV secretion system protein virB5
RRL10_RS25935 (RRL10_25935) 26852..27079 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
RRL10_RS25940 (RRL10_25940) 27095..28135 + 1041 WP_001749958 type IV secretion system protein virB6
RRL10_RS25945 (RRL10_25945) 28218..28364 + 147 WP_001257173 conjugal transfer protein TraN -
RRL10_RS25950 (RRL10_25950) 28354..29052 + 699 WP_000646594 virB8 family protein virB8
RRL10_RS25955 (RRL10_25955) 29063..29947 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
RRL10_RS25960 (RRL10_25960) 29947..31107 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
RRL10_RS25965 (RRL10_25965) 31149..32144 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
RRL10_RS25970 (RRL10_25970) 32144..32677 + 534 WP_000792636 phospholipase D family protein -
RRL10_RS25975 (RRL10_25975) 32851..33057 - 207 WP_315690158 DUF6710 family protein -
RRL10_RS25980 (RRL10_25980) 33074..35902 - 2829 Protein_43 Tn3 family transposase -

Host bacterium

ID   16440 GenBank   NZ_CP135452
Plasmid name   pIsolateL_B Incompatibility group   IncN
Plasmid size   85586 bp Coordinate of oriT [Strand]   72417..72517 [+]
Host baterium   Citrobacter freundii strain isolateL

Cargo genes

Drug resistance gene   aac(6')-Ib-cr, ARR-3, dfrA27, aadA16, qacE, sul1, qnrB6, blaKPC-3
Virulence gene   -
Metal resistance gene   arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -