Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121115
Name   oriT_pF621-IMP in_silico
Organism   Citrobacter portucalensis strain F621
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137172 (39696..39796 [+], 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_pF621-IMP
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13332 GenBank   WP_012561166
Name   mobF_R2X24_RS24150_pF621-IMP 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   7381 GenBank   WP_000706094
Name   WP_000706094_pF621-IMP 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   15621 GenBank   WP_000342688
Name   t4cp2_R2X24_RS24155_pF621-IMP 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: 15387..25712

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R2X24_RS23980 (R2X24_23980) 11232..12665 - 1434 WP_001288432 DNA cytosine methyltransferase -
R2X24_RS23985 (R2X24_23985) 12764..13036 + 273 Protein_13 IS1 family transposase -
R2X24_RS23990 (R2X24_23990) 13047..13253 - 207 WP_001749967 hypothetical protein -
R2X24_RS23995 (R2X24_23995) 13258..13695 - 438 WP_020325134 restriction endonuclease -
R2X24_RS24000 (R2X24_24000) 13955..14266 - 312 WP_001452736 hypothetical protein -
R2X24_RS24005 (R2X24_24005) 14302..14616 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
R2X24_RS24010 (R2X24_24010) 14613..14957 - 345 WP_001749964 hypothetical protein -
R2X24_RS24015 (R2X24_24015) 14973..15344 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
R2X24_RS24020 (R2X24_24020) 15387..16121 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
R2X24_RS24025 (R2X24_24025) 16130..16411 + 282 WP_000440698 transcriptional repressor KorA -
R2X24_RS24030 (R2X24_24030) 16421..16714 + 294 WP_001749962 hypothetical protein virB2
R2X24_RS24035 (R2X24_24035) 16764..17081 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
R2X24_RS24040 (R2X24_24040) 17081..19681 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
R2X24_RS24045 (R2X24_24045) 19699..20412 + 714 WP_001749960 type IV secretion system protein virB5
R2X24_RS24050 (R2X24_24050) 20420..20647 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
R2X24_RS24055 (R2X24_24055) 20663..21703 + 1041 WP_001749958 type IV secretion system protein virB6
R2X24_RS24060 (R2X24_24060) 21786..21932 + 147 WP_001257173 conjugal transfer protein TraN -
R2X24_RS24065 (R2X24_24065) 21922..22620 + 699 WP_000646594 virB8 family protein virB8
R2X24_RS24070 (R2X24_24070) 22631..23515 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
R2X24_RS24075 (R2X24_24075) 23515..24675 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
R2X24_RS24080 (R2X24_24080) 24717..25712 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
R2X24_RS24085 (R2X24_24085) 25712..26245 + 534 WP_000792636 phospholipase D family protein -
R2X24_RS24090 (R2X24_24090) 26419..26706 - 288 Protein_34 DUF6710 family protein -
R2X24_RS24095 (R2X24_24095) 26973..27152 + 180 Protein_35 helix-turn-helix domain-containing protein -
R2X24_RS24100 (R2X24_24100) 27217..27921 + 705 WP_001067855 IS6-like element IS26 family transposase -
R2X24_RS24105 (R2X24_24105) 27975..28606 - 632 Protein_37 transposase -
R2X24_RS24110 (R2X24_24110) 29001..29657 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
R2X24_RS24115 (R2X24_24115) 29976..30590 - 615 WP_014839983 recombinase family protein -

Host bacterium

ID   21543 GenBank   NZ_CP137172
Plasmid name   pF621-IMP Incompatibility group   IncN
Plasmid size   52865 bp Coordinate of oriT [Strand]   39696..39796 [+]
Host baterium   Citrobacter portucalensis strain F621

Cargo genes

Drug resistance gene   blaIMP-4, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -