Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116532
Name   oriT_pF3021-IMP in_silico
Organism   Citrobacter freundii strain F3021
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137122 (36035..36135 [+], 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_pF3021-IMP
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10556 GenBank   WP_284246358
Name   TrwC_R2X28_RS00240_pF3021-IMP insolico UniProt ID   _
Length   74 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 74 a.a.        Molecular weight: 7978.70 Da        Isoelectric Point: 4.3059

>WP_284246358.1 relaxase domain-containing protein [Citrobacter freundii]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESGEHKKYWGSVSYAAIAGP
FPSL

  Protein domains



No domain identified.



  Protein structure



No available structure.




Auxiliary protein

ID   6198 GenBank   WP_000706094
Name   WP_000706094_pF3021-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   12337 GenBank   WP_000342688
Name   t4cp2_R2X28_RS00245_pF3021-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: 15386..35468

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R2X28_RS00080 (R2X28_00080) 11231..12664 - 1434 WP_001288432 DNA cytosine methyltransferase -
R2X28_RS00085 (R2X28_00085) 12763..13035 + 273 Protein_13 IS1 family transposase -
R2X28_RS00090 (R2X28_00090) 13046..13252 - 207 WP_001749967 hypothetical protein -
R2X28_RS00095 (R2X28_00095) 13257..13904 - 648 WP_015344958 restriction endonuclease -
R2X28_RS00100 (R2X28_00100) 13954..14265 - 312 WP_001452736 hypothetical protein -
R2X28_RS00105 (R2X28_00105) 14301..14615 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
R2X28_RS00110 (R2X28_00110) 14612..14956 - 345 WP_001749964 hypothetical protein -
R2X28_RS00115 (R2X28_00115) 14972..15343 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
R2X28_RS00120 (R2X28_00120) 15386..16120 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
R2X28_RS00125 (R2X28_00125) 16129..16410 + 282 WP_000440698 transcriptional repressor KorA -
R2X28_RS00130 (R2X28_00130) 16420..16713 + 294 WP_001749962 hypothetical protein virB2
R2X28_RS00135 (R2X28_00135) 16763..17080 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
R2X28_RS00140 (R2X28_00140) 17080..19680 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
R2X28_RS00145 (R2X28_00145) 19698..20411 + 714 WP_001749960 type IV secretion system protein virB5
R2X28_RS00150 (R2X28_00150) 20419..20646 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
R2X28_RS00155 (R2X28_00155) 20662..21702 + 1041 WP_001749958 type IV secretion system protein virB6
R2X28_RS00160 (R2X28_00160) 21785..21931 + 147 WP_001257173 conjugal transfer protein TraN -
R2X28_RS00165 (R2X28_00165) 21921..22619 + 699 WP_000646594 virB8 family protein virB8
R2X28_RS00170 (R2X28_00170) 22630..23514 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
R2X28_RS00175 (R2X28_00175) 23514..24674 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
R2X28_RS00180 (R2X28_00180) 24716..25711 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
R2X28_RS00185 (R2X28_00185) 25711..26244 + 534 WP_000792636 phospholipase D family protein -
R2X28_RS00190 (R2X28_00190) 26418..26705 - 288 Protein_34 DUF6710 family protein -
R2X28_RS00195 (R2X28_00195) 26972..27151 + 180 Protein_35 helix-turn-helix domain-containing protein -
R2X28_RS00200 (R2X28_00200) 27216..27920 + 705 WP_001067855 IS6-like element IS26 family transposase -
R2X28_RS00205 (R2X28_00205) 27974..28605 - 632 Protein_37 transposase -
R2X28_RS00210 (R2X28_00210) 29000..29656 + 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
R2X28_RS00215 (R2X28_00215) 29975..30589 - 615 WP_014839983 recombinase family protein -
R2X28_RS00220 (R2X28_00220) 30751..30933 + 183 Protein_40 DUF4158 domain-containing protein -
R2X28_RS00225 (R2X28_00225) 31069..31614 + 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -
R2X28_RS00230 (R2X28_00230) 31751..32323 + 573 WP_001493762 recombinase family protein -
R2X28_RS00235 (R2X28_00235) 32360..33751 + 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
R2X28_RS00240 (R2X28_00240) 33715..33939 - 225 WP_284246358 relaxase domain-containing protein -
R2X28_RS00245 (R2X28_00245) 33939..35468 - 1530 WP_000342688 type IV secretion system DNA-binding domain-containing protein virb4
R2X28_RS00250 (R2X28_00250) 35470..35760 - 291 WP_000706094 hypothetical protein -
R2X28_RS00255 (R2X28_00255) 36377..36796 + 420 WP_001749974 plasmid stabilization protein StbA -
R2X28_RS00260 (R2X28_00260) 36805..37521 + 717 WP_001749973 StbB family protein -
R2X28_RS00265 (R2X28_00265) 37523..37891 + 369 WP_000414913 plasmid stabilization protein StbC -
R2X28_RS00270 (R2X28_00270) 38073..38417 + 345 WP_000999874 hypothetical protein -
R2X28_RS00275 (R2X28_00275) 38528..38848 - 321 WP_001749971 protein CcgAII -
R2X28_RS00280 (R2X28_00280) 38903..39082 - 180 WP_000214483 protein CcgAI -
R2X28_RS00285 (R2X28_00285) 39809..40318 - 510 WP_000129958 antirestriction protein ArdA -

Host bacterium

ID   16965 GenBank   NZ_CP137122
Plasmid name   pF3021-IMP Incompatibility group   IncN
Plasmid size   49204 bp Coordinate of oriT [Strand]   36035..36135 [+]
Host baterium   Citrobacter freundii strain F3021

Cargo genes

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