Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120459
Name   oriT_pNY2385-IMP in_silico
Organism   Citrobacter freundii strain NY2385
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP096922 (49045..49145 [+], 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_pNY2385-IMP
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12883 GenBank   WP_270158060
Name   mobF_M2J86_RS24335_pNY2385-IMP insolico UniProt ID   _
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120175.31 Da        Isoelectric Point: 6.5229

>WP_270158060.1 MobF family relaxase [Citrobacter freundii]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWFDSLTNSGMRADKARFA
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



No available structure.




Auxiliary protein

ID   7258 GenBank   WP_000706094
Name   WP_000706094_pNY2385-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   15132 GenBank   WP_000342688
Name   t4cp2_M2J86_RS24340_pNY2385-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: 15426..23554

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
M2J86_RS24135 (M2J86_24005) 11271..12704 - 1434 WP_001288432 DNA cytosine methyltransferase -
M2J86_RS24140 (M2J86_24010) 12803..13075 + 273 Protein_13 IS1 family transposase -
M2J86_RS24145 (M2J86_24015) 13086..13292 - 207 WP_001749967 hypothetical protein -
M2J86_RS24150 (M2J86_24020) 13297..13944 - 648 WP_015344958 restriction endonuclease -
M2J86_RS24155 (M2J86_24025) 13994..14305 - 312 WP_001452736 hypothetical protein -
M2J86_RS24160 (M2J86_24030) 14341..14655 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
M2J86_RS24165 (M2J86_24035) 14652..14996 - 345 WP_001749964 hypothetical protein -
M2J86_RS24170 (M2J86_24040) 15012..15383 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
M2J86_RS24175 (M2J86_24045) 15426..16160 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
M2J86_RS24180 (M2J86_24050) 16169..16450 + 282 WP_000440698 transcriptional repressor KorA -
M2J86_RS24185 (M2J86_24055) 16460..16753 + 294 WP_001749962 hypothetical protein virB2
M2J86_RS24190 (M2J86_24060) 16803..17120 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
M2J86_RS24195 (M2J86_24065) 17120..19720 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
M2J86_RS24200 (M2J86_24070) 19738..20451 + 714 WP_001749960 type IV secretion system protein virB5
M2J86_RS24205 (M2J86_24075) 20459..20686 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
M2J86_RS24210 (M2J86_24080) 20702..21742 + 1041 WP_001749958 type IV secretion system protein virB6
M2J86_RS24215 21825..21971 + 147 WP_001257173 conjugal transfer protein TraN -
M2J86_RS24220 (M2J86_24085) 21961..22659 + 699 WP_000646594 virB8 family protein virB8
M2J86_RS24225 (M2J86_24090) 22670..23554 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
M2J86_RS24230 (M2J86_24095) 23554..24231 + 678 Protein_31 conjugal transfer protein TraF -
M2J86_RS24235 (M2J86_24100) 24264..27269 - 3006 WP_013213984 Tn3-like element Tn3 family transposase -
M2J86_RS24240 (M2J86_24105) 27432..27989 + 558 WP_001217881 recombinase family protein -

Host bacterium

ID   20888 GenBank   NZ_CP096922
Plasmid name   pNY2385-IMP Incompatibility group   IncN
Plasmid size   62214 bp Coordinate of oriT [Strand]   49045..49145 [+]
Host baterium   Citrobacter freundii strain NY2385

Cargo genes

Drug resistance gene   blaIMP-4, blaKPC-2, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -