Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119090
Name   oriT_pCA71-IMP in_silico
Organism   Citrobacter amalonaticus strain CA71
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP064181 (26701..26801 [-], 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_pCA71-IMP
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12056 GenBank   WP_012561166
Name   mobF_ISX58_RS23895_pCA71-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   6891 GenBank   WP_001749975
Name   WP_001749975_pCA71-IMP insolico UniProt ID   A0A5C2CVS6
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A5C2CVS6


T4CP

ID   14119 GenBank   WP_000342688
Name   t4cp2_ISX58_RS23890_pCA71-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: 40785..51110

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ISX58_RS23930 (ISX58_23930) 35907..36521 + 615 WP_014839983 recombinase family protein -
ISX58_RS23935 (ISX58_23935) 36840..37496 - 657 WP_001516695 quinolone resistance pentapeptide repeat protein QnrS1 -
ISX58_RS23940 (ISX58_23940) 37891..38522 + 632 Protein_45 transposase -
ISX58_RS23945 (ISX58_23945) 38576..39280 - 705 WP_001067855 IS6-like element IS26 family transposase -
ISX58_RS23950 (ISX58_23950) 39345..39524 - 180 Protein_47 helix-turn-helix domain-containing protein -
ISX58_RS24450 39791..40078 + 288 Protein_48 DUF6710 family protein -
ISX58_RS23960 (ISX58_23960) 40252..40785 - 534 WP_000792636 phospholipase D family protein -
ISX58_RS23965 (ISX58_23965) 40785..41780 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
ISX58_RS23970 (ISX58_23970) 41822..42982 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
ISX58_RS23975 (ISX58_23975) 42982..43866 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
ISX58_RS23980 (ISX58_23980) 43877..44575 - 699 WP_000646594 virB8 family protein virB8
ISX58_RS24455 44565..44723 - 159 WP_012561180 hypothetical protein -
ISX58_RS23985 (ISX58_23985) 44794..45834 - 1041 WP_001749958 type IV secretion system protein virB6
ISX58_RS23990 (ISX58_23990) 45850..46077 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
ISX58_RS23995 (ISX58_23995) 46085..46798 - 714 WP_001749960 type IV secretion system protein virB5
ISX58_RS24000 (ISX58_24000) 46816..49284 - 2469 WP_224743086 VirB4 family type IV secretion/conjugal transfer ATPase virb4
ISX58_RS24005 (ISX58_24005) 49416..49733 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
ISX58_RS24010 (ISX58_24010) 49783..50076 - 294 WP_001749962 hypothetical protein virB2
ISX58_RS24015 (ISX58_24015) 50086..50367 - 282 WP_000440698 transcriptional repressor KorA -
ISX58_RS24020 (ISX58_24020) 50376..51110 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
ISX58_RS24025 (ISX58_24025) 51219..51524 + 306 WP_000960954 H-NS family nucleoid-associated regulatory protein -
ISX58_RS24030 (ISX58_24030) 51540..51884 + 345 WP_001749964 hypothetical protein -
ISX58_RS24035 (ISX58_24035) 51881..52195 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
ISX58_RS24040 (ISX58_24040) 52231..52542 + 312 WP_001452736 hypothetical protein -

Host bacterium

ID   19522 GenBank   NZ_CP064181
Plasmid name   pCA71-IMP Incompatibility group   IncN
Plasmid size   52790 bp Coordinate of oriT [Strand]   26701..26801 [-]
Host baterium   Citrobacter amalonaticus strain CA71

Cargo genes

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