Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120422
Name   oriT_p31A20001_F_KPC_KPC in_silico
Organism   Citrobacter freundii strain 31A20CPO001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ821187 (51195..51293 [+], 99 nt)
oriT length   99 nt
IRs (inverted repeats)      24..31, 34..41  (TAACCGGC..GCCGGTTA)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  TCCTGCCCGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 99 nt

>oriT_p31A20001_F_KPC_KPC
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12859 GenBank   WP_011114057
Name   traI_SLH58_RS00220_p31A20001_F_KPC_KPC insolico UniProt ID   A0A4P7LSA6
Length   746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82038.71 Da        Isoelectric Point: 10.7900

>WP_011114057.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Bacteria]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
LQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)


  Protein structure


Source ID Structure
AlphaFold DB A0A4P7LSA6


T4CP

ID   15105 GenBank   WP_011342945
Name   t4cp2_SLH58_RS00070_p31A20001_F_KPC_KPC insolico UniProt ID   _
Length   852 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 852 a.a.        Molecular weight: 93952.10 Da        Isoelectric Point: 6.3901

>WP_011342945.1 MULTISPECIES: VirB4 family type IV secretion/conjugal transfer ATPase [Pseudomonadota]
MIEAIAIAIAVLGAVLLLILFARIRAVDAELKLKKHRAKDAGLADLLNYAAAVDDGVIVGKNGSFMAAWL
YKGDDNASSTEEQREMVSFRINQALAGLGNGWMVHVDAVRRPAPNYSERGVSSFPDSVSFAIDEERRRLF
EGLGAMFEGYFVLTVTWFPPVLAQRKFVELMFDDDAVAPDHTARTTGLIAQFKREITSLESRLSSAVKMT
RLRGQKVVSEEGREVTHDDFLSWLQFCVTGLHHPVMLPSNPMYLDAVIGGQELWGGVVPKIGRKFIQVVA
IEGFPLESTPGVLSALAELPSEYRWSSRFIFMDQHESLKHLDKFRKKWKQKIRGFFDQVFNTNTGSINQD
AAAMVGDAEAAIAEVNSGLVAAGYYTSVVVLMDEDRERLAASALLVEKAVNRLAFAARIETINTLDAYLG
SLPGHGVENVRRPLINTMNLADLLPTSSIWTGSATAPCPMYPPLSPALMHCVTVGATPFRLNLHVRDLGH
TFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMSMYPLAAGIRAATKGKSGLHFTVAADDDRLAFC
PLQFLETKGDRAWAMEWIDTILALNGVNTTPAQRNEIGNAIMSMHASGARTLSEFSVTIQDEAIREAIKQ
YTVDGSMGHLLDAEEDGLSLSDFTVFEIEELMNLGEKFALPVLLYLFRRIERALKGQPSVIILDEAWLML
GHPAFRAKIREWLKVLRKANCLVLMATQSLSDAANSGILDVIVESTATKIFLPNVYARDEDTSALYRRMG
LNARQIEILATAIPKRQYYYVSENGRRLYDLALGPMALAFVGASDKESVATIKSLEAKFGHEWVHEWLAG
RGLNLNDYLEAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(626-754)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(218-431)

  Protein structure



No available structure.



ID   15106 GenBank   WP_000694765
Name   t4cp2_SLH58_RS00215_p31A20001_F_KPC_KPC insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 69897.09 Da        Isoelectric Point: 8.2993

>WP_000694765.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Bacteria]
MKIKMNNAVGPQVRTAKPKPSKLLPVLGAASMVGGLQAATQFFAHTFAYHATLGPNVGHVYAPWSILHWT
YKWYSQYPDEIMKAGSMGMLVSTVGLLGVAVAKVVTSNSSKANEYLHGSARWAEKKDIQAAGLLPRERNV
LEIVTGKAAPTATGVYVGGWQDKDGNFFYLRHSGPEHVLTYAPTRSGKGVGLVVPTLLSWGASSVITDLK
GELWALTAGWRQKHAKNKVLRFEPASTSGGVCWNPLDEIRLGTEYEVGDVQNLATLIVDPDGKGLDSHWQ
KTAFALLVGVILHALYKAKDDGGTATLPSVDAMLADPNRDIGELWMEMATYGHVDGQNHHAIGSAARDMM
DRPEEEAGSVLSTAKSYLALYRDPVVARNVSRSDFRIKQLMHEDDPVSLYIVTQPNDKARLRPLVRVMVN
MIVRLLADKMDFEGGRPVAHYKHRLLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRET
GYGHDESITSNCHVQNAYPPNRVETAEHLSRLTGQTTVVKEQITTSGRRTAAMLGQVSRTYQEVQRPLLT
PDECLRMPGPKKNAQGEIEEAGDMVIYVAGYPAIYGKQPLYFKDPVFSARAAIPAPKVSDRLRAVAQAET
EGEGITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(121-620)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9674..20351

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SLH58_RS00035 (ILEDJCEM_00006) 5519..6523 + 1005 WP_022542389 IS110-like element IS4321 family transposase -
SLH58_RS00040 (ILEDJCEM_00007) 7280..8500 - 1221 WP_011114072 plasmid replication initiator TrfA -
SLH58_RS00045 (ILEDJCEM_00008) 8547..8888 - 342 WP_000019167 single-stranded DNA-binding protein -
SLH58_RS00050 (ILEDJCEM_00009) 9002..9364 + 363 WP_010890126 transcriptional regulator -
SLH58_RS00055 (ILEDJCEM_00010) 9674..10636 + 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
SLH58_RS00060 (ILEDJCEM_00011) 10653..11117 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
SLH58_RS00065 (ILEDJCEM_00012) 11121..11432 + 312 WP_001207961 conjugal transfer protein TrbD virB3
SLH58_RS00070 (ILEDJCEM_00013) 11429..13987 + 2559 WP_011342945 VirB4 family type IV secretion/conjugal transfer ATPase virb4
SLH58_RS00075 (ILEDJCEM_00014) 13984..14766 + 783 WP_006122481 conjugal transfer protein TrbF virB8
SLH58_RS00080 (ILEDJCEM_00015) 14784..15683 + 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
SLH58_RS00085 (ILEDJCEM_00016) 15686..16174 + 489 WP_006122479 conjugal transfer protein TrbH -
SLH58_RS00090 (ILEDJCEM_00017) 16179..17600 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
SLH58_RS00095 (ILEDJCEM_00018) 17621..18385 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
SLH58_RS00100 (ILEDJCEM_00019) 18395..18622 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
SLH58_RS00105 (ILEDJCEM_00020) 18633..20351 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
SLH58_RS00110 (ILEDJCEM_00021) 20369..20956 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
SLH58_RS00115 (ILEDJCEM_00022) 20970..21605 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
SLH58_RS00120 (ILEDJCEM_00023) 21634..21900 + 267 WP_010890140 hypothetical protein -
SLH58_RS00125 (ILEDJCEM_00024) 21900..22598 + 699 WP_011114053 TraX family protein -
SLH58_RS00130 (ILEDJCEM_00025) 22614..23045 + 432 WP_319382215 OmpA family protein -
SLH58_RS00135 (ILEDJCEM_00026) 23200..23874 + 675 WP_011178411 DNA methylase -
SLH58_RS00140 (ILEDJCEM_00027) 24121..25134 - 1014 WP_000845048 class 1 integron integrase IntI1 -

Host bacterium

ID   20851 GenBank   NZ_OQ821187
Plasmid name   p31A20001_F_KPC_KPC Incompatibility group   IncP1
Plasmid size   71058 bp Coordinate of oriT [Strand]   51195..51293 [+]
Host baterium   Citrobacter freundii strain 31A20CPO001

Cargo genes

Drug resistance gene   blaKPC-2, sul1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -