Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121837
Name   oriT_pRetIE4771b in_silico
Organism   Rhizobium etli bv. mimosae str. IE4771
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP006988 (370942..370983 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pRetIE4771b
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACGCCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13782 GenBank   WP_040140651
Name   traA_IE4771_RS24220_pRetIE4771b insolico UniProt ID   A0A060I4Y1
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122414.44 Da        Isoelectric Point: 9.5561

>WP_040140651.1 Ti-type conjugative transfer relaxase TraA [Rhizobium etli]
MAVPHFSVSVVARGSGRSAVLSAAYRHCTKMEFEREARTIDYTRKQGLLHEEFVVPTDAPEWLRSMIADR
SVSGASEAFWNRVEDFEKRSDAQLAKDVTIALPIELTAEQNIALVRDFVEQHITVKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKIAVTGPDGNPIRNDAGKIVYELWAGSIDDFNTFRDGWFACQNRHLALAG
LDIYVDGRSFEKQGIELEPTIHLGVGTKAIERKSDGASDPVELERLELQEARRSENVRRIDRNPELVLAL
IMREKSVFDERDVAKILHRYVDDAALFQSLMVRILLCPETFRIECERIDLATGIRVPAKYTTRDMIRLEA
EMANRAVWLSQRSSHGVRDAVLAATFERHERLSDEQRTAIEHVAGPERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGAALAGKAAEGLEKEAGIISRTLASWELRWNQGRDQLDGKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGRAVDAYR
ANGKIIGSDLKADAVDNLIAAWDRDYDPAKTSLILAHLRRDVRMLNQMARIKLIERGVLDQGTMFKTADG
GRNFAVGDQIVFLKNEGSLGVKNGMLAKVVETGPGRITARIGERENARQVLVEQRFYNNLDHGYATTIHK
SQGATIDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKNGGLIPMLSRRNAKETTLDYEKSDFY
RQALRFAEARGLHLVNVARTLVRDRLEWVVSQKQKLANLGARLAAVAGKLGLIRGAAQSPTQNNTKEAKP
MVSGITTFAKSVDQAIEDKIAADPGLKKQWEEVSTRFHLVYAQPESAFKAVNVDAMLKDETAQKSTLAKL
GSEPESFGALKGKTGILASRSDRQEREKAGTNAPALARNLERYLRQRAEAERKFEVEERAVRLKVSIDIP
ALSPNAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLSLAAKEPNGQTFSA
VTSGMTAGQKTEVQSAWNSMRTVQQLAAHERTTEALKQAETLRQAKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(859-955)


  Protein structure


Source ID Structure
AlphaFold DB A0A060I4Y1


T4CP

ID   16114 GenBank   WP_040140646
Name   traG_IE4771_RS24205_pRetIE4771b insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 70940.14 Da        Isoelectric Point: 9.5637

>WP_040140646.1 Ti-type conjugative transfer system protein TraG [Rhizobium etli]
MNRIVLFVAPVALMTVAAVCLTGIEHWLSAFGKTEAAHQTLGRVGIAFPYLAAALVGIVFLFASAGAIRI
KAAGWGVIAGGVATILIAAIRETIRLSALADKVPAGKSILSYVDPATLIGAGAAAMASCFALRVALAGNA
PFTSAAPKRIRGKRALHGEANWMKLPEAATLFSDTGGIVVGERYRVDKDSTAARAFRADERETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVAPMVSAHRTSANRDLFVLDPK
SPETGFNALDWIGKFGGTKEEDIASVASWIMSDSGGTRGVRDDFFRASALQLLTAMIADVCLSGHTEKVK
QTLRQVRANLSEPEPKLRQRLQEIYDNSDSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYAAL
VSGKTFSTGDLAVGSTDVFINIDLRTLETHAGLARVIIGSFLNAIYNRDGSMKGRALFLLDEVARLGYMR
ILETARDAGRKYGITLTMIYQSIGQMRETYGGHDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIIFTAGNSPLRCGRAIWFRRDDMKACVGTN
RFHQLKGGPEANLIEPARSAASKADREK

  Protein domains


Predicted by InterproScan.

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

(161-633)

  Protein structure



No available structure.



ID   16115 GenBank   WP_040140668
Name   t4cp2_IE4771_RS24300_pRetIE4771b insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91762.62 Da        Isoelectric Point: 6.2213

>WP_040140668.1 conjugal transfer protein TrbE [Rhizobium etli]
MVALTRFRAAGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATVLERNELSRQINTILSRLG
SGWMIQVEAVRIPTFDYPSDDRCHFPDAVTRAIDAERRAHFGREQGHFESKHALILTYRPLESKKTALSK
YIYSDDESRKKTYADTVLFIFKNAVREIEQYFANTLSIRRMETRETFERGGERVARYDELLQFVRFCVTG
ENHPIRLPDAPMYLDWLATAELEHGLTPKVESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFLF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATEAFLGSLPGNWYCNIREPLINTSNLADLVPLNSVWS
GNPTAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSALLPLTLAVGGEHYEIGGDHNGAERALAFCPLSELSNDADRAWATEWIEMLLALQGVAITPDHRN
AISRQIGLMASAAGRSLSDFVSGVQMRVIKDALHHYTVDGPMGQLLDAEQDGLSPVAVQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRAKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYQRIGFNERQIEIVSNAIPKREYYVVTPDGRRLFDMALGP
VALSFVGASGKEDLKRIRALRSEHGRDWPIHWLQSRGVHDAASLLNFE

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 376108..389218

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IE4771_RS24225 (IE4771_PB00378) 374371..374937 + 567 WP_080711056 conjugative transfer signal peptidase TraF -
IE4771_RS24230 (IE4771_PB00379) 374927..376090 + 1164 WP_040140653 conjugal transfer protein TraB -
IE4771_RS24235 (IE4771_PB00380) 376108..376719 + 612 WP_040140655 TraH family protein virB1
IE4771_RS24240 (IE4771_PB00381) 376734..377111 - 378 WP_040140657 DUF5615 family PIN-like protein -
IE4771_RS24245 (IE4771_PB00382) 377108..377740 - 633 WP_040140659 DUF433 domain-containing protein -
IE4771_RS24250 (IE4771_PB00383) 377950..378171 - 222 WP_010046230 helix-turn-helix domain-containing protein -
IE4771_RS24255 (IE4771_PB00384) 378368..378685 + 318 WP_010046233 transcriptional repressor TraM -
IE4771_RS24260 (IE4771_PB00385) 378689..379393 - 705 WP_040140791 autoinducer binding domain-containing protein -
IE4771_RS24265 (IE4771_PB00386) 379715..381016 - 1302 WP_040140660 IncP-type conjugal transfer protein TrbI virB10
IE4771_RS24270 (IE4771_PB00387) 381028..381465 - 438 WP_010060774 conjugal transfer protein TrbH -
IE4771_RS24275 (IE4771_PB00388) 381469..382281 - 813 WP_040140662 P-type conjugative transfer protein TrbG virB9
IE4771_RS24280 (IE4771_PB00389) 382298..382960 - 663 WP_010060772 conjugal transfer protein TrbF virB8
IE4771_RS24285 (IE4771_PB00390) 382985..384163 - 1179 WP_040140666 P-type conjugative transfer protein TrbL virB6
IE4771_RS24290 (IE4771_PB00391) 384166..384342 - 177 WP_010060768 entry exclusion protein TrbK -
IE4771_RS24295 (IE4771_PB00392) 384336..385139 - 804 WP_040140667 P-type conjugative transfer protein TrbJ virB5
IE4771_RS24300 (IE4771_PB00393) 385111..387567 - 2457 WP_040140668 conjugal transfer protein TrbE virb4
IE4771_RS24305 (IE4771_PB00394) 387576..387875 - 300 WP_040140669 conjugal transfer protein TrbD virB3
IE4771_RS24310 (IE4771_PB00395) 387868..388251 - 384 WP_040140671 TrbC/VirB2 family protein virB2
IE4771_RS24315 (IE4771_PB00396) 388241..389218 - 978 WP_040140672 P-type conjugative transfer ATPase TrbB virB11
IE4771_RS24320 (IE4771_PB00397) 389238..389855 - 618 WP_040140673 acyl-homoserine-lactone synthase TraI -
IE4771_RS24325 (IE4771_PB00399) 390243..391457 + 1215 WP_040140795 plasmid partitioning protein RepA -
IE4771_RS24330 (IE4771_PB00400) 391454..392479 + 1026 WP_040140674 plasmid partitioning protein RepB -
IE4771_RS24335 (IE4771_PB00401) 392635..393846 + 1212 WP_010058593 plasmid replication protein RepC -

Host bacterium

ID   22264 GenBank   NZ_CP006988
Plasmid name   pRetIE4771b Incompatibility group   -
Plasmid size   393846 bp Coordinate of oriT [Strand]   370942..370983 [+]
Host baterium   Rhizobium etli bv. mimosae str. IE4771

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   LinG, dxnH, linJ
Symbiosis gene   nifA, nifH, mLTONO_5203, nodD, fixN, fixO, nodA, nodB, nodC, nodS, nodU, nodI, nodJ, nodH, nifT, nifB, fixX, fixC, fixB, fixA, nifW, nifS, nifD, nifK, nifE, nifX
Anti-CRISPR   AcrIC6