Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102475
Name   oriT_pRg502a in_silico
Organism   Rhizobium grahamii CCGE 502
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AEYE02000038 (268505..268540 [-], 36 nt)
oriT length   36 nt
IRs (inverted repeats)      21..26, 31..36  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 36 nt

>oriT_pRg502a
ATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1844 GenBank   WP_016558652
Name   traA_RGCCGE502_RS33385_pRg502a insolico UniProt ID   S3H423
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122325.33 Da        Isoelectric Point: 10.0652

>WP_016558652.1 Ti-type conjugative transfer relaxase TraA [Rhizobium grahamii]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPKWLRATIADR
SVSGACEAFWNSVETFEKRVDAQLAKDVTVGLPVELSTAQNIELVRDFVELHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKVAVTSPDGRPVRNDAGKIVYELWAGNLDDFNVFRDGWFACQNRHLARAG
LEIRVDGRSFEKQGIELTPTIHLGVGAKAIERKSAEAERDPSLERLELQEGRRAENARRIQRRPELVLDL
ITREKSVFDERDVAKILHRYIDDADLFQNLMARILQSPETLRLERERIEFSSGLRVPAKYTTRDLVRLEA
QMASRSIWLDQRSSHSVADAVRDAVFAHHLRLSDEQKTAIAHATGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSTWELRWKQGRNRLDDKTVFVLDEAGMVSSRQMALFVE
AATKSGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYVELETIYRQREQWMRDASLDLARGNIGRAVEAYR
AQGYVSGADLKADVVQALIADWNRDYDPQKSSLILAHLRRDVRMLNDMARAKLVERGLVADGFAFLTEDG
HRKFAAGDQIVFLKNEGSLGVKNGMLARVLEAAPGRIVAEVGEGQHRRPVTVEQRFYANVDHGYATTIHK
SQGATVESVKVLASLSLDRHLAYVAMTRHREDLALYYGRRSFAKAGGLVPILSRRQAKETTLEYASGRFY
AQALRFAEARGLHLVNVARTVVRDRLEWTVRQNSKLGELGARLATIAGRLGPSARAANTTQSHSIKEAKP
MVSGITTFPKSLEQAVEDRLAADPSLKKQWEEVSARFHLVYAQPEGAFKAVNVDAMLKNEAAAKVTIARI
GSKPETFGALKGKTGLLAVHADKQARKKAVTNAPALARNLERYLRQRTEAEHKYEAEERAVRLKVSLDIP
ALSPTAKQTLERVRDAINRNDLPAGVEYALADKMVKSELEGFARAVSARFGERTFLPLAAKDTTGRIFQS
VTSSMSAGQKAEVQSAWSTMRTVQQLSAHERTTEALKQAETLRQTKSQGLWLK

  Protein domains


Predicted by InterproScan.

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

(859-955)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(691-735)

AAA domain (AAA_30)

(382-568)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure


Source ID Structure
AlphaFold DB S3H423


T4CP

ID   1435 GenBank   WP_016558635
Name   t4cp2_RGCCGE502_RS33315_pRg502a 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: 91387.09 Da        Isoelectric Point: 6.0149

>WP_016558635.1 conjugal transfer protein TrbE [Rhizobium grahamii]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATALERNELSRQINSILSRLG
SGWMIQVEAIRIPTIDYPSNDRCHFPDPVTRAIDAERRAHFAREQGHFESKHAIFLTYRPLESKKTALSK
YIYSDAGSRKRSYADTVLFVFKNAIREIEQYLANNLSIRRMETREVSEREGTRSARYDELLQFVRFCITG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENQFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFLF
LDADEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETADAIAQASSQLVAYGYYTPVIVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTNNLADLIPLNAVWA
GSPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIVAQFRRYENAQVFA
FDKGNSLLPLTLAGGGDHYEIGGDTEGEGRALAFCPLSELGSDADRAWASEWIEMLVALQGVTTTPDYRN
AISRQVGLMTTAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLSLGALQTFEIEHLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRAKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIDIVAAATPKREYYVATPDGRRLFDMTLGP
VALSFVGASGKNDLKSIRALIAEYGRDWPIHWLNTRGVHDAASLLNFE

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.



ID   1436 GenBank   WP_016558655
Name   traG_RGCCGE502_RS33400_pRg502a insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 69424.15 Da        Isoelectric Point: 8.8983

>WP_016558655.1 Ti-type conjugative transfer system protein TraG [Rhizobium grahamii]
MTRILLLVAPCALMMLTAIGMTGIEHWLSHFGKSDAARQMLGRAGIALPYVAASIVGIFFPFASAGSVRI
RTAGWGVVTGATATLVLAVLREASRLSAFLGQIPAGKSIFNYLDPATTIGAATVLLSALLGTRVAIAGNA
AFARPEPKRIVGKRAVHGEADWMKLSQAEKLFAESGGIVIGERYRVDRDSSAAHSFRADSAETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVSKHRCDANRDVFVLDPK
QSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVREDFFRASALQLLTALIADTCLSGHTPEND
QTLRQVRKNLSEPEPQLRQRLQEIYDDSSSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGKAFTTGDLADGKTDVFINVDLKALETHAGLARVIIGSFLNAIYNRNGEMPGRALFLLDEVARLGYMR
ILETARDAGRKYGITLTTIYQSIGQMRETYGGRDAASKWFESASWISFAAINDSETADYISRRCGMTTVE
IDQVSRSVQSQRSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACVKPN
SFFRDTADKP

  Protein domains


Predicted by InterproScan.

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

(161-632)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 250329..263382

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RGCCGE502_RS38590 245442..245543 - 102 Protein_240 replication initiation protein RepC -
RGCCGE502_RS33280 (RGCCGE502_33751) 245599..246813 - 1215 WP_016558628 plasmid replication protein RepC -
RGCCGE502_RS33285 (RGCCGE502_33756) 246999..248006 - 1008 WP_016558629 plasmid partitioning protein RepB -
RGCCGE502_RS33290 (RGCCGE502_33761) 248104..249336 - 1233 WP_019280633 plasmid partitioning protein RepA -
RGCCGE502_RS33295 (RGCCGE502_33766) 249694..250317 + 624 WP_016558631 acyl-homoserine-lactone synthase TraI -
RGCCGE502_RS33300 (RGCCGE502_33771) 250329..251306 + 978 WP_016558632 P-type conjugative transfer ATPase TrbB virB11
RGCCGE502_RS33305 (RGCCGE502_33776) 251296..251673 + 378 WP_016558633 TrbC/VirB2 family protein virB2
RGCCGE502_RS33310 (RGCCGE502_33781) 251666..251965 + 300 WP_016558634 conjugal transfer protein TrbD virB3
RGCCGE502_RS33315 (RGCCGE502_33786) 251976..254432 + 2457 WP_016558635 conjugal transfer protein TrbE virb4
RGCCGE502_RS33320 (RGCCGE502_33791) 254404..255207 + 804 WP_016558636 P-type conjugative transfer protein TrbJ virB5
RGCCGE502_RS33325 (RGCCGE502_33796) 255201..256391 + 1191 WP_016558637 P-type conjugative transfer protein TrbL virB6
RGCCGE502_RS33330 (RGCCGE502_33801) 256414..257076 + 663 WP_016558638 conjugal transfer protein TrbF virB8
RGCCGE502_RS33335 (RGCCGE502_33806) 257093..257917 + 825 WP_016558639 P-type conjugative transfer protein TrbG virB9
RGCCGE502_RS33340 (RGCCGE502_33811) 257905..258342 + 438 WP_016558640 conjugal transfer protein TrbH -
RGCCGE502_RS33345 (RGCCGE502_33816) 258353..259675 + 1323 WP_016558641 IncP-type conjugal transfer protein TrbI virB10
RGCCGE502_RS33350 (RGCCGE502_33821) 259896..260600 + 705 WP_016558642 autoinducer binding domain-containing protein -
RGCCGE502_RS33355 (RGCCGE502_33826) 260604..260924 - 321 WP_016558643 transcriptional repressor TraM -
RGCCGE502_RS33360 (RGCCGE502_33831) 261121..261357 + 237 WP_016558644 helix-turn-helix transcriptional regulator -
RGCCGE502_RS38595 (RGCCGE502_33841) 261528..261746 - 219 WP_016558646 hypothetical protein -
RGCCGE502_RS38600 (RGCCGE502_33846) 261743..262354 - 612 WP_019280635 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
RGCCGE502_RS33370 (RGCCGE502_33856) 262768..263382 - 615 WP_016558649 TraH family protein virB1
RGCCGE502_RS33375 (RGCCGE502_33861) 263398..264561 - 1164 WP_016558650 conjugal transfer protein TraB -
RGCCGE502_RS33380 (RGCCGE502_33866) 264551..265117 - 567 WP_016558651 conjugative transfer signal peptidase TraF -

Host bacterium

ID   2919 GenBank   NZ_AEYE02000038
Plasmid name   pRg502a Incompatibility group   -
Plasmid size   413761 bp Coordinate of oriT [Strand]   268505..268540 [-]
Host baterium   Rhizobium grahamii CCGE 502

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   linJ, dxnH
Symbiosis gene   mLTONO_5203, nifX, nifN, nifE, nifK, nifD, nifH, nifS, nifW, fixA, fixB, fixC, fixX, nifB, fixQ, fixO, fixN, nodD, nifT, nodJ, nodI, nodU, nodC, nodA, nodE, nodM
Anti-CRISPR   -