Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107574
Name   oriT_pRspNXC24b in_silico
Organism   Rhizobium sp. NXC24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP024313 (466151..466186 [+], 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_pRspNXC24b
ATCCGAAGGGCGCAATTATACGTCGCTGACGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5088 GenBank   WP_104825954
Name   traA_NXC24_RS23965_pRspNXC24b insolico UniProt ID   _
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122648.62 Da        Isoelectric Point: 10.0159

>WP_104825954.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. NXC24]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPNWLRAMIADR
SVSGASEAFWNSVETFEKRVDAQLAKDVTIALPVELSTARNIELVRDFVERHITSNGMVADWVYHDAPGN
PHVHLMTTLRPLAEDGFGAKKIAVTGPDGKPVRNDASKIVYELWAGSLDDFNAFRDGWFACQNRHLARAG
LDLRVDGRSFEKQGIDLTPTIHLGVGAKAIERKSAEAERLPSLERLELQEERRAENARRIRRRPELVLDL
ITREKSVFDERDVAKILHRYIDDAGLFQSLMARILQSSDTLRLERERIEFSSGQRVPARYTTRELIRLEA
ELANRAIWLSQRSSHGVADAVREATFAHHLRLSDEQRTAIAHVIGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLVKEAGIVSRTLSSWELRWNQGRNQLDDRTVFVLDEAGMVSSRQMALFVE
AATKSGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMREASLDLARGNIGKAVEAYR
AQGRISEADLKADAVQALIADWNRDYDPQKSSLILAHLRREVRMLNDMTRAKLIERGLVAEGFAFRTEDG
HRKFAAGDQIVFLKNEGSLGVKNGMLAKVVEAAPGRIVAEVGEGEHRRQVTVEQRFYANLDHGYAITIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLSFYYGRRSFAKAGGLISILSRGQAKETTLDYASGRFY
AQALRFADARGLHLVNVARTVVRDRLEWTVRQKSKLAELGARLATIAGRLGLFAGAAKTTQSHRINEAKP
MVSGITTFPKSLEQAVEDRLAADPGLKKQWEEVSTRFHLVYAQPESAFKAVNVNAMLKDESIAKSTLARI
GSEPERFGALKGKTGILASHADRQEREKAQTNAPALARNLERYLRQRAEAERKFEVEERALRLKVSIDIP
ALSQGAKQILERVRDAIDRNDLPAGLEYALADKMMKAELEGFAKAVSERFGERIFLSLAAKDPIGQTFNA
VTSGMTAGQKAEVQAAWSSMRTVQQLAAHERTTEALKHAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-569)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

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

(859-955)


  Protein structure



No available structure.




T4CP

ID   5300 GenBank   WP_104825899
Name   traG_NXC24_RS23950_pRspNXC24b 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: 69307.09 Da        Isoelectric Point: 8.5372

>WP_104825899.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. NXC24]
MTRMLLFVAPCTLMMLTAIGMTGIEDWLAQFGKSDAARQMLGRAGIALPYVAASVVGIVFLFASAGSVRI
RTAGWGVVTGSIATLVIAALREASRLSAFLGQVPAGKSIFNYLDPATAIGAAAVVMSALFGTRVAIAGNA
AFARAEPKRIVGKRALHGEADWMKLAHAEKLFAESGGIVIGERYRVDRDSCAAQSVRADSPETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVSKHRGDANRDVFVLDPK
YSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRTSALQLLTALIADVCLSGHTTESD
QTLRQVRKNLSEPEPQLRQRLQEIYDDSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGKTFTTGDLADGKTDVFINVDLKTLETHAGLARVIIGSFLNAIYNRNGEMPGRALFLLDEVARLGYMR
ILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACVKPN
AFFRDSADNP

  Protein domains


Predicted by InterproScan.

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

(161-632)

  Protein structure



No available structure.



ID   5301 GenBank   WP_104825913
Name   t4cp2_NXC24_RS24035_pRspNXC24b 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: 91783.79 Da        Isoelectric Point: 6.5141

>WP_104825913.1 conjugal transfer protein TrbE [Rhizobium sp. NXC24]
MVALKRFRATDPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATALERNELSRHINTILSRLG
SGWMIQVEAVRIPTFDYPSDDRCHFPDAVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKTYADTVLFFFKNAVREIEQYFANTLSIRRMETREAVERGGVRVARYDELLQFVRFCITG
DNHPIRLPDAPMYLDWIATAELEHGLTPKIESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIARASSQLVAYGYYTPVVVL
FDLDRKALQEKAEAIRRLVQAEGFGARIETLNATDAFLGSLPGNWYCNVREPLINTSNLADLIPLNSVWS
GHPVAPCPFYPPSSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLAAGGDHYEIGGDTQKAEKALAFCPLSDLSSDVDRAWAAEWIEMLIALQGVTITPDHRN
AISRQIGLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLSLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIILDEGWVPLGHPKFRDKIREWLKVLRRLNCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAGEPGTREFYERIGFNETQIEIVSNAIPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRTLSSKHGRDWPIHWLRTRGVHDAAALLNLE

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 472578..484447

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NXC24_RS23970 (NXC24_PB00502) 469572..470138 + 567 WP_104825901 conjugative transfer signal peptidase TraF -
NXC24_RS23975 (NXC24_PB00503) 470128..471291 + 1164 WP_104825902 conjugal transfer protein TraB -
NXC24_RS35900 471955..472309 + 355 Protein_429 transposase -
NXC24_RS23985 (NXC24_PB00506) 472578..473186 + 609 WP_104825903 TraH family protein virB1
NXC24_RS23990 (NXC24_PB00507) 473448..473684 - 237 WP_104825904 helix-turn-helix transcriptional regulator -
NXC24_RS23995 (NXC24_PB00508) 473934..474248 + 315 WP_104825905 transcriptional repressor TraM -
NXC24_RS24000 (NXC24_PB00509) 474252..474956 - 705 WP_104825906 autoinducer binding domain-containing protein -
NXC24_RS24005 (NXC24_PB00510) 475115..476416 - 1302 WP_104825907 IncP-type conjugal transfer protein TrbI virB10
NXC24_RS24010 (NXC24_PB00511) 476427..476861 - 435 WP_104825908 conjugal transfer protein TrbH -
NXC24_RS24015 (NXC24_PB00512) 476865..477677 - 813 WP_104825909 P-type conjugative transfer protein TrbG virB9
NXC24_RS24020 (NXC24_PB00513) 477694..478356 - 663 WP_104825910 conjugal transfer protein TrbF virB8
NXC24_RS24025 (NXC24_PB00514) 478381..479559 - 1179 WP_104825911 P-type conjugative transfer protein TrbL virB6
NXC24_RS24030 (NXC24_PB00515) 479564..480367 - 804 WP_104825912 P-type conjugative transfer protein TrbJ virB5
NXC24_RS24035 (NXC24_PB00516) 480339..482795 - 2457 WP_104825913 conjugal transfer protein TrbE virb4
NXC24_RS24040 (NXC24_PB00517) 482805..483104 - 300 WP_104825914 conjugal transfer protein TrbD virB3
NXC24_RS24045 (NXC24_PB00518) 483097..483480 - 384 WP_104825915 TrbC/VirB2 family protein virB2
NXC24_RS24050 (NXC24_PB00519) 483470..484447 - 978 WP_104825916 P-type conjugative transfer ATPase TrbB virB11
NXC24_RS24055 (NXC24_PB00520) 484444..485082 - 639 WP_104825917 acyl-homoserine-lactone synthase TraI -
NXC24_RS24060 (NXC24_PB00521) 485459..486679 + 1221 WP_104825918 plasmid partitioning protein RepA -
NXC24_RS24065 (NXC24_PB00522) 486739..487710 + 972 WP_104825919 plasmid partitioning protein RepB -
NXC24_RS24070 (NXC24_PB00523) 487872..489086 + 1215 WP_104825920 plasmid replication protein RepC -

Host bacterium

ID   8009 GenBank   NZ_CP024313
Plasmid name   pRspNXC24b Incompatibility group   -
Plasmid size   489086 bp Coordinate of oriT [Strand]   466151..466186 [+]
Host baterium   Rhizobium sp. NXC24

Cargo genes

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