Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107588
Name   oriT_pRspNXC14a in_silico
Organism   Rhizobium sp. NXC14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021031 (505380..505421 [+], 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_pRspNXC14a
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACGCCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5099 GenBank   WP_085780560
Name   traA_NXC14_RS24210_pRspNXC14a insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 122053.29 Da        Isoelectric Point: 9.8788

>WP_085780560.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. NXC14]
MAAPHFSVSVVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVVPTDAPEWLRSMIANR
SVSGASGAFWNRVEDFEKRSDAQLAKDVTIALPIELTAEQNIALVRDFVEQHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKIAVTGPDGNPIRNDAGKIVYELWAGSIDDFNAFRDAWFACQNRHLALAG
LDIHVDGRSFKKQGIDFEPTIHLGVGTKAIERKADGASKPLELERLELQDARRHENVRRIDRNPELVLAM
IMREKSVFDERDVAKILHRYVDDAALFQSLMIRILLCPETFRIEREQIALASGIRVPAKYTTRGMIRLEA
EMANRAVWLSQRSSHGVRDAVLAATFARHEHLSEEQKIAIEHVASGERIAAVIGRAGAGKTTMMNAAREA
WEAAGYRVVGAALAGKAAEGLEKEAGIISRTLASWELRWNQGRDQLDGKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGKTVDAYR
ANGKIIGSDLKADAVDNLIAAWDRDYDPAKTSLILAHLRRDVHMLNQMARIKLIERGVLDQGTMFKTADG
ERNFAVGDQIVFLKNEASLGVKNGMLAKVVEVGAGRITARIGDGENARLVLVEQRFYNNLDHGYATTIHK
SQGATVDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRPFAKNGGLIPILSRRNAKETTLDYEKSAFY
RQALRFAEARGLHIVNVARTVVRDRLEWIVNQKQKLANLGARLVAVAGRLGMVRGVAQSPTQNSAKEAKP
MVSGITTFAKSVDRAIEDKVAADPGLKKQWEEVSTRFHLVYAQPVSAFKAVNVDAMLKDETVAKSTLAKI
GSDPERFGALRGKTGILASRADREEREKAQTNAPALARNLERYLRQRAEAERKFEVEERADRLKVSIDIP
ALSPNAKQKLERVRDAIDRHDLPAGLEYALADKMVKAELEGFARAVSERFGERTFLSLAAKDANGQTFNA
VTSGMTAGQKAEVQAAWNSMRTVQQLAAHERTTEALKQAETLRQTKSQGLSP

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(859-955)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   5318 GenBank   WP_085780557
Name   traG_NXC14_RS24195_pRspNXC14a 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: 71242.31 Da        Isoelectric Point: 8.7174

>WP_085780557.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. NXC14]
MNRILLFIAPAALMIVVVVGLTGIEHWLSQFGKTEGARQTLGRAGIALPYASAGLVGIVFLFASAGSIRI
KTTGWGVVAGGVATVLIAAIREAMRLSALTDEVPAGKSILSYVDPATLIGAGAAAMASCFALRVALAGNA
AFARAEPKRIRGKRALHGEADWMKLADAEKLLADAGGIVVGERYRVDKDSTAARSFRADNPETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVVPMVSAHRTNFNRDLFVLDPK
NPETGFNALDWIGQFGGTKEEDIASVASWIMSDSGGTRGVRDDFFRASALQLLTAMIADVCLSGHTEKES
QTLRQVRANLSEPEPKLRQRLQEIYDNSDSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYAAL
VSGKTFSTGDLADGKTDIFINIDLKTLETHAGLARVIIGSFLNAIYNRDGSMKGRALFLLDEVARLGYMR
ILETARDAGRKYGITLIMIYQSIGQMRETFGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSCSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGTN
RFHRLEETPGTYPVEPARSAASKTDREK

  Protein domains


Predicted by InterproScan.

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

(161-633)

  Protein structure



No available structure.



ID   5319 GenBank   WP_085780574
Name   t4cp2_NXC14_RS24300_pRspNXC14a 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: 91641.48 Da        Isoelectric Point: 6.1927

>WP_085780574.1 conjugal transfer protein TrbE [Rhizobium sp. NXC14]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAVRIPTFDYPSDDHCHFPDAVTRAIDAERRAHFGREQGHFESKHALILTYRPLESKKTTLSK
YIYSDDESRKKTYADTVLFIFKNAVREIEQYFANALSILRMETREAVERGGERVARYDELLQFVRFCVTG
ENHPIRLPGAPMYLDWLATAELEHGLTPKVESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFLF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIVL
FDNDREALQEKAEAIRRLIQAEGFGARIETLNATEAFLGSLPGNWYCNIREPLINTSNLADLVPLNSVWS
GNPTAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSALLPLTLAVGGEHYEIGGDHNGAERALAFCPLSELSNDADRAWATEWIEMLVALQGVAITPDHRN
AISRQIGLMASAAGRSLSDFVSGVQMRVIKDALHHYTVDGPMGQLLDAEQDGLSLVAVQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATHSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYQRIGFNERQIEIVSNAIPKREYYVVTPDGRRLFDMALGP
VALSFVGASGKEDLKRIRALRSEHGRDWPIHWLQSRGVHDAASLLNFE

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 510539..525435

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NXC14_RS24215 (NXC14_PA00545) 508806..509372 + 567 WP_085780561 conjugative transfer signal peptidase TraF -
NXC14_RS24220 (NXC14_PA00546) 509362..510522 + 1161 WP_085780562 conjugal transfer protein TraB -
NXC14_RS24225 (NXC14_PA00547) 510539..511147 + 609 WP_085780563 TraH family protein virB1
NXC14_RS24230 (NXC14_PA00548) 511164..511541 - 378 WP_085780564 DUF5615 family PIN-like protein -
NXC14_RS24235 (NXC14_PA00549) 511538..512170 - 633 WP_085780565 DUF433 domain-containing protein -
NXC14_RS24240 (NXC14_PA00550) 512352..512564 - 213 WP_085780566 helix-turn-helix transcriptional regulator -
NXC14_RS24245 (NXC14_PA00551) 512761..513075 + 315 WP_085780567 transcriptional repressor TraM -
NXC14_RS24250 (NXC14_PA00552) 513152..513886 - 735 WP_085777969 IS21-like element helper ATPase IstB -
NXC14_RS24255 (NXC14_PA00553) 513828..515385 - 1558 Protein_493 IS21 family transposase -
NXC14_RS24265 (NXC14_PA00556) 515948..517249 - 1302 WP_085780568 IncP-type conjugal transfer protein TrbI virB10
NXC14_RS24270 (NXC14_PA00557) 517261..517698 - 438 WP_085780569 conjugal transfer protein TrbH -
NXC14_RS24275 (NXC14_PA00558) 517702..518514 - 813 WP_085780570 P-type conjugative transfer protein TrbG virB9
NXC14_RS24280 (NXC14_PA00559) 518532..519194 - 663 WP_085780571 conjugal transfer protein TrbF virB8
NXC14_RS24285 (NXC14_PA00560) 519219..520397 - 1179 WP_085780572 P-type conjugative transfer protein TrbL virB6
NXC14_RS24295 (NXC14_PA00562) 520570..521373 - 804 WP_085780573 P-type conjugative transfer protein TrbJ virB5
NXC14_RS24300 (NXC14_PA00563) 521345..523801 - 2457 WP_085780574 conjugal transfer protein TrbE virb4
NXC14_RS24305 (NXC14_PA00564) 523811..524110 - 300 WP_085780575 conjugal transfer protein TrbD virB3
NXC14_RS24310 (NXC14_PA00565) 524103..524468 - 366 WP_085780576 TrbC/VirB2 family protein virB2
NXC14_RS24315 (NXC14_PA00566) 524458..525435 - 978 WP_085780577 P-type conjugative transfer ATPase TrbB virB11
NXC14_RS24320 (NXC14_PA00567) 525455..526072 - 618 WP_085780578 acyl-homoserine-lactone synthase TraI -
NXC14_RS24325 (NXC14_PA00569) 526461..527675 + 1215 WP_085780579 plasmid partitioning protein RepA -
NXC14_RS24330 (NXC14_PA00570) 527672..528697 + 1026 WP_085780580 plasmid partitioning protein RepB -
NXC14_RS24335 (NXC14_PA00572) 528854..530065 + 1212 WP_085780581 plasmid replication protein RepC -

Host bacterium

ID   8023 GenBank   NZ_CP021031
Plasmid name   pRspNXC14a Incompatibility group   -
Plasmid size   530065 bp Coordinate of oriT [Strand]   505380..505421 [+]
Host baterium   Rhizobium sp. NXC14

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   LinG, dxnH, linJ
Symbiosis gene   nodH, nodM, nodD, nifA, nifH, mLTONO_5203, nodA, nodB, nodC, nodS, nodU, nodI, nodJ, nifT, nifZ, nifB, fixX, fixC, fixB, fixA, nifW, nifS, nifD, nifK, nifE, nifN, nifX
Anti-CRISPR   AcrIIA7