Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102782
Name   oriT_pRspN871b in_silico
Organism   Rhizobium sp. N871
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013592 (215833..215861 [+], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_pRspN871b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2054 GenBank   WP_064811989
Name   traA_AMK04_RS24035_pRspN871b insolico UniProt ID   A0A192M522
Length   1565 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1565 a.a.        Molecular weight: 172913.26 Da        Isoelectric Point: 7.2379

>WP_064811989.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVRDFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETLNAWKIAWAETANR
HLALADHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLAEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPQEIEAETGKVSEPAMFTTREMLRIE
YDMAQSARVLSERRGFGVSERIVTVAIERVESIESGDPKTPFRLDAEQVDAVRHVTGDGDIAAIVGLAGA
GKSTLLAAARLAWEGEGHRVIGAALAGKAAEGLQHSSGIKSRTLASWELAWANGRDTLHRGDVLVIDEAG
MVASQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREAWARNASRLFA
RGEVEKGLDAYARHGHLVEAGSREETIDRIVSDWAAARREAIERSTSEGGDGRLRGDELLVLAHTNDDVR
KLNEALRSVMTQEGALGESRSFRSERGAREFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVVSTG
DKRGDPLLSILLDNGRKLVFSEDSYRHVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDR
VDLYAAKEDFAAKPEWGRKPRVDHAAGVTGELVETGEAKFRPDDEDADDSPYADVRADGGTVHRLWGVSL
PKALEEAGIQEGDTVMLRKDGVERVKVQITVVDEKTGHKHYEEREVDRNVWTASQVETASARQERIERES
HRSELFNPLVERLSRSGAKTTTLDFESEASYRAHANDFARRRGLDHLSLAAAEMEESLTRRWAWIAEKRE
QVAKLWERASVALGFAIERERRVAYNEERSQTMVEATSSDARTASHSVSGASAAETRYLIPPATSFVSSV
EEDARLAQLASPAWTEREVILRPLLQKIYRDPDAALVSLNALASDIGVAPRRLADDLAVAPGRLGRMRGS
ELIVDGRAAREERNVAVAGVKELLPIARAHATEFRRNAERFELREQTRRAHMSLSIPALSERAMARLMEI
EAVRRQGGDDAYKTAFALTAKDRSVVQEIKAVSEALTARFGWSAFSAKADAIAERNIVERMPEDLTDERR
GKLTRLFEAVRRFAEEQHLAERRDRSKIVAGASVDLRTGTEKGVGKENVPIPPMLAAVTEFKVPVDDEAR
SRALASPLYRQQRAALANAATTIWRDPAEVVGKIEELLQKGFAAERIGAAVTNNPAAYGALRGSDRLMDR
MLASGRERKEATRTVPEAAARLRALGAAYANALNSERQAITDERRRMAVAIPALSKAAEEALAHLTVEVS
KDSRKLNVSAASLDPGIGREFAAVSRALDERFGRNALVRGDKDIANVVPPAQRGAFAAMQERLKVLQQTV
RLQSSEQIIVERRQQTANRSRGINL

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(394-579)

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

(1334-1425)

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

(1072-1143)


  Protein structure



No available structure.




T4CP

ID   1710 GenBank   WP_064811988
Name   traG_AMK04_RS24020_pRspN871b insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 70745.97 Da        Isoelectric Point: 9.5675

>WP_064811988.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MGLRGKPHPSLLLVLVPIAVTTITIYIVGWRWPGLAAGMSGKIEHWFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLYFLGVAAFYALREFGRLAPAVQAEVITWDRALSYLDMVAVIAAVAGFMAVAMSARI
SVVVPDEIKRARRGIFGDADWLPMRAAGKLFPPEGEIVVGERYRVDKEIVHALPFDANDRSTWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYSGPLICLDPSTEVAPMVAEHRARALKREVMVLDPT
NPIMGFNVLDGIEASKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYEGRRS
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIARVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKG
SSRNIGWDTKNNASRRSENVTFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDQAAK
VNRFVKPVL

  Protein domains


Predicted by InterproScan.

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

(168-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 196072..205660

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMK04_RS33680 192556..192782 - 227 Protein_184 chaperonin GroEL -
AMK04_RS23895 (AMK04_PB00172) 193077..193997 + 921 WP_064811974 zincin-like metallopeptidase domain-containing protein -
AMK04_RS23900 194108..194290 - 183 WP_016737443 hypothetical protein -
AMK04_RS23905 (AMK04_PB00173) 195062..195433 - 372 WP_042120136 hypothetical protein -
AMK04_RS23910 (AMK04_PB00174) 195532..196068 + 537 WP_064811975 hypothetical protein -
AMK04_RS23915 (AMK04_PB00175) 196072..196731 + 660 WP_064811976 lytic transglycosylase domain-containing protein virB1
AMK04_RS23920 (AMK04_PB00176) 196728..197027 + 300 WP_009997887 TrbC/VirB2 family protein virB2
AMK04_RS23925 (AMK04_PB00177) 197033..197371 + 339 WP_009997888 type IV secretion system protein VirB3 virB3
AMK04_RS23930 (AMK04_PB00178) 197364..199730 + 2367 WP_064811977 VirB4 family type IV secretion system protein virb4
AMK04_RS23935 (AMK04_PB00179) 199727..200428 + 702 WP_064811978 P-type DNA transfer protein VirB5 virB5
AMK04_RS23940 (AMK04_PB00180) 200425..200658 + 234 WP_010007459 EexN family lipoprotein -
AMK04_RS23945 (AMK04_PB00181) 200662..201594 + 933 WP_040111793 type IV secretion system protein virB6
AMK04_RS33685 (AMK04_PB00182) 201634..201915 + 282 WP_080771758 hypothetical protein -
AMK04_RS23950 (AMK04_PB00183) 201917..202588 + 672 WP_064811979 virB8 family protein virB8
AMK04_RS23955 (AMK04_PB00184) 202585..203442 + 858 WP_064811980 P-type conjugative transfer protein VirB9 virB9
AMK04_RS23960 (AMK04_PB00185) 203451..204623 + 1173 WP_064811981 type IV secretion system protein VirB10 virB10
AMK04_RS23965 (AMK04_PB00186) 204632..205660 + 1029 WP_010008207 P-type DNA transfer ATPase VirB11 virB11
AMK04_RS23970 (AMK04_PB00187) 205704..206282 - 579 WP_064811982 PIN domain-containing protein -
AMK04_RS23975 (AMK04_PB00188) 206272..206718 - 447 WP_225881772 DNA-binding protein -
AMK04_RS23980 (AMK04_PB00190) 207230..208420 - 1191 WP_064811984 DUF1173 domain-containing protein -
AMK04_RS33690 208731..208990 + 260 Protein_204 toprim domain-containing protein -
AMK04_RS23990 (AMK04_PB00191) 209376..209642 + 267 WP_004676093 hypothetical protein -
AMK04_RS23995 (AMK04_PB00192) 209639..210037 + 399 WP_064811986 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   3225 GenBank   NZ_CP013592
Plasmid name   pRspN871b Incompatibility group   -
Plasmid size   433056 bp Coordinate of oriT [Strand]   215833..215861 [+]
Host baterium   Rhizobium sp. N871

Cargo genes

Drug resistance gene   -
Virulence gene   hsiC1/vipB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nifX, nifN, nifE, nifK, nifD, nifH, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nodD, nodJ, nodI, nodS, nodC, fixO, fixN, mLTONO_5203, nodA
Anti-CRISPR   -