Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102762
Name   oriT_pRspN621b in_silico
Organism   Rhizobium sp. N621
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013497 (218473..218501 [+], 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_pRspN621b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2037 GenBank   WP_064811989
Name   traA_AMK00_RS23655_pRspN621b 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   1690 GenBank   WP_064811988
Name   traG_AMK00_RS23640_pRspN621b 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: 198712..208300

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMK00_RS33210 195196..195422 - 227 Protein_188 chaperonin GroEL -
AMK00_RS23515 (AMK00_PB00172) 195717..196637 + 921 WP_064811974 zincin-like metallopeptidase domain-containing protein -
AMK00_RS23520 196748..196930 - 183 WP_016737443 hypothetical protein -
AMK00_RS23525 (AMK00_PB00173) 197702..198073 - 372 WP_042120136 hypothetical protein -
AMK00_RS23530 (AMK00_PB00174) 198172..198708 + 537 WP_064811975 hypothetical protein -
AMK00_RS23535 (AMK00_PB00175) 198712..199371 + 660 WP_064811976 lytic transglycosylase domain-containing protein virB1
AMK00_RS23540 (AMK00_PB00176) 199368..199667 + 300 WP_009997887 TrbC/VirB2 family protein virB2
AMK00_RS23545 (AMK00_PB00177) 199673..200011 + 339 WP_009997888 type IV secretion system protein VirB3 virB3
AMK00_RS23550 (AMK00_PB00178) 200004..202370 + 2367 WP_064811977 VirB4 family type IV secretion system protein virb4
AMK00_RS23555 (AMK00_PB00179) 202367..203068 + 702 WP_064811978 P-type DNA transfer protein VirB5 virB5
AMK00_RS23560 (AMK00_PB00180) 203065..203298 + 234 WP_010007459 EexN family lipoprotein -
AMK00_RS23565 (AMK00_PB00181) 203302..204234 + 933 WP_040111793 type IV secretion system protein virB6
AMK00_RS33215 (AMK00_PB00182) 204274..204555 + 282 WP_080771758 hypothetical protein -
AMK00_RS23570 (AMK00_PB00183) 204557..205228 + 672 WP_064811979 virB8 family protein virB8
AMK00_RS23575 (AMK00_PB00184) 205225..206082 + 858 WP_064811980 P-type conjugative transfer protein VirB9 virB9
AMK00_RS23580 (AMK00_PB00185) 206091..207263 + 1173 WP_064811981 type IV secretion system protein VirB10 virB10
AMK00_RS23585 (AMK00_PB00186) 207272..208300 + 1029 WP_010008207 P-type DNA transfer ATPase VirB11 virB11
AMK00_RS23590 (AMK00_PB00187) 208344..208922 - 579 WP_064811982 PIN domain-containing protein -
AMK00_RS23595 (AMK00_PB00188) 208912..209358 - 447 WP_225881772 DNA-binding protein -
AMK00_RS23600 (AMK00_PB00190) 209870..211060 - 1191 WP_064811984 DUF1173 domain-containing protein -
AMK00_RS33220 211371..211630 + 260 Protein_208 toprim domain-containing protein -
AMK00_RS23610 (AMK00_PB00191) 212016..212282 + 267 WP_004676093 hypothetical protein -
AMK00_RS23615 (AMK00_PB00192) 212279..212677 + 399 WP_064811986 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   3205 GenBank   NZ_CP013497
Plasmid name   pRspN621b Incompatibility group   -
Plasmid size   439584 bp Coordinate of oriT [Strand]   218473..218501 [+]
Host baterium   Rhizobium sp. N621

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   -