Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102780
Name   oriT_pRphaR620b in_silico
Organism   Rhizobium phaseoli strain R620
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013544 (147649..147677 [+], 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_pRphaR620b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2052 GenBank   WP_064811989
Name   traA_AMC86_RS23700_pRphaR620b 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   1708 GenBank   WP_064826107
Name   traG_AMC86_RS23685_pRphaR620b 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: 70731.94 Da        Isoelectric Point: 9.5675

>WP_064826107.1 Ti-type conjugative transfer system protein TraG [Rhizobium phaseoli]
MGLRGKPHPSLLLVLVPIAVTTITIYIVGWRWPGLAAGMSGKIEHWFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLYFLGVAAFYALREFGRLAPAVQAEVITWDRALSYLDMVAVIAAVAGFMAVAMSARI
SVVVPDEIKRARRGIFGDADWLPMRAAGKLFPPEGEIVVGERYRVDKEIVHALPFDANDRSTWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYSGPLICLDPSTEVAPMVAEHRARALKREVMVLDPT
NPIMGFNVLDGIEASKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYEGRRS
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDVVSGKKDVFLNIPASILRSYPGIARVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
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: 127885..137473

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC86_RS33875 122898..123124 - 227 Protein_112 chaperonin GroEL -
AMC86_RS23555 (AMC86_PB00103) 123419..124339 + 921 WP_064811974 zincin-like metallopeptidase domain-containing protein -
AMC86_RS23560 124450..124632 - 183 WP_016737443 hypothetical protein -
AMC86_RS23565 (AMC86_PB00104) 125534..126607 - 1074 WP_064826106 IS110 family transposase -
AMC86_RS23570 (AMC86_PB00106) 126875..127246 - 372 WP_042120136 hypothetical protein -
AMC86_RS23575 (AMC86_PB00107) 127345..127881 + 537 WP_064811975 hypothetical protein -
AMC86_RS23580 (AMC86_PB00108) 127885..128544 + 660 WP_064811976 lytic transglycosylase domain-containing protein virB1
AMC86_RS23585 (AMC86_PB00109) 128541..128840 + 300 WP_009997887 TrbC/VirB2 family protein virB2
AMC86_RS23590 (AMC86_PB00110) 128846..129184 + 339 WP_009997888 type IV secretion system protein VirB3 virB3
AMC86_RS23595 (AMC86_PB00111) 129177..131543 + 2367 WP_064811977 VirB4 family type IV secretion system protein virb4
AMC86_RS23600 (AMC86_PB00112) 131540..132241 + 702 WP_064811978 P-type DNA transfer protein VirB5 virB5
AMC86_RS23605 (AMC86_PB00113) 132238..132471 + 234 WP_010007459 EexN family lipoprotein -
AMC86_RS23610 (AMC86_PB00114) 132475..133407 + 933 WP_040111793 type IV secretion system protein virB6
AMC86_RS33880 (AMC86_PB00115) 133447..133728 + 282 WP_080771758 hypothetical protein -
AMC86_RS23615 (AMC86_PB00116) 133730..134401 + 672 WP_064811979 virB8 family protein virB8
AMC86_RS23620 (AMC86_PB00117) 134398..135255 + 858 WP_064811980 P-type conjugative transfer protein VirB9 virB9
AMC86_RS23625 (AMC86_PB00118) 135264..136436 + 1173 WP_064811981 type IV secretion system protein VirB10 virB10
AMC86_RS23630 (AMC86_PB00119) 136445..137473 + 1029 WP_010008207 P-type DNA transfer ATPase VirB11 virB11
AMC86_RS23635 (AMC86_PB00120) 137517..138095 - 579 WP_064811982 PIN domain-containing protein -
AMC86_RS23640 (AMC86_PB00121) 138085..138531 - 447 WP_225881772 DNA-binding protein -
AMC86_RS23645 (AMC86_PB00123) 139043..140233 - 1191 WP_064811984 DUF1173 domain-containing protein -
AMC86_RS33885 140544..140806 + 263 Protein_133 toprim domain-containing protein -
AMC86_RS23655 (AMC86_PB00124) 141192..141458 + 267 WP_004676093 hypothetical protein -
AMC86_RS23660 (AMC86_PB00125) 141455..141853 + 399 WP_064811986 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   3223 GenBank   NZ_CP013544
Plasmid name   pRphaR620b Incompatibility group   -
Plasmid size   355825 bp Coordinate of oriT [Strand]   147649..147677 [+]
Host baterium   Rhizobium phaseoli strain R620

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, a9174_31165, nodD, nodJ, nodI, nodS, nodC, nodB, nodZ, fixG, fixO, fixN, mLTONO_5203, nodA
Anti-CRISPR   -