Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102904
Name   oriT_pRetBra5b in_silico
Organism   Rhizobium phaseoli Brasil 5 strain Bra5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP020898 (147060..147088 [+], 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_pRetBra5b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2182 GenBank   WP_064811989
Name   traA_Bra5_RS23785_pRetBra5b 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   1854 GenBank   WP_064811988
Name   traG_Bra5_RS23770_pRetBra5b 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: 127299..136887

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Bra5_RS33935 123783..124009 - 227 Protein_108 chaperonin GroEL -
Bra5_RS23635 (Bra5_PB00112) 124304..125224 + 921 WP_064811974 zincin-like metallopeptidase domain-containing protein -
Bra5_RS23640 (Bra5_PB00113) 125335..125517 - 183 WP_016737443 hypothetical protein -
Bra5_RS23645 (Bra5_PB00115) 126289..126660 - 372 WP_042120136 hypothetical protein -
Bra5_RS23650 (Bra5_PB00116) 126759..127295 + 537 WP_085743930 hypothetical protein -
Bra5_RS23655 (Bra5_PB00117) 127299..127958 + 660 WP_064811976 lytic transglycosylase domain-containing protein virB1
Bra5_RS23660 (Bra5_PB00118) 127955..128254 + 300 WP_009997887 TrbC/VirB2 family protein virB2
Bra5_RS23665 (Bra5_PB00119) 128260..128598 + 339 WP_009997888 type IV secretion system protein VirB3 virB3
Bra5_RS23670 (Bra5_PB00120) 128591..130957 + 2367 WP_085743931 VirB4 family type IV secretion system protein virb4
Bra5_RS23675 (Bra5_PB00121) 130954..131655 + 702 WP_064811978 P-type DNA transfer protein VirB5 virB5
Bra5_RS23680 (Bra5_PB00122) 131652..131885 + 234 WP_010007459 EexN family lipoprotein -
Bra5_RS23685 (Bra5_PB00123) 131889..132821 + 933 WP_040111793 type IV secretion system protein virB6
Bra5_RS33940 (Bra5_PB00124) 132861..133142 + 282 WP_080771758 hypothetical protein -
Bra5_RS23695 (Bra5_PB00125) 133144..133815 + 672 WP_064811979 virB8 family protein virB8
Bra5_RS23700 (Bra5_PB00126) 133812..134669 + 858 WP_064811980 P-type conjugative transfer protein VirB9 virB9
Bra5_RS23705 (Bra5_PB00127) 134678..135850 + 1173 WP_064811981 type IV secretion system protein VirB10 virB10
Bra5_RS23710 (Bra5_PB00128) 135859..136887 + 1029 WP_010008207 P-type DNA transfer ATPase VirB11 virB11
Bra5_RS23715 (Bra5_PB00129) 136931..137509 - 579 WP_064811982 PIN domain-containing protein -
Bra5_RS23720 (Bra5_PB00130) 137499..137945 - 447 WP_225881772 DNA-binding protein -
Bra5_RS23725 (Bra5_PB00132) 138457..139647 - 1191 WP_064811984 DUF1173 domain-containing protein -
Bra5_RS33945 139958..140217 + 260 Protein_128 toprim domain-containing protein -
Bra5_RS23735 (Bra5_PB00134) 140603..140869 + 267 WP_004676093 hypothetical protein -
Bra5_RS23740 (Bra5_PB00135) 140866..141264 + 399 WP_010002510 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   3347 GenBank   NZ_CP020898
Plasmid name   pRetBra5b Incompatibility group   -
Plasmid size   392817 bp Coordinate of oriT [Strand]   147060..147088 [+]
Host baterium   Rhizobium phaseoli Brasil 5 strain Bra5

Cargo genes

Drug resistance gene   -
Virulence gene   hsiC1/vipB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixN, fixO, nodC, nodS, nodI, nodJ, nodD, a9174_31165, nifH, nifT, nifZ, nifB, nifA, fixX, fixC, fixB, fixA, nifW, nifS, nifD, nifK, nifE, nifN, nifX, mLTONO_5203, nodA
Anti-CRISPR   -