Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102488
Name   oriT_pRphCh2410d in_silico
Organism   Rhizobium phaseoli Ch24-10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AHJU02000028 (972323..972351 [-], 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_pRphCh2410d
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1852 GenBank   WP_046977228
Name   traA_RPHASCH2410_RS29705_pRphCh2410d insolico UniProt ID   _
Length   1543 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1543 a.a.        Molecular weight: 170684.10 Da        Isoelectric Point: 7.1240

>WP_046977228.1 Ti-type conjugative transfer relaxase TraA [Rhizobium phaseoli]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGASELMHEELALPDQIPAWLKMAMDG
RSIAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVSGNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEDGKPLRVVTPDRPNGRIVYKVWAGDKETMKAWKVAWAETANR
HLALAGHDIRLDGRSYAEQGLDGVAQKHLGPEKAALARQGRELFFAPAHLARRQEMADRLLAEPELLLKQ
LGNERSTFDEKDIAKALHRYVDDPVEFANIRARLMASDELVMLKPQEMDAGTGKVSEPAVFTTRDMLRIE
YHMAESARRLSNRSGYAVSRKHVAAAIERIESDDPKNLFRLDAEQVDAIRHVTGDSGTAAVVGLAGAGKS
TLLAAARLAWESEGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVLVIDEAGMVS
SQQMARVLKIAEEAEIKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQEWARDASRLFARGE
VEKGLDAYAQQGHLVEAGTREEAINRIVADWSEARRKAFGRSVAEGRDGHLRGDELLVLAHTNADVHKLN
EALREVMKAEQALSDSRTFQTARGAREFAVGDRIIFLENARFLEPRARHSGPQYVKNGMLGTVVATGDKR
GDPLLSVLLDNGRNVVFSEDSYRNVDHGYAATIHKSQGATVDRTFVLATGMMDRHLTYVSMTRHRDRADL
YAAKEDFAARPEWGHKARVDHAAGVTGELVEAGEAKFRPDDEDADDSPYADIRTDDGSVHRLWGVSLPKA
LEQAGISEGDTITLRKDGVERVKVQIAVVDEATGQKRYEEREVGRNVWTAKQIETAEARQERIERESHRP
DVFSRLVERLARSGSKTTTLDFESEAGYRAHADDFARRRGLDHLSLAAAEMEEGVSRRLAWIAEKRGQIA
KLWERASVALGFAIERERRVAYNEERSETMIGAISSEERYLMPPATDFRRSLDEDARLAQLSSPAWKERE
AILRPLLETIYRDPDAALVRLNALASYTGTEPRGLADNLAVAPDRLGRLRGSELIVEGRAARDERDVAMA
ALEELLPLVRGHATEFRRNAERFELREQTRRASMSLSVPALSEQAMARLMEIEAVRTQGGDDAYKTAFAL
AAEDRSVVQEVKAVSEALTARFGWSAFTAKADAMAERNMVERMPEDLSAGRREELIRLFEAVKRFAEEQH
LAERRDRSKIVAAASAVPGAAPGKQTVTVLPMLAAVTEFKTSVDDEARSRAIAAPLYRQQRAALAEAARM
IWRDPAATVDNIESLLEKGFAADRIAAAVTNDPAAYGALRGSDRLMDRMLASGRERKDAVQAVPEAAARL
RSLGSAYVNVLDAERQAIAEERRRMAVAIPGLSKAAEGVLMRLTTEVKNNGRTRNAAAGSLDPSIHREFD
AVSRALDERFGRSAIVRGEKDLLNRMPPAQRAAFAAMQEKLKVLQQTVRWESSEKIVSELRSRTVNRGRG
IEL

  Protein domains


Predicted by InterproScan.

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

(1313-1404)

MobA/MobL family (MobA_MobL)

(17-248)

AAA domain (AAA_30)

(391-577)


  Protein structure



No available structure.




T4CP

ID   1444 GenBank   WP_046977229
Name   traG_RPHASCH2410_RS29720_pRphCh2410d 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: 70437.30 Da        Isoelectric Point: 9.2555

>WP_046977229.1 Ti-type conjugative transfer system protein TraG [Rhizobium phaseoli]
MIARGKPHPSLLFVFAPVVVTAIAVYIAGWRWPGLAAGMPGRMEYWFLRAAPVPALLFGPLAGLLTVWAL
PLHRRRPVAMTSLLCYLGVSASYAMREFARLGPSVQTGVMTWDRALSYLDMVAVLGAVAGFLAVAVSARI
SVVVPDEINRARRGTFGDADWLSMAAAAKLFPPDGEIVVGERYRVDKEIVHQLPFDANDRGTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHALGREVMVLDPT
NPIMGFNVLDGIETSRQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFRRRALFMLDEVDLLGYMRVL
EEARDRGRKYGVSMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAVKALDTARTVSAQCGEMTVEVKG
SSRNLGWNSRNGGTRKSESVSFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDGVAK
ANRFVKPVP

  Protein domains


Predicted by InterproScan.

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

(165-632)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 983749..993305

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RPHASCH2410_RS29755 (RPHASCH2410_PD04885) 979319..979501 + 183 WP_016735269 hypothetical protein -
RPHASCH2410_RS29760 (RPHASCH2410_PD04890) 979634..980674 - 1041 WP_016735270 toprim domain-containing protein -
RPHASCH2410_RS29765 (RPHASCH2410_PD04895) 981037..982227 + 1191 WP_016735272 DUF1173 domain-containing protein -
RPHASCH2410_RS29770 (RPHASCH2410_PD04900) 982670..983263 + 594 WP_037146723 DUF433 domain-containing protein -
RPHASCH2410_RS29775 (RPHASCH2410_PD04905) 983278..983730 + 453 WP_016735273 PIN domain-containing protein -
RPHASCH2410_RS29780 (RPHASCH2410_PD04910) 983749..984744 - 996 WP_037146721 P-type DNA transfer ATPase VirB11 virB11
RPHASCH2410_RS29785 (RPHASCH2410_PD04915) 984753..985928 - 1176 WP_016735275 type IV secretion system protein VirB10 virB10
RPHASCH2410_RS29790 (RPHASCH2410_PD04920) 985937..986791 - 855 WP_016735276 P-type conjugative transfer protein VirB9 virB9
RPHASCH2410_RS29795 (RPHASCH2410_PD04925) 986788..987459 - 672 WP_037146717 virB8 family protein virB8
RPHASCH2410_RS35430 (RPHASCH2410_PD04930) 987453..987740 - 288 WP_016737562 hypothetical protein -
RPHASCH2410_RS29805 (RPHASCH2410_PD04935) 987781..988713 - 933 WP_046977230 type IV secretion system protein virB6
RPHASCH2410_RS29810 (RPHASCH2410_PD04940) 988716..988949 - 234 WP_016735278 EexN family lipoprotein -
RPHASCH2410_RS29815 (RPHASCH2410_PD04945) 988946..989647 - 702 WP_016735279 P-type DNA transfer protein VirB5 virB5
RPHASCH2410_RS29820 (RPHASCH2410_PD04950) 989644..992010 - 2367 WP_046977231 VirB4 family type IV secretion system protein virb4
RPHASCH2410_RS29825 (RPHASCH2410_PD04955) 992003..992341 - 339 WP_016735282 type IV secretion system protein VirB3 virB3
RPHASCH2410_RS29830 (RPHASCH2410_PD04960) 992347..992646 - 300 WP_016735283 TrbC/VirB2 family protein virB2
RPHASCH2410_RS29835 (RPHASCH2410_PD04965) 992643..993305 - 663 WP_016735284 transglycosylase SLT domain-containing protein virB1
RPHASCH2410_RS29840 (RPHASCH2410_PD04970) 993309..993845 - 537 WP_016735285 hypothetical protein -
RPHASCH2410_RS29845 (RPHASCH2410_PD04975) 993944..994315 + 372 WP_016735286 hypothetical protein -
RPHASCH2410_RS29850 (RPHASCH2410_PD04985) 994668..995858 - 1191 WP_016735288 hypothetical protein -
RPHASCH2410_RS29855 (RPHASCH2410_PD04990) 995932..996588 - 657 WP_016735289 hypothetical protein -

Host bacterium

ID   2932 GenBank   NZ_AHJU02000028
Plasmid name   pRphCh2410d Incompatibility group   -
Plasmid size   1099763 bp Coordinate of oriT [Strand]   972323..972351 [-]
Host baterium   Rhizobium phaseoli Ch24-10

Cargo genes

Drug resistance gene   -
Virulence gene   gmd
Metal resistance gene   hupE2
Degradation gene   -
Symbiosis gene   fixB, fixA
Anti-CRISPR   AcrIIA8