Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102777
Name   oriT_pRphaN161b in_silico
Organism   Rhizobium phaseoli strain N161
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013587 (177632..177660 [+], 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_pRphaN161b
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2049 GenBank   WP_029875464
Name   traA_AMC78_RS24305_pRphaN161b insolico UniProt ID   A0A2A5KKZ8
Length   1558 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1558 a.a.        Molecular weight: 172030.24 Da        Isoelectric Point: 7.1540

>WP_029875464.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPATEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETMKAWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLSEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPQEIEAETGKVSEPAVFTTREMLRIE
YDMAQSARVLSERRGFGVSERNVTVAIERVESGDPKNPFRLDAEQVDAVRHVTGDGGIAAIVGLAGAGKS
TLLAAARLAWESEGHRVIGAALAGKAAEGLQDSSGIKSRTLASWELAWGNGRDTLHRGDVLVIDEAGMVA
SQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELVGVRRQREAWARNASRLFARGE
VEKGLDAYARHGHLVEAGSREETIDRIVSDWAAARREAIERSTSEGGDGRLRGDELLVLAHTNDDVRKLN
EALRSVMTQEGALSESRSFRSERGVREFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVVSTGDKR
GDPLLSVLLDNGRKLVFSEDSYRHVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDRVDL
YAAKEDFAAKPEWGRKPRVDHATGVTGELVETGEAKFRPDDEDADDSPYADVRADDGTVHRLWGVSLPKA
LEEAGIQEGDTVTLRKDGVERVKVQIAVVDEKTGHKHYEEREVDRNVWTASQVETASARQERIERESHRP
ELFNPLVERLSRSGAKTTTLDFESEASYRAHANDFARRRGLDHLSLAAAEMEQSLTRRWAWIAAKREQVE
KLWERASVALGFAIERERRVAYNEERSQTMVEATSSDARTASHSVSGASAAETRYLIPPATSFVSSVEED
ARLAQLASPAWTEREVILRPLLQKIYRDPDAALVSLNALASDIGVAPRRLADDLAAAPGRLGRLRGSELI
VDGRAAREERNLAVAAVKELLPMARAHATEFRRNAERFELREQTRRAHMSLSIPALSERAMARLMEIEAV
RSQGGDDAYKTAFALAAKDRSVVREIKAVSEALTARFGWSAFSAKADAIAERNIVERMPEDLTDEWRGKL
TRLFDAVRRFADEQHLAERRDRSKVVAGASADLSKEPGTEKIIMPPMFAAVTEFKVPIDDEARSRALASP
VYRQQRAALANAATTIWRDPAEVVGKIEELLQKGFAAERIGAAVTNNPAAYGALRGSDRLMDRMLTSGRE
RKEAVAAVPEAAARLRALGAAHLNALDAERQAITDERRRMAVAIPALSKAAEEALAHLTVEVSKDSRKLS
VSAASLDPGIGREFAAVSRALDERFGRNALVRGDKDIANVVPPAQRGAFAAMQERLKVLQQTVRLQSSEQ
IIVERRQQTANRSRGINL

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(391-576)

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

(1327-1418)

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

(1069-1140)


  Protein structure



No available structure.




T4CP

ID   1704 GenBank   WP_012489500
Name   traG_AMC78_RS24290_pRphaN161b 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: 70607.76 Da        Isoelectric Point: 9.5676

>WP_012489500.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MGLRGKPHPSLLLVLVPIAVTTITIYIVGWRWPGLAAGMSGKIEHWFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLYFLGVAAFYALREFGRLAPAVQAEVITWDRALSYLDMVAVIAAVAGFMAVAMSARI
SVVVPDEIKRARRGIFGDADWLPMTAAGKLFPPEGEIVVGERYRVDKEIVHALPFDANDRSTWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYSGPLICLDPSTEVAPMVAGHRARALKREVMVLDPT
NPIMGFNVLDGIEASKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYEGRRS
LRSLRQIVSEPEPSVLAMLRDIQEHSGSAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNISASILRSYPGIARVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKG
SSRNIGWDTKNNASRRSENVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDQAAK
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: 157873..167460

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC78_RS34505 154367..154593 - 227 Protein_139 chaperonin GroEL -
AMC78_RS24165 (AMC78_PB00123) 154888..155808 + 921 WP_029875459 zincin-like metallopeptidase domain-containing protein -
AMC78_RS24170 155919..156101 - 183 WP_009993909 hypothetical protein -
AMC78_RS24175 (AMC78_PB00125) 156863..157234 - 372 WP_012489483 hypothetical protein -
AMC78_RS24180 (AMC78_PB00126) 157333..157869 + 537 WP_012489484 hypothetical protein -
AMC78_RS24185 (AMC78_PB00127) 157873..158514 + 642 WP_009991940 transglycosylase SLT domain-containing protein virB1
AMC78_RS24190 (AMC78_PB00128) 158529..158828 + 300 WP_009991942 TrbC/VirB2 family protein virB2
AMC78_RS24195 (AMC78_PB00129) 158834..159172 + 339 WP_010068249 type IV secretion system protein VirB3 virB3
AMC78_RS24200 (AMC78_PB00130) 159165..161531 + 2367 WP_029875460 VirB4 family type IV secretion system protein virb4
AMC78_RS24205 (AMC78_PB00131) 161528..162229 + 702 WP_009996884 P-type DNA transfer protein VirB5 virB5
AMC78_RS24210 (AMC78_PB00132) 162226..162459 + 234 WP_064836762 EexN family lipoprotein -
AMC78_RS24215 (AMC78_PB00133) 162462..163394 + 933 WP_009996881 type IV secretion system protein virB6
AMC78_RS34510 (AMC78_PB00134) 163434..163715 + 282 WP_012489488 hypothetical protein -
AMC78_RS24220 (AMC78_PB00135) 163717..164388 + 672 WP_029875461 virB8 family protein virB8
AMC78_RS24225 (AMC78_PB00136) 164385..165242 + 858 WP_009996879 P-type conjugative transfer protein VirB9 virB9
AMC78_RS24230 (AMC78_PB00137) 165251..166423 + 1173 WP_012489490 type IV secretion system protein VirB10 virB10
AMC78_RS24235 (AMC78_PB00138) 166432..167460 + 1029 WP_012489491 P-type DNA transfer ATPase VirB11 virB11
AMC78_RS24240 (AMC78_PB00139) 167504..168076 - 573 WP_010067915 PIN domain-containing protein -
AMC78_RS24245 (AMC78_PB00140) 168066..168512 - 447 WP_029875463 hypothetical protein -
AMC78_RS24250 (AMC78_PB00142) 169025..170215 - 1191 WP_012489493 DUF1173 domain-containing protein -
AMC78_RS34515 170526..170785 + 260 Protein_159 toprim domain-containing protein -
AMC78_RS24255 (AMC78_PB00144) 171173..171439 + 267 WP_004676093 hypothetical protein -
AMC78_RS24260 (AMC78_PB00145) 171436..171834 + 399 WP_008536014 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   3220 GenBank   NZ_CP013587
Plasmid name   pRphaN161b Incompatibility group   -
Plasmid size   395855 bp Coordinate of oriT [Strand]   177632..177660 [+]
Host baterium   Rhizobium phaseoli strain N161

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   -