Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107595
Name   oriT_pRheCIAT894c in_silico
Organism   Rhizobium sp. CIAT894
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP020950 (229850..229878 [+], 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_pRheCIAT894c
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5105 GenBank   WP_071088540
Name   traA_RHEC894_RS25135_pRheCIAT894c insolico UniProt ID   A0A437N6N5
Length   1558 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1558 a.a.        Molecular weight: 172057.27 Da        Isoelectric Point: 7.2379

>WP_071088540.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [unclassified Rhizobium]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPATEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETMRAWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLSEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPQEIEAETGKVSEPAVFTTREMLRIE
YDMAQSARVLSERRGFGVSERNVTVAIERVESGDPKNPFRLDAEQVDAVRHVTGDGGIAAIVGLAGAGKS
TLLAAARLAWESEGHRVIGAALAGKAAEGLQDSSGIKSRTLASWELAWGNGRDTLHRGDVLVIDEAGMVA
SQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELVGVRRQREAWARNASRLFARGE
VEKGLDAYARHGHLVEAGSREETIDRIVSDWAAARREAIERSTSEGGDGRLRGDELLVLAHTNDDVRKLN
EALRSVMTQEGALSESRSFRSERGVREFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVVSTGDKR
GDPLLSVLLDNGRKLVFSEDSYRHVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDRVDL
YAAKEDFAAKPEWGRKPRVDHATGVTGELVETGEAKFRPDDEDADDSPYADVRADDGTVHRLWGVSLPKA
LEEAGIQEGDTVTLRKDGVERVKVQIAVVDEKTGHKHYEEREVDRNVWTASQVETASARQERIERESHRP
ELFNPLVERLSRSGAKTTTLDFESEASYRAHANDFARRRGLDHLSLAAAEMEQSLTRRWAWIAAKREQVE
KLWERASVALGFAIERERRVAYNEERSQTMVEATSSDARTASHSVSGASAAETRYLIPPATSFVSSVEED
ARLAQLASPAWTEREVILRPLLQKIYRDPDAALVSLNALASDIGVAPRRLADDLAAAPGRLGRLRGSELI
VDGRAAREERNLAVAAVKELLPMARAHATEFRRNAERFELREQTRRAHMSLSIPALSERAMARLMEIEAV
RSQGGDDAYKTAFALAAKDRSVVREIKAVSEALTARFGWSAFSAKADAIAERNIVERMPEDLTDEWRGKL
TRLFDAVRRFADEQHLAERRDRSKVVAGASADLSKEPGTEKIIMPPMFAAVTEFKVPIDDEARSRALASP
VYRQQRAALANAATTIWRDPAEVVGKIEELLQKGFAAERIGAAVTNNPAAYGALRGSDRLMDRMLTSGRE
RKEAVAAVPEAAARLRALGAAHLNALDAQRQAITDERRRMAVAIPALSKAAEEALAHLTVEVSKDSRKLS
VSAASLDPGIGREFAAVSRALDERFGRNALVRGDKDIANVVPPAQRGAFAAMQERLKVLQQTVRLQSSEQ
IIVERRQQTANRSRGINL

  Protein domains


Predicted by InterproScan.

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)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   5327 GenBank   WP_012489500
Name   traG_RHEC894_RS25120_pRheCIAT894c 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: 210091..219678

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RHEC894_RS33545 206585..206811 - 227 Protein_191 chaperonin GroEL -
RHEC894_RS24985 (RHEC894_PC00203) 207106..208026 + 921 WP_029875459 zincin-like metallopeptidase domain-containing protein -
RHEC894_RS24990 208137..208319 - 183 WP_009993909 hypothetical protein -
RHEC894_RS24995 (RHEC894_PC00206) 209081..209452 - 372 WP_012489483 hypothetical protein -
RHEC894_RS25000 (RHEC894_PC00207) 209551..210087 + 537 WP_012489484 hypothetical protein -
RHEC894_RS25005 (RHEC894_PC00208) 210091..210732 + 642 WP_012489485 transglycosylase SLT domain-containing protein virB1
RHEC894_RS25010 (RHEC894_PC00209) 210747..211046 + 300 WP_009991942 TrbC/VirB2 family protein virB2
RHEC894_RS25015 (RHEC894_PC00210) 211052..211390 + 339 WP_010068249 type IV secretion system protein VirB3 virB3
RHEC894_RS25020 (RHEC894_PC00211) 211383..213749 + 2367 WP_029875460 VirB4 family type IV secretion system protein virb4
RHEC894_RS25025 (RHEC894_PC00212) 213746..214447 + 702 WP_012489487 P-type DNA transfer protein VirB5 virB5
RHEC894_RS25030 (RHEC894_PC00213) 214444..214677 + 234 WP_009996882 EexN family lipoprotein -
RHEC894_RS25035 (RHEC894_PC00214) 214680..215612 + 933 WP_009996881 type IV secretion system protein virB6
RHEC894_RS33550 (RHEC894_PC00215) 215652..215933 + 282 WP_012489488 hypothetical protein -
RHEC894_RS25045 (RHEC894_PC00216) 215935..216606 + 672 WP_029875461 virB8 family protein virB8
RHEC894_RS25050 (RHEC894_PC00217) 216603..217460 + 858 WP_009996879 P-type conjugative transfer protein VirB9 virB9
RHEC894_RS25055 (RHEC894_PC00218) 217469..218641 + 1173 WP_012489490 type IV secretion system protein VirB10 virB10
RHEC894_RS25060 (RHEC894_PC00219) 218650..219678 + 1029 WP_012489491 P-type DNA transfer ATPase VirB11 virB11
RHEC894_RS25065 (RHEC894_PC00220) 219722..220294 - 573 WP_010067915 PIN domain-containing protein -
RHEC894_RS25070 (RHEC894_PC00221) 220284..220730 - 447 WP_029875463 hypothetical protein -
RHEC894_RS25075 (RHEC894_PC00223) 221243..222433 - 1191 WP_012489493 DUF1173 domain-containing protein -
RHEC894_RS33555 222744..223003 + 260 Protein_211 toprim domain-containing protein -
RHEC894_RS25080 (RHEC894_PC00225) 223391..223657 + 267 WP_004676093 hypothetical protein -
RHEC894_RS25085 (RHEC894_PC00226) 223654..224052 + 399 WP_008536014 type II toxin-antitoxin system VapC family toxin -

Host bacterium

ID   8030 GenBank   NZ_CP020950
Plasmid name   pRheCIAT894c Incompatibility group   -
Plasmid size   464024 bp Coordinate of oriT [Strand]   229850..229878 [+]
Host baterium   Rhizobium sp. CIAT894

Cargo genes

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