Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103487
Name   oriT_pBS3a in_silico
Organism   Rhizobium phaseoli strain S3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP064932 (258004..258032 [+], 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_pBS3a
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2609 GenBank   WP_046977193
Name   traA_HER27_RS23020_pBS3a insolico UniProt ID   A0A192TMB6
Length   1560 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1560 a.a.        Molecular weight: 172207.61 Da        Isoelectric Point: 6.9611

>WP_046977193.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGAKKVPVLGEDGKPLRVVTPDRPNGKIVYKVWAGDKETMKAWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLSEPELLLKQ
LGNERSTFDEREIAKALHRYVDDPVDFANIRVRLMASDQLVILKPQEIEAETGKVSEPAMFTTREMLRIE
YDMAQSARVLSERRGFGVSERNVKVAIESVESGDPKTPFRLDAEQVDAVRHVTGDSGIAAVVGLAGAGKS
TLLAAARLAWEGEGHRVIGAALAGKAAEGLQDSSGIKSRTLASWELAWANGRDTLHRGDVLVIDEAGMVA
SQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREAWARNASRLFARGE
VEKGLDAYAQQGHLVEAGTREETIDRIVVDWTEARKHAIGRSISEGRDGRLRGDELLVLAHTNDDVRKLN
EALREVMAGDNALGESRSFRTERGARKFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVVSTGDKR
GGPLLSVLLDNGNKVVFGEDSYRNVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDRVDL
YAAIEDFEAKPEWGRKAGVDHAAGVTGELVETGEAKFRPDDEDADDSPYADIRTDGGAVHRLWGVSLPKA
LEEASIMEGDTVTLRKDGVERVKVQIAVVDEKTGHKHYEEREVDRNVWTASQVETASARQERIERESHRP
ELFNLLVERLSRSGAKTTTLDFESEASYRAHANDFARRRGLDHLSLAAAEMEESLTRRWAWIAAKREQVE
KLWERASVALGFAIERERRVAYNEERSQTMVEATSSDARTASHSVSGASADETRYLIPPATSFVSSVEED
ARLAQLASPAWTEREVILRPLLEKIYRDPDAALVSLNALASDIGVAARRLADDLAAAPGRLGRLRGSELI
VDGRAAREERNLAVAAVKELLPMARAHATEFRRNAERFDLREQTRRAHMSLSIPALSERAMARLMEIEAV
RRQGGDDAYKSAFALAAEDRSVVQEIKAVSEALTARFGWSAFSAKADAIAERNIVERMPEDLTDERRGKL
TRLFEAVRRFAEEQHLAERRDRSKVVAGASVDLETEKGVGKENVPIPPMLAAVTEFKVPVDDEARSRALS
APLYRQQRVALANAATTIWRDPAEVVGKIEELLQKGFAADRIGAAVANDPAAYAALRGSDRLVDRMLASG
RERKEAVAAVPEAAARLRALGAAYANALNSERQAITEERRRMGVAIPALSKAAEEALARLTAEARKDSRG
LRVSAVPLDPGIGREFAAVSRALDERFGRNAIVRGEKDLVSRLPPAQRRAFEAMQERLKVLQQTVRLQSS
EQITAERRQRAASRARGINL

  Protein domains


Predicted by InterproScan.

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

(1330-1420)

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

(1070-1140)

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(391-577)


  Protein structure



No available structure.




T4CP

ID   2410 GenBank   WP_046977192
Name   traG_HER27_RS23005_pBS3a 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: 70708.95 Da        Isoelectric Point: 9.2487

>WP_046977192.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MGLRGKPHPSLLLVLAPIAVTTITIYIVGWRWPGLAVGMSGRMEYWFLRAAPVLPLMFGPLAGLLTVWAL
PLHRRRPVAMASLLCFLGIAAYYALREFGRLAPTVQARVVPWDRALSYLDMVAVIAAVAGFMAVAVSARI
SVVVPDEIKRARRGIFGDADWLPMAAAGKLFPPDGEIVVGERYRVDKEIIHALPFDVNDRSTWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALIYTGPMICLDPSTEVAPMVVEHRTNALGREVMVLDPT
NPIMGFNVLDGIEASKQKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYEGRRS
LRSLRQIVSEPEPSVLAMLRDIQEHSGSAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNISASILRSYPGIARVIIGSLINAMVQADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNLSAQCGEMTVEVKG
SSRNIGWDTKNNASRRSENVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKEMDQAAK
VNRFVKPVL

  Protein domains


Predicted by InterproScan.

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

(171-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 237276..246871

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HER27_RS33030 234051..234277 - 227 Protein_223 chaperonin GroEL -
HER27_RS22875 (HER27_022875) 234572..235492 + 921 WP_004673402 zincin-like metallopeptidase domain-containing protein -
HER27_RS22880 (HER27_022880) 236266..236637 - 372 WP_042120136 hypothetical protein -
HER27_RS22885 (HER27_022885) 236736..237272 + 537 WP_011053366 hypothetical protein -
HER27_RS22890 (HER27_022890) 237276..237944 + 669 WP_064820013 lytic transglycosylase domain-containing protein virB1
HER27_RS22895 (HER27_022895) 237941..238240 + 300 WP_007636189 TrbC/VirB2 family protein virB2
HER27_RS22900 (HER27_022900) 238246..238584 + 339 WP_011053369 type IV secretion system protein VirB3 virB3
HER27_RS22905 (HER27_022905) 238577..240940 + 2364 WP_167860844 VirB4 family type IV secretion system protein virb4
HER27_RS22910 (HER27_022910) 240937..241638 + 702 WP_011053371 P-type DNA transfer protein VirB5 virB5
HER27_RS22915 (HER27_022915) 241635..241868 + 234 WP_008537008 EexN family lipoprotein -
HER27_RS22920 (HER27_022920) 241871..242803 + 933 WP_064820015 type IV secretion system protein virB6
HER27_RS33035 242845..243126 + 282 WP_081278376 hypothetical protein -
HER27_RS22925 (HER27_022925) 243128..243799 + 672 WP_064820016 virB8 family protein virB8
HER27_RS22930 (HER27_022930) 243796..244653 + 858 WP_064820017 P-type conjugative transfer protein VirB9 virB9
HER27_RS22935 (HER27_022935) 244662..245834 + 1173 WP_064820018 type IV secretion system protein VirB10 virB10
HER27_RS22940 (HER27_022940) 245843..246871 + 1029 WP_064820019 P-type DNA transfer ATPase VirB11 virB11
HER27_RS22945 (HER27_022945) 246915..247493 - 579 WP_064820020 PIN domain-containing protein -
HER27_RS22950 (HER27_022950) 247483..247929 - 447 WP_225882822 DNA-binding protein -
HER27_RS22955 (HER27_022955) 248443..249633 - 1191 WP_064820021 DUF1173 domain-containing protein -
HER27_RS33040 249943..250200 + 258 Protein_242 toprim domain-containing protein -
HER27_RS22965 (HER27_022965) 250525..251465 + 941 Protein_243 DUF2493 domain-containing protein -
HER27_RS22970 (HER27_022970) 251550..251816 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   3930 GenBank   NZ_CP064932
Plasmid name   pBS3a Incompatibility group   -
Plasmid size   446029 bp Coordinate of oriT [Strand]   258004..258032 [+]
Host baterium   Rhizobium phaseoli strain S3

Cargo genes

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