Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102768
Name   oriT_pRphaN671d in_silico
Organism   Rhizobium phaseoli strain N671
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013578 (235004..235032 [+], 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_pRphaN671d
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2041 GenBank   WP_046977193
Name   traA_AMC80_RS26475_pRphaN671d 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   1695 GenBank   WP_046977192
Name   traG_AMC80_RS26460_pRphaN671d 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: 214273..223871

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC80_RS26330 (AMC80_PD00173) 211047..211274 - 228 Protein_193 chaperonin GroEL -
AMC80_RS26335 (AMC80_PD00174) 211569..212489 + 921 WP_037145473 zincin-like metallopeptidase domain-containing protein -
AMC80_RS26340 (AMC80_PD00175) 213263..213634 - 372 WP_042120136 hypothetical protein -
AMC80_RS26345 (AMC80_PD00176) 213733..214269 + 537 WP_011053366 hypothetical protein -
AMC80_RS26350 (AMC80_PD00177) 214273..214941 + 669 WP_064820013 lytic transglycosylase domain-containing protein virB1
AMC80_RS26355 (AMC80_PD00178) 214938..215237 + 300 WP_007636189 TrbC/VirB2 family protein virB2
AMC80_RS26360 (AMC80_PD00179) 215243..215581 + 339 WP_011053369 type IV secretion system protein VirB3 virB3
AMC80_RS26365 (AMC80_PD00180) 215574..217940 + 2367 WP_064820014 VirB4 family type IV secretion system protein virb4
AMC80_RS26370 (AMC80_PD00181) 217937..218638 + 702 WP_011053371 P-type DNA transfer protein VirB5 virB5
AMC80_RS26375 (AMC80_PD00182) 218635..218868 + 234 WP_008537008 EexN family lipoprotein -
AMC80_RS26380 (AMC80_PD00183) 218871..219803 + 933 WP_064820015 type IV secretion system protein virB6
AMC80_RS35695 (AMC80_PD00184) 219845..220126 + 282 WP_081278376 hypothetical protein -
AMC80_RS26385 (AMC80_PD00185) 220128..220799 + 672 WP_064820016 virB8 family protein virB8
AMC80_RS26390 (AMC80_PD00186) 220796..221653 + 858 WP_064820017 P-type conjugative transfer protein VirB9 virB9
AMC80_RS26395 (AMC80_PD00187) 221662..222834 + 1173 WP_064820018 type IV secretion system protein VirB10 virB10
AMC80_RS26400 (AMC80_PD00188) 222843..223871 + 1029 WP_064820019 P-type DNA transfer ATPase VirB11 virB11
AMC80_RS26405 (AMC80_PD00189) 223915..224493 - 579 WP_064832806 PIN domain-containing protein -
AMC80_RS26410 (AMC80_PD00190) 224483..224929 - 447 WP_225882822 DNA-binding protein -
AMC80_RS26415 (AMC80_PD00192) 225443..226633 - 1191 WP_064820021 DUF1173 domain-containing protein -
AMC80_RS35700 226943..227200 + 258 Protein_212 toprim domain-containing protein -
AMC80_RS26425 (AMC80_PD00193) 227525..228465 + 941 Protein_213 DUF2493 domain-containing protein -
AMC80_RS26430 (AMC80_PD00194) 228550..228816 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   3211 GenBank   NZ_CP013578
Plasmid name   pRphaN671d Incompatibility group   -
Plasmid size   459642 bp Coordinate of oriT [Strand]   235004..235032 [+]
Host baterium   Rhizobium phaseoli strain N671

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, a9174_31165, nodD, nodJ, nodI, nodS, nodC, nodB, nodZ, fixG, fixO, fixN, mLTONO_5203, nodA
Anti-CRISPR   -