Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102776
Name   oriT_pRphaN831c in_silico
Organism   Rhizobium phaseoli strain N831
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013566 (230059..230087 [+], 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_pRphaN831c
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2048 GenBank   WP_046977193
Name   traA_AMC82_RS25560_pRphaN831c 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   1703 GenBank   WP_046977192
Name   traG_AMC82_RS25545_pRphaN831c 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: 209351..218930

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC82_RS34490 205839..206065 - 227 Protein_185 chaperonin GroEL -
AMC82_RS25415 (AMC82_PC00167) 206359..207279 + 921 WP_016737442 zincin-like metallopeptidase domain-containing protein -
AMC82_RS25420 207390..207572 - 183 WP_016737443 hypothetical protein -
AMC82_RS25425 (AMC82_PC00168) 208341..208712 - 372 WP_007636193 hypothetical protein -
AMC82_RS25430 (AMC82_PC00169) 208811..209347 + 537 WP_016737444 hypothetical protein -
AMC82_RS25435 (AMC82_PC00170) 209351..210019 + 669 WP_016737445 transglycosylase SLT domain-containing protein virB1
AMC82_RS25440 (AMC82_PC00171) 210016..210315 + 300 WP_007636189 TrbC/VirB2 family protein virB2
AMC82_RS25445 (AMC82_PC00172) 210321..210659 + 339 WP_011053369 type IV secretion system protein VirB3 virB3
AMC82_RS25450 (AMC82_PC00173) 210652..213018 + 2367 WP_046977188 VirB4 family type IV secretion system protein virb4
AMC82_RS25455 (AMC82_PC00174) 213015..213716 + 702 WP_016737448 P-type DNA transfer protein VirB5 virB5
AMC82_RS25460 (AMC82_PC00175) 213713..213928 + 216 WP_016737449 EexN family lipoprotein -
AMC82_RS25465 (AMC82_PC00176) 213931..214863 + 933 WP_046977189 type IV secretion system protein virB6
AMC82_RS34495 214905..215186 + 282 WP_016737561 hypothetical protein -
AMC82_RS25470 (AMC82_PC00177) 215188..215859 + 672 WP_046977190 virB8 family protein virB8
AMC82_RS25475 (AMC82_PC00178) 215856..216713 + 858 WP_016737451 P-type conjugative transfer protein VirB9 virB9
AMC82_RS25480 (AMC82_PC00179) 216722..217894 + 1173 WP_016737452 type IV secretion system protein VirB10 virB10
AMC82_RS25485 (AMC82_PC00180) 217902..218930 + 1029 WP_046977191 P-type DNA transfer ATPase VirB11 virB11
AMC82_RS25490 (AMC82_PC00181) 218974..219552 - 579 WP_016737454 PIN domain-containing protein -
AMC82_RS25495 (AMC82_PC00182) 219542..219988 - 447 WP_029532409 hypothetical protein -
AMC82_RS25500 (AMC82_PC00184) 220498..221688 - 1191 WP_016737456 DUF1173 domain-containing protein -
AMC82_RS33670 221999..222258 + 260 Protein_205 toprim domain-containing protein -
AMC82_RS25505 (AMC82_PC00185) 222581..223521 + 941 Protein_206 DUF2493 domain-containing protein -
AMC82_RS25510 (AMC82_PC00186) 223606..223872 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   3219 GenBank   NZ_CP013566
Plasmid name   pRphaN831c Incompatibility group   -
Plasmid size   453258 bp Coordinate of oriT [Strand]   230059..230087 [+]
Host baterium   Rhizobium phaseoli strain N831

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   -