Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102744
Name   oriT_pRetR611c in_silico
Organism   Rhizobium phaseoli strain R611
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013550 (199985..200013 [+], 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_pRetR611c
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2021 GenBank   WP_046977193
Name   traA_AMC85_RS26190_pRetR611c 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   1670 GenBank   WP_046977192
Name   traG_AMC85_RS26175_pRetR611c 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: 179254..188852

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC85_RS34005 176029..176255 - 227 Protein_163 chaperonin GroEL -
AMC85_RS26050 (AMC85_PC00150) 176550..177470 + 921 WP_004673402 zincin-like metallopeptidase domain-containing protein -
AMC85_RS26055 (AMC85_PC00151) 178244..178615 - 372 WP_042120136 hypothetical protein -
AMC85_RS26060 (AMC85_PC00152) 178714..179250 + 537 WP_011053366 hypothetical protein -
AMC85_RS26065 (AMC85_PC00153) 179254..179922 + 669 WP_064820013 lytic transglycosylase domain-containing protein virB1
AMC85_RS26070 (AMC85_PC00154) 179919..180218 + 300 WP_007636189 TrbC/VirB2 family protein virB2
AMC85_RS26075 (AMC85_PC00155) 180224..180562 + 339 WP_011053369 type IV secretion system protein VirB3 virB3
AMC85_RS26080 (AMC85_PC00156) 180555..182921 + 2367 WP_064830109 VirB4 family type IV secretion system protein virb4
AMC85_RS26085 (AMC85_PC00157) 182918..183619 + 702 WP_011053371 P-type DNA transfer protein VirB5 virB5
AMC85_RS26090 (AMC85_PC00158) 183616..183849 + 234 WP_008537008 EexN family lipoprotein -
AMC85_RS26095 (AMC85_PC00159) 183852..184784 + 933 WP_064820015 type IV secretion system protein virB6
AMC85_RS34010 (AMC85_PC00160) 184826..185107 + 282 WP_081278376 hypothetical protein -
AMC85_RS26100 (AMC85_PC00161) 185109..185780 + 672 WP_064820016 virB8 family protein virB8
AMC85_RS26105 (AMC85_PC00162) 185777..186634 + 858 WP_064820017 P-type conjugative transfer protein VirB9 virB9
AMC85_RS26110 (AMC85_PC00163) 186643..187815 + 1173 WP_064820018 type IV secretion system protein VirB10 virB10
AMC85_RS26115 (AMC85_PC00164) 187824..188852 + 1029 WP_064820019 P-type DNA transfer ATPase VirB11 virB11
AMC85_RS26120 (AMC85_PC00165) 188896..189474 - 579 WP_064820020 PIN domain-containing protein -
AMC85_RS26125 (AMC85_PC00166) 189464..189910 - 447 WP_225882822 DNA-binding protein -
AMC85_RS26130 (AMC85_PC00168) 190424..191614 - 1191 WP_064820021 DUF1173 domain-containing protein -
AMC85_RS34015 191924..192181 + 258 Protein_182 toprim domain-containing protein -
AMC85_RS26140 192506..193446 + 941 Protein_183 DUF2493 domain-containing protein -
AMC85_RS26145 (AMC85_PC00171) 193531..193797 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   3187 GenBank   NZ_CP013550
Plasmid name   pRetR611c Incompatibility group   -
Plasmid size   414080 bp Coordinate of oriT [Strand]   199985..200013 [+]
Host baterium   Rhizobium phaseoli strain R611

Cargo genes

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