Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102772
Name   oriT_pRphaN931c in_silico
Organism   Rhizobium phaseoli strain N931
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013555 (230058..230086 [+], 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_pRphaN931c
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2045 GenBank   WP_046977193
Name   traA_AMC84_RS25575_pRphaN931c 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   1700 GenBank   WP_046977192
Name   traG_AMC84_RS25560_pRphaN931c 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: 209350..218929

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC84_RS34505 205838..206064 - 227 Protein_183 chaperonin GroEL -
AMC84_RS25430 (AMC84_PC00167) 206358..207278 + 921 WP_016737442 zincin-like metallopeptidase domain-containing protein -
AMC84_RS25435 207389..207571 - 183 WP_016737443 hypothetical protein -
AMC84_RS25440 (AMC84_PC00168) 208340..208711 - 372 WP_007636193 hypothetical protein -
AMC84_RS25445 (AMC84_PC00169) 208810..209346 + 537 WP_016737444 hypothetical protein -
AMC84_RS25450 (AMC84_PC00170) 209350..210018 + 669 WP_016737445 transglycosylase SLT domain-containing protein virB1
AMC84_RS25455 (AMC84_PC00171) 210015..210314 + 300 WP_007636189 TrbC/VirB2 family protein virB2
AMC84_RS25460 (AMC84_PC00172) 210320..210658 + 339 WP_011053369 type IV secretion system protein VirB3 virB3
AMC84_RS25465 (AMC84_PC00173) 210651..213017 + 2367 WP_046977188 VirB4 family type IV secretion system protein virb4
AMC84_RS25470 (AMC84_PC00174) 213014..213715 + 702 WP_016737448 P-type DNA transfer protein VirB5 virB5
AMC84_RS25475 (AMC84_PC00175) 213712..213927 + 216 WP_016737449 EexN family lipoprotein -
AMC84_RS25480 (AMC84_PC00176) 213930..214862 + 933 WP_046977189 type IV secretion system protein virB6
AMC84_RS34510 214904..215185 + 282 WP_016737561 hypothetical protein -
AMC84_RS25485 (AMC84_PC00177) 215187..215858 + 672 WP_046977190 virB8 family protein virB8
AMC84_RS25490 (AMC84_PC00178) 215855..216712 + 858 WP_016737451 P-type conjugative transfer protein VirB9 virB9
AMC84_RS25495 (AMC84_PC00179) 216721..217893 + 1173 WP_016737452 type IV secretion system protein VirB10 virB10
AMC84_RS25500 (AMC84_PC00180) 217901..218929 + 1029 WP_046977191 P-type DNA transfer ATPase VirB11 virB11
AMC84_RS25505 (AMC84_PC00181) 218973..219551 - 579 WP_016737454 PIN domain-containing protein -
AMC84_RS25510 (AMC84_PC00182) 219541..219987 - 447 WP_029532409 hypothetical protein -
AMC84_RS25515 (AMC84_PC00184) 220497..221687 - 1191 WP_016737456 DUF1173 domain-containing protein -
AMC84_RS33685 221998..222257 + 260 Protein_203 toprim domain-containing protein -
AMC84_RS25520 222580..223520 + 941 Protein_204 DUF2493 domain-containing protein -
AMC84_RS25525 (AMC84_PC00187) 223605..223871 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   3215 GenBank   NZ_CP013555
Plasmid name   pRphaN931c Incompatibility group   -
Plasmid size   453545 bp Coordinate of oriT [Strand]   230058..230086 [+]
Host baterium   Rhizobium phaseoli strain N931

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   -