Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102784
Name   oriT_pRphaN841d in_silico
Organism   Rhizobium phaseoli strain N841
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013561 (211509..211537 [+], 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_pRphaN841d
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2056 GenBank   WP_046977193
Name   traA_AMC83_RS26140_pRphaN841d 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   1712 GenBank   WP_046977192
Name   traG_AMC83_RS26125_pRphaN841d 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: 190800..200379

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMC83_RS35455 187288..187514 - 227 Protein_178 chaperonin GroEL -
AMC83_RS26000 (AMC83_PD00159) 187808..188728 + 921 WP_016737442 zincin-like metallopeptidase domain-containing protein -
AMC83_RS26005 188839..189021 - 183 WP_016737443 hypothetical protein -
AMC83_RS26010 (AMC83_PD00161) 189790..190161 - 372 WP_007636193 hypothetical protein -
AMC83_RS26015 (AMC83_PD00162) 190260..190796 + 537 WP_016737444 hypothetical protein -
AMC83_RS26020 (AMC83_PD00163) 190800..191468 + 669 WP_016737445 transglycosylase SLT domain-containing protein virB1
AMC83_RS26025 (AMC83_PD00164) 191465..191764 + 300 WP_007636189 TrbC/VirB2 family protein virB2
AMC83_RS26030 (AMC83_PD00165) 191770..192108 + 339 WP_011053369 type IV secretion system protein VirB3 virB3
AMC83_RS26035 (AMC83_PD00166) 192101..194467 + 2367 WP_046977188 VirB4 family type IV secretion system protein virb4
AMC83_RS26040 (AMC83_PD00167) 194464..195165 + 702 WP_016737448 P-type DNA transfer protein VirB5 virB5
AMC83_RS26045 (AMC83_PD00168) 195162..195377 + 216 WP_016737449 EexN family lipoprotein -
AMC83_RS26050 (AMC83_PD00169) 195380..196312 + 933 WP_046977189 type IV secretion system protein virB6
AMC83_RS35460 196354..196635 + 282 WP_016737561 hypothetical protein -
AMC83_RS26055 (AMC83_PD00170) 196637..197308 + 672 WP_046977190 virB8 family protein virB8
AMC83_RS26060 (AMC83_PD00171) 197305..198162 + 858 WP_016737451 P-type conjugative transfer protein VirB9 virB9
AMC83_RS26065 (AMC83_PD00172) 198171..199343 + 1173 WP_016737452 type IV secretion system protein VirB10 virB10
AMC83_RS26070 (AMC83_PD00173) 199351..200379 + 1029 WP_046977191 P-type DNA transfer ATPase VirB11 virB11
AMC83_RS26075 (AMC83_PD00174) 200423..201001 - 579 WP_016737454 PIN domain-containing protein -
AMC83_RS26080 (AMC83_PD00175) 200991..201437 - 447 WP_029532409 hypothetical protein -
AMC83_RS26085 (AMC83_PD00177) 201947..203137 - 1191 WP_016737456 DUF1173 domain-containing protein -
AMC83_RS34535 203448..203707 + 260 Protein_198 toprim domain-containing protein -
AMC83_RS26090 (AMC83_PD00178) 204030..204970 + 941 Protein_199 DUF2493 domain-containing protein -
AMC83_RS26095 (AMC83_PD00179) 205055..205321 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   3227 GenBank   NZ_CP013561
Plasmid name   pRphaN841d Incompatibility group   -
Plasmid size   433209 bp Coordinate of oriT [Strand]   211509..211537 [+]
Host baterium   Rhizobium phaseoli strain N841

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, fixO, fixN, mLTONO_5203, nodA
Anti-CRISPR   -