Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102487
Name   oriT_pRphCh2410c in_silico
Organism   Rhizobium phaseoli Ch24-10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AHJU02000025 (367464..367492 [+], 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_pRphCh2410c
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1851 GenBank   WP_046977193
Name   traA_RPHASCH2410_RS24825_pRphCh2410c 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   1443 GenBank   WP_046977192
Name   traG_RPHASCH2410_RS24810_pRphCh2410c 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: 346755..356334

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RPHASCH2410_RS35195 343243..343469 - 227 Protein_337 chaperonin GroEL -
RPHASCH2410_RS24685 (RPHASCH2410_PC01705) 343763..344683 + 921 WP_016737442 zincin-like metallopeptidase domain-containing protein -
RPHASCH2410_RS24690 344794..344976 - 183 WP_016737443 hypothetical protein -
RPHASCH2410_RS24695 (RPHASCH2410_PC01715) 345745..346116 - 372 WP_007636193 hypothetical protein -
RPHASCH2410_RS24700 (RPHASCH2410_PC01720) 346215..346751 + 537 WP_016737444 hypothetical protein -
RPHASCH2410_RS24705 (RPHASCH2410_PC01725) 346755..347423 + 669 WP_016737445 transglycosylase SLT domain-containing protein virB1
RPHASCH2410_RS24710 (RPHASCH2410_PC01730) 347420..347719 + 300 WP_007636189 TrbC/VirB2 family protein virB2
RPHASCH2410_RS24715 (RPHASCH2410_PC01735) 347725..348063 + 339 WP_011053369 type IV secretion system protein VirB3 virB3
RPHASCH2410_RS24720 (RPHASCH2410_PC01740) 348056..350422 + 2367 WP_046977188 VirB4 family type IV secretion system protein virb4
RPHASCH2410_RS24725 (RPHASCH2410_PC01745) 350419..351120 + 702 WP_016737448 P-type DNA transfer protein VirB5 virB5
RPHASCH2410_RS24730 (RPHASCH2410_PC01750) 351117..351332 + 216 WP_016737449 EexN family lipoprotein -
RPHASCH2410_RS24735 (RPHASCH2410_PC01755) 351335..352267 + 933 WP_046977189 type IV secretion system protein virB6
RPHASCH2410_RS35200 (RPHASCH2410_PC01760) 352309..352590 + 282 WP_016737561 hypothetical protein -
RPHASCH2410_RS24740 (RPHASCH2410_PC01765) 352592..353263 + 672 WP_046977190 virB8 family protein virB8
RPHASCH2410_RS24745 (RPHASCH2410_PC01770) 353260..354117 + 858 WP_016737451 P-type conjugative transfer protein VirB9 virB9
RPHASCH2410_RS24750 (RPHASCH2410_PC01775) 354126..355298 + 1173 WP_016737452 type IV secretion system protein VirB10 virB10
RPHASCH2410_RS24755 (RPHASCH2410_PC01780) 355306..356334 + 1029 WP_046977191 P-type DNA transfer ATPase VirB11 virB11
RPHASCH2410_RS24760 (RPHASCH2410_PC01785) 356378..356956 - 579 WP_016737454 PIN domain-containing protein -
RPHASCH2410_RS24765 (RPHASCH2410_PC01790) 356946..357392 - 447 WP_029532409 hypothetical protein -
RPHASCH2410_RS24770 (RPHASCH2410_PC01795) 357902..359092 - 1191 WP_016737456 DUF1173 domain-containing protein -
RPHASCH2410_RS34140 359403..359662 + 260 Protein_357 toprim domain-containing protein -
RPHASCH2410_RS24775 359985..360925 + 941 Protein_358 DUF2493 domain-containing protein -
RPHASCH2410_RS24780 (RPHASCH2410_PC01810) 361010..361276 + 267 WP_004676093 hypothetical protein -

Host bacterium

ID   2931 GenBank   NZ_AHJU02000025
Plasmid name   pRphCh2410c Incompatibility group   -
Plasmid size   425928 bp Coordinate of oriT [Strand]   367464..367492 [+]
Host baterium   Rhizobium phaseoli Ch24-10

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   -