Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120828
Name   oriT_pRlX4 in_silico
Organism   Rhizobium leguminosarum strain TP16
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140866 (1058131..1058159 [+], 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_pRlX4
AGGGCGCAATATACGTCGCTGTCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13138 GenBank   WP_327209874
Name   traA_U8Q02_RS35940_pRlX4 insolico UniProt ID   _
Length   1536 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1536 a.a.        Molecular weight: 169739.69 Da        Isoelectric Point: 7.0749

>WP_327209874.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAIMFVRAQVIGRGAGRSVVSAAAYRHRARMMDEQAGTSFSYRGGASELVHEELALPDQIPAWLRSAISG
QSVAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVRDNLTAKGMVADWVYHDKDG
NPHIHLMTTLRPLAEEGFGPKKVPVRGEDGKPLRVVTPDRPNGKVVYKLWAGDKETMKGWKIAWAETASR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARRDAEMYFAPADLARRQDMADRLLADPALLLKQ
LSNERSTFDERDIAKALHRTVDDPADFANIRARLMASDDLIMLKPQQIDAETGKASEPAVFTTREMLRIE
YDMGRSARVLAERRGFAVSDRVVAAAIRQVETQDPENSFRLDPEQVDAIHHITRDDGIAAVVGLAGAGKS
TLLAAARVAWESDGRRVIGAALAGKAAEGLEDSSGIRSRTLAAWELAWASERELLERGNVLVIDEAGMVS
SQQMARLLDIAEQAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQPWAREASRLFARGE
TGKGLDAYAQQGHLIEAGTRVETIDRIVADWSQARKQAIQNSTTAGNDGRLRGDELLVLAHTNEDVKYLN
EALRSVMVGEGALGEDRAFRTERGARAFAAGDRIIFLENARFVEPRATRLGPQHVKNGMLGTVVSTGDKR
GDAVLSIRLDSGRDVVISESSYRNVDHGYAATIHKSQGATVERTFVLATGMMDQHLTYVSMTRHRDRVDL
YAAKDDFEAKPEWGRKPHVDHAAGVTGALVETGQAKFRPNDEDADDSPYADVRTDDGTLHRLWGVSLPKA
LEEGGVSEGDTVTLRKDGVERVTIKVAIVDEQTGQKRFEEREVDRNVWTARRIETAAERQQRIERESHRP
DVFKQLVERLSRSGAKTTTLDFESEAGYRAHADDFARRRGLDHLSLAAAGAEESLSRRWAGIAEKREQLA
KLWERASVALGFTIERERRIAYNEERAEPQTVLEADVARGRYLIPPTTGFARSAEEDAQLAQLSSPAWKE
REAILRPVLETIYRDPDAALVALNALSSDTSVEPRRLADDLAKAPERLGRLRGSELIVDGRAARDERNAA
ITPLTDLLPLVRAHATQFRRNAERFESHEQQRRAHMALPIPALSEKAMARLTEIEAVRRQGGDDAYKAAF
ALAAKDRSIVQEVKAVSEALTARFGWRAFTSKADAVGERNMIERMPEDLASSRGEKLTRLFEDVKRFADE
QHLAERRDRSKIVAGASADQGMENVPMLAAVTEFRTGIDEEARSRVLSDPLYRQQRAALAAVASAIWRDP
VGAVGKIEELLQKGFAGERIAAAVTNDPAAYGALRGSDRLMDRMLAAGRERKEAVQAVPEAAARLRSLGP
AYVNVLDAERQAIAEERRRMAVAIPALSTAAEDVLMRLTAEAKNNDRKLTASAAPLDPSIRREFAAVSRA
LDERFGRNAIIRGEKDLINRVPPAQRNAFEAMQDRLKVLQRTVRMESSEQIISERHQRAVSRGISL

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-576)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1305-1399)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1049-1126)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   15418 GenBank   WP_018245175
Name   traG_U8Q02_RS35925_pRlX4 insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 70387.17 Da        Isoelectric Point: 8.8045

>WP_018245175.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MALKGRLHPSLLLVFVPIAVTAISVYIIGWRWPALAHGLSGKIEYWFLQAAPVPALLFGPLAGLLTVWAL
PLHRRRPIAVASLLCFLVVAGFYALREYGRLVPSVERGIVTWDQALSYLDLVAVIGALAGFMTVAVAARI
SVVVPEAVKRARGGTFGDADWLSMSAAARLFPPDGEIVVGERYRVDKETVHQVPFDPKDRSTWGQGGKAP
LLTYSQDFDSTHMLFFAGSGGYKTTSNVLPTALRYSGPLICLDPSTEVAPMVVEHRTRILGRDVMVLDPT
NPIMSFNVLDGIEHSMRKEEDIVGIAHMLLSESLRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYAGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSESAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFRSSDIVSAKTDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGGFSRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLLYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVQG
RSRNIGWDTKGGGTRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMDEQAK
ANRFVRS

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(161-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 663885..673476

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U8Q02_RS33895 (U8Q02_33875) 659255..659785 - 531 WP_018245413 TadE/TadG family type IV pilus assembly protein -
U8Q02_RS33900 (U8Q02_33880) 659782..661143 - 1362 WP_026188666 TadE/TadG family type IV pilus assembly protein -
U8Q02_RS33905 (U8Q02_33885) 661832..662245 + 414 WP_018245411 hypothetical protein -
U8Q02_RS33910 (U8Q02_33890) 662312..662557 + 246 WP_018245410 hypothetical protein -
U8Q02_RS33915 (U8Q02_33895) 662741..662896 - 156 WP_155256966 hypothetical protein -
U8Q02_RS33920 (U8Q02_33900) 662897..663250 - 354 WP_018245409 hypothetical protein -
U8Q02_RS33925 (U8Q02_33905) 663342..663881 + 540 WP_018245408 hypothetical protein -
U8Q02_RS33930 (U8Q02_33910) 663885..664547 + 663 WP_018245407 lytic transglycosylase domain-containing protein virB1
U8Q02_RS33935 (U8Q02_33915) 664544..664843 + 300 WP_018245406 TrbC/VirB2 family protein virB2
U8Q02_RS33940 (U8Q02_33920) 664849..665187 + 339 WP_018245405 type IV secretion system protein VirB3 virB3
U8Q02_RS33945 (U8Q02_33925) 665180..667546 + 2367 WP_018245404 VirB4 family type IV secretion/conjugal transfer ATPase virb4
U8Q02_RS33950 (U8Q02_33930) 667546..668244 + 699 WP_018245403 P-type DNA transfer protein VirB5 virB5
U8Q02_RS33955 (U8Q02_33935) 668241..668465 + 225 WP_018245402 EexN family lipoprotein -
U8Q02_RS33960 (U8Q02_33940) 668469..669389 + 921 WP_027690921 type IV secretion system protein virB6
U8Q02_RS33965 (U8Q02_33945) 669442..669726 + 285 WP_018245400 hypothetical protein -
U8Q02_RS33970 (U8Q02_33950) 669728..670399 + 672 WP_018245399 virB8 family protein virB8
U8Q02_RS33975 (U8Q02_33955) 670396..671253 + 858 WP_018245398 P-type conjugative transfer protein VirB9 virB9
U8Q02_RS33980 (U8Q02_33960) 671263..672438 + 1176 WP_327209823 type IV secretion system protein VirB10 virB10
U8Q02_RS33985 (U8Q02_33965) 672445..673476 + 1032 WP_018245396 P-type DNA transfer ATPase VirB11 virB11
U8Q02_RS33990 (U8Q02_33970) 673573..674028 + 456 WP_018245395 NUDIX hydrolase -
U8Q02_RS33995 (U8Q02_33975) 674025..675047 + 1023 WP_327209824 PHB depolymerase family esterase -
U8Q02_RS34000 (U8Q02_33980) 675129..675356 + 228 Protein_622 hypothetical protein -
U8Q02_RS34005 (U8Q02_33985) 675512..675727 - 216 WP_327209825 DUF3072 domain-containing protein -
U8Q02_RS34010 (U8Q02_33990) 675974..676885 - 912 WP_327209826 LysR family transcriptional regulator -
U8Q02_RS34015 (U8Q02_33995) 676985..677746 + 762 WP_327209827 SDR family NAD(P)-dependent oxidoreductase -

Host bacterium

ID   21257 GenBank   NZ_CP140866
Plasmid name   pRlX4 Incompatibility group   -
Plasmid size   1125900 bp Coordinate of oriT [Strand]   1058131..1058159 [+]
Host baterium   Rhizobium leguminosarum strain TP16

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixA, fixB
Anti-CRISPR   AcrIF22