Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119532
Name   oriT_HAMBI 105|unnamed in_silico
Organism   Agrobacterium tumefaciens strain HAMBI 105
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP139999 (54844..54872 [+], 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_HAMBI 105|unnamed
AGGGCGCAATATACGTCGCTCGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12342 GenBank   WP_114836199
Name   traA_U0027_RS24110_HAMBI 105|unnamed insolico UniProt ID   _
Length   1541 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1541 a.a.        Molecular weight: 170827.34 Da        Isoelectric Point: 7.8700

>WP_114836199.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRARMMDEQVGTSFSYRGGASELVHEELALPDQIPAWLKSAIDG
KSVAGASEALWNAVDVFEKRADAQLARELIIALPEELTRAENIALVREFVADNFTSKGMVADWVFHDKDG
NPHIHLMTALRPLTEEGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETMKTWKIAWADTANR
HLALACHEIRLDGRSYAEQGLAGIAQKHLGPEKAALARKGIERYFAPGDLARRQEIADRLLANPELLLKQ
LANERSTFDERDIARALHRYVDDPTDFANIRARLMASDDLVLLKPQQIDAETDKAAEPAVFTTREILRIE
YDMARSANVLSKRPGFAVSADAVAAAIRKVETEDPQKPFRLGPQQVDAVRHVTGDNGIAAVVGLAGAGKS
TLLAAARVAWESEGRRVIGAALAGKAAEGLEDSSGIRSRTLASLELAWASGRDLLERGNVFVIDEAGMIS
SQQMGRVLKVAEDAGAKVVLVGDAMQLQPIQAGAAFRAISDRIGFAELAGVRRQRQEWARDASRLFARGN
VRDGLDAYAQQGRITEAETRAEIVERIVADWTDARRNLLQNTTDRGDAPRLRGDELLVLAHTNEDVKRLN
ESLRKVMMEEGVLTDARAFQTARGAREFAAGDRIIFLENARFVEPRARHLGPQYVKNGMLGTVVSTGDKR
GGSLLSIRLDNSRDVVISEDSYRNIDHGYAATIHKSQGATIDRTFVLATGMMDQHLTYVSMTRHRIRADL
YAAREDFELRPEWGRKPRADHAAGVTGELVETGEAKFRPQDEDAKQSPYADVKTDNGAVHRLWGVSLPKA
LEEGGISEGDTVTLRKDGVERVKVKVTVVDEQTGEKRAEEREVERNIWTAELKETADAREQRIEQESHRP
ELFSQLVDRLGRSGAKTTTLDFESEEGYRAHAEDFARRRGIDMAAGIGEGVSGRLAWIAEKRGQVAKLWE
RASIALGFAIERERRIAYNEDRTETPAPEIPTTGQYLIPPTTRFARGVDEDARRAQLASERWKERDAILG
PVLEKIYRDPDAALARLNALASDATNEPRKFADDLAAAPDRLGRLRGSDLMVDGRAARDERKTATAALSE
LVPMARAHATEFRRQAERFGIREEQRRAHMSLSIPMLSKPAMARLVEIEEIRERGGDDAYKTAFAYAVED
RQLVQEVKAVTDALTARFGWSAFTTKADAVAERNMAERMPEDLAPERREKLLRLFTVVRRFSEEQHLAEK
QDRSKIVAGASVEVGQEAIPMLPMLAAVTEFKTPVEDEARIRAGAVAHYRHHRAALADTAALIWRDPAGA
VAKIEELVGKGFAGERIAAAVSNDPAAYGALRGSDRMMDRMFAAGRERKEAVQAVPEAASRVRSLGASWA
IALDTETRAVTEERRRMAVAVPGLSQTAEDALRTLVADVRKQKKDKGENIRRDVAARSLDPRIIREFAAV
SRALDERFGRNAILRGEKDVVNRVSPAQRRAFEAMRERLLILQQVVRTTSSQEIIAERQRQDIDRTRGFT
R

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-578)

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

(1305-1396)

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

(1052-1121)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   14485 GenBank   WP_114836202
Name   traG_U0027_RS24095_HAMBI 105|unnamed 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: 70501.47 Da        Isoelectric Point: 9.4541

>WP_114836202.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MALKGKLHPSLLLVFVPIVVTAISVYIVGWRWKGLATGMSGKTAYWFLRATPLPALLFGPLAGLLTVSAL
PMHRRRPIAMVSLLCFLGVVGFYALREYGRLAPSVGRGVVSWDYALSYLDMVAVVGALCGFMAVAASARI
STVVPEQVKRARRATFGDADWLSMSAAGKLFPADGEIVVGERYRVDKEIVHELPFDPNDRSTWGQGGKAP
LLTYNQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIETSRQKEEDIVGVAHMLLSESMRFESSTGSYFQSQAHNLLTGLLDHVMLSPDYAGRRN
LRSLRQIVSEPEPSVLTMLRDIQENSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGRKDVFLNIPASILRSYPGIGRVIIGALINAMTQADGAFKRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKG
SSRNIGWDMKNSASRKSENVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMDAAAR
VNRFVKLGS

  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: 16032..25643

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U0027_RS23835 (U0027_23830) 12088..12375 + 288 WP_080821105 hypothetical protein -
U0027_RS23840 (U0027_23835) 12382..12768 + 387 WP_114836239 hypothetical protein -
U0027_RS23845 (U0027_23840) 12806..13519 - 714 WP_114836238 IS6 family transposase -
U0027_RS23850 (U0027_23845) 13916..14113 - 198 WP_162791770 hypothetical protein -
U0027_RS23855 (U0027_23850) 14131..14574 - 444 WP_114836235 hypothetical protein -
U0027_RS23860 (U0027_23855) 15041..15391 - 351 WP_114836234 MarR family transcriptional regulator -
U0027_RS23865 (U0027_23860) 15490..16029 + 540 WP_114836233 hypothetical protein -
U0027_RS23870 (U0027_23865) 16032..16706 + 675 WP_114836232 lytic transglycosylase domain-containing protein virB1
U0027_RS23875 (U0027_23870) 16703..17002 + 300 WP_114836231 TrbC/VirB2 family protein virB2
U0027_RS23880 (U0027_23875) 17009..17347 + 339 WP_114836230 type IV secretion system protein VirB3 virB3
U0027_RS23885 (U0027_23880) 17340..19706 + 2367 WP_114836229 VirB4 family type IV secretion/conjugal transfer ATPase virb4
U0027_RS23890 (U0027_23885) 19703..20404 + 702 WP_114836228 P-type DNA transfer protein VirB5 virB5
U0027_RS23895 (U0027_23890) 20401..20634 + 234 WP_114836227 EexN family lipoprotein -
U0027_RS23900 (U0027_23895) 20639..21571 + 933 WP_114836226 type IV secretion system protein virB6
U0027_RS23905 (U0027_23900) 21611..21892 + 282 WP_114836225 hypothetical protein -
U0027_RS23910 (U0027_23905) 21894..22565 + 672 WP_114836224 virB8 family protein virB8
U0027_RS23915 (U0027_23910) 22562..23419 + 858 WP_114836223 P-type conjugative transfer protein VirB9 virB9
U0027_RS23920 (U0027_23915) 23428..24603 + 1176 WP_114836222 type IV secretion system protein VirB10 virB10
U0027_RS23925 (U0027_23920) 24612..25643 + 1032 WP_114836221 P-type DNA transfer ATPase VirB11 virB11
U0027_RS23930 (U0027_23925) 25852..26550 + 699 WP_236762449 hypothetical protein -
U0027_RS23935 (U0027_23930) 26547..27134 + 588 WP_114836220 RES family NAD+ phosphorylase -
U0027_RS23940 (U0027_23935) 27367..27573 + 207 WP_162791769 hypothetical protein -
U0027_RS23945 (U0027_23940) 27670..27930 + 261 WP_114836219 hypothetical protein -
U0027_RS23950 (U0027_23945) 28114..28298 - 185 Protein_33 transposon DNA-invertase -

Host bacterium

ID   19962 GenBank   NZ_CP139999
Plasmid name   HAMBI 105|unnamed Incompatibility group   -
Plasmid size   410809 bp Coordinate of oriT [Strand]   54844..54872 [+]
Host baterium   Agrobacterium tumefaciens strain HAMBI 105

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7