Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103891
Name   oriT_pI in_silico
Organism   Agrobacterium tumefaciens strain 183
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP029046 (145816..145844 [+], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
 4..9, 20..25  (GCGCAA..TTGCGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_pI
AGGGCGCAATATACGTCGCTTGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2894 GenBank   WP_128287202
Name   traA_DC439_RS24680_pI insolico UniProt ID   _
Length   1545 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1545 a.a.        Molecular weight: 170737.35 Da        Isoelectric Point: 7.7226

>WP_128287202.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQIGSSFSYRGGARELVHEELALPDKVPTWLKTAVDG
KTVAAASEALWNAVDAFETRADAQLARELIIALPEELTRAENISLVREFVADSFTSKGMVADWVFHDKDG
NPHIHLMMTLRPLTEEGFGPKKVQVAGADGEPLRVITPDRPNGKIVYKIWAGDKETMKGWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVEMYFAPADLARRQEMADRLLAEPELLLKQ
LANERSTFDERDIAKALHRYVDDPADFANIRARLMTSNDLVLLKPQRMDDQSGKVTEPAVFTTREILRIE
FDMAQSAEVLSKRTGFGVADAKIAAAVRQVETADPEKPFKLDAEQVDAVRHVTGENAVAAVVGLAGAGKS
TLLAAARVAWERDHRGVFGAALAGKAAEGLEDSSGIKSRTLASWELAWANGCDLLQRGNVFVIDEAGMVS
SQQMARVLKVVEEAGAKAVLVGDAMQLQPIQAGAAFRAIGDRIGFAELAGVRRQREEWAREASRLFARGE
VEKGLDAYAAHGRLVESETRDEIIGRMVSDWADARRALVQASRDQENPPRLRGDELLVLAHTNDDVRKLN
EALRKVMLDDGALTGAREFHTARGAREFATGDRIIFLENARFLEPRAKRLGPQYVKNGMLGTIVATGDKR
AGPLLSVRLDNGRDVIISEDSYTNVDHGYAATIHKSQGATVDRTFVLATGMMDQHLTYVSMTRHRDRADL
YAAREDFQPKLEWGRAARADHAAGVTGELVETGLAKFRPNDEDADESPYADMKTDDGAVHRLWGVSLPKA
LEEGGVSEGDTVTLRKDGVERVTVTVPVIDENTGKKSFEERTVDRNVWTAKLKETADVRRERIERESHRP
ELFKQLVERLGRSGAKTTTLDFESEEGYQAHARDFARRRGIDMAAGVAAGIEEGLSRRFTWIAEKREQVA
RLWERASVALGFAIERERSVSYNEARAATVSADIPVGGYHLIPPTTTFTRSVEHDARRAQLLSERWKERE
AILRPVLDKVYRDPDAALIRLNALASNSNIEPRKLADDLAMAPNRLGRLRGSDLMVDGRAARDERSAAMA
ALNDLVPLARAHATEFRRNEDRFQDREKTRRAHMALSIPAISKRAMARLVEIEAVRKQGGDDAYKTAFSF
AAEDREIVQEVKAVSDALNARFGWSAFTAKADAAAERNVAERMPEDLPDDRREKLVRLFEVVRHFSDEQH
LAEKQDRSKIVAGASVEAGKESMAMLPMLAAVTEFKTPVDEEARTRALAVPHYRHHLAALAETAGRIWRD
PAGAVGKIEELIVKGIASERIAAAVTNDPAAYGALRGSDRIMEKLLAVGRERKGALQAVPEAASRVRSLG
ASWASALDAESEAIREERRRMSVAIPGVSPAAEGALLHLVADLKKQRQEKAKSARIETAARSLDPDIARE
FAAVSRALDERFGRNAILRGETDVINRVSPAQRRAFEAMRERLQVVQQTVRTHGSQEIISERQRRAIDRA
RGLTR

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-578)

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

(1309-1400)

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

(1048-1125)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   2738 GenBank   WP_128287199
Name   traG_DC439_RS24665_pI 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: 70523.40 Da        Isoelectric Point: 9.0190

>WP_128287199.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTIRAKPHPSLLLILVPITVTAFAVYVVGWRWPELAAEMTGKAQYWFLRASPVPALLFGPLAGLLTVLAL
PLHRRRPIAMATLICFLSVACLYGLREFGRLSPSVESGAVTWNQALSFIDMVAVMGSVAGFMATAVSARI
STVVSEPVKRARRGTFGDADWLPMSAAGRLFPDDGEIVVGERYRVDKEIVHEMPFDPNDPATWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVIPTALRYSGPLICLDPSTEVAPMVVEHRRERLGRQVMVLDPT
NPIMGFNVLDGIETSEQKEQDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYEGRRN
LRSLRQIVSEPETSVLAMLRDVQQHSASKFISETLGVFVNMTEQTFSGVYSTASKDTQWLSLDNYAALAC
GNTFKPSDLTRGKKDVFLNIPASILRSYPGIGRVIVGSLINAMIEADGAFQRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLLYQSVGQLERHFGKDGAVSWIDGCAFASYAAIKALETARNVSAQCGEMTVEVKG
SSRNIGWDTKNSASRKSESLNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKTMNEAAK
VNRFVKP

  Protein domains


Predicted by InterproScan.

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

(168-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 73484..83077

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DC439_RS24305 (DC439_24350) 69155..70027 - 873 WP_128287142 sugar ABC transporter permease -
DC439_RS24310 (DC439_24355) 70204..71517 - 1314 WP_128287143 sugar ABC transporter substrate-binding protein -
DC439_RS24315 (DC439_24360) 72057..73190 + 1134 WP_233282957 hypothetical protein -
DC439_RS24320 (DC439_24365) 73484..74485 - 1002 WP_128287144 P-type DNA transfer ATPase VirB11 virB11
DC439_RS24325 (DC439_24370) 74494..75666 - 1173 WP_128287145 type IV secretion system protein VirB10 virB10
DC439_RS24330 (DC439_24375) 75680..76534 - 855 WP_161974293 P-type conjugative transfer protein VirB9 virB9
DC439_RS24335 (DC439_24380) 76531..77202 - 672 WP_128287146 virB8 family protein virB8
DC439_RS24340 (DC439_24385) 77206..77472 - 267 WP_128287147 hypothetical protein -
DC439_RS24345 (DC439_24390) 77509..78444 - 936 WP_128287148 type IV secretion system protein virB6
DC439_RS24350 (DC439_24395) 78449..78682 - 234 WP_128287149 EexN family lipoprotein -
DC439_RS24355 (DC439_24400) 78679..79377 - 699 WP_128287150 P-type DNA transfer protein VirB5 virB5
DC439_RS24360 (DC439_24405) 79377..81758 - 2382 WP_128287151 VirB4 family type IV secretion system protein virb4
DC439_RS24365 (DC439_24410) 81751..82092 - 342 WP_128287152 type IV secretion system protein VirB3 virB3
DC439_RS24370 (DC439_24415) 82095..82394 - 300 WP_128287153 TrbC/VirB2 family protein virB2
DC439_RS24375 (DC439_24420) 82391..83077 - 687 WP_128287266 lytic transglycosylase domain-containing protein virB1
DC439_RS24380 (DC439_24425) 83080..83619 - 540 WP_128287154 hypothetical protein -
DC439_RS24385 (DC439_24430) 83713..84075 + 363 WP_128287155 transcriptional regulator -
DC439_RS27295 (DC439_24435) 84179..84553 - 375 WP_337587109 acyl-homoserine-lactone synthase -
DC439_RS24395 (DC439_24440) 84983..86206 + 1224 WP_170212275 plasmid partitioning protein RepA -
DC439_RS24400 (DC439_24445) 86285..87280 + 996 WP_128287156 plasmid partitioning protein RepB -

Host bacterium

ID   4331 GenBank   NZ_CP029046
Plasmid name   pI Incompatibility group   -
Plasmid size   210169 bp Coordinate of oriT [Strand]   145816..145844 [+]
Host baterium   Agrobacterium tumefaciens strain 183

Cargo genes

Drug resistance gene   -
Virulence gene   katA
Metal resistance gene   -
Degradation gene   benC, benB, benA
Symbiosis gene   -
Anti-CRISPR   -