Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121968
Name   oriT_pAt2788b in_silico
Organism   Agrobacterium fabrum strain 2788
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP116686 (97660..97702 [+], 43 nt)
oriT length   43 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 43 nt

>oriT_pAt2788b
GGATCCAAGGGCGCAATTATACGTCGCTGATGCGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13845 GenBank   WP_173993878
Name   traA_G6L39_RS26005_pAt2788b insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123700.22 Da        Isoelectric Point: 9.6646

>WP_173993878.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium fabrum]
MAIAHFSASIVSRGGGRSVVLSAAYRHCAKMEYEREARTIDYTRKEGLLHEEFLLPADAPKWVRAMIADR
SVAGASEAFWNKVEAFEKRSDAQLARDLTIALPLELTPEQNIALVRDFAEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGSKKVAVIGEDGQPVRTKSGKILYELWAGSTDDFNSLRDGWFERLNHHLSLGG
IDLRIDGRSYEKQGIELEPTIHLGVGAKAIERKAEEQGVRPELERLELNEQRRSENTRRILNNPAIVLDV
ITREKSVFDERDVAKVLHRYVDDPAVFQQLMLRIILNPEVLRLQRDTIDFSTGERVPARYSTRAMIRLEA
TMVRQALWLSNRDGQAVSDAALDATFRRHERLSQEQKTAIERIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWNRGRDVLDDKAVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREEWMRKASLDLARGDVEKALTAYD
TNVRITGTRLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNIMAREKLVGRGIVGEGHVFKTVDG
VRQFDVGDQIVFLKNETSLGVKNGMIAHVTEAAPNRIVAVVGEGDQRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLAKVLSRKNAKETTLDYERGKRY
REALRFAESRGLNIVQVARTLLRDQLDWTLRQKTKLVDLGQRLAVFAERLGLHHPLKTQTMKEAAPMVAG
IRAFSGSVADTVEQKLDTDPALRQQWEEVSTRFAYVFADPETAFRAMNFDAMLVDKETAKLALQTLTTAP
ASIGPLKGKTGILASKTEREDRRVADLNVPALKRDLEQYLRMRETAAQRLQADEQALRQRVSIDIPALSP
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNQAVTERFGERTLLTNAAREPSGKLFDKLSDG
MQPEQKERLKEVWPIMRTSQQLAAHERTVQTLRQAEDLRLAQRQTPVMKQ

  Protein domains


Predicted by InterproScan.

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-567)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(691-736)


  Protein structure



No available structure.




T4CP

ID   16207 GenBank   WP_173993872
Name   traG_G6L39_RS25990_pAt2788b insolico UniProt ID   _
Length   656 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 656 a.a.        Molecular weight: 70487.46 Da        Isoelectric Point: 9.3993

>WP_173993872.1 Ti-type conjugative transfer system protein TraG [Agrobacterium fabrum]
MTASKVLLAVIPATTMIVVVVLMPGVEYWLAAFGKTAQAKLMLGRIGLALPYATAAVIGTIFLFAANGAA
GIKAAGWGVVSGNGVAILIALLREGVRLAGIAGDSPKGQSVLGYADPATMLGASTTFLAGVFALRVAMKG
NAAFAKAAPRRIRGKRAVHGEADWMKVQEAAKLFPDPGGIVVGERYRVDRDSVATVSFRADDPSTWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSSEVAPMVSEHRRKAGRKVIILD
PSASGVGFNALDWIGRHGSTKEEDIVAVATWIMTDNPRSASARDDFFRASAMQLLTALIADVCLSGHTDE
EDQTLRRVRTNLSEPEPQLRARLTKIYEQSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVVGSLLNAIYNRNGDVKGRALFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSRQLSRRPLILPHEVLRMRADEQIVFTSGNPPLRCGRAIWFRRKDMSASVG
DNRFHKQITDGVKSYKAAPTTDSEET

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   16208 GenBank   WP_173993995
Name   t4cp2_G6L39_RS26380_pAt2788b insolico UniProt ID   _
Length   822 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 822 a.a.        Molecular weight: 91787.79 Da        Isoelectric Point: 5.5968

>WP_173993995.1 conjugal transfer protein TrbE [Agrobacterium fabrum]
MVALKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAIRVPTGDYPTEAESHFPDPVTRAIDNERRAHFQKEKGHFESRHALILTWRPPESRRSGLTR
YVYSDAASRSATYADTMLQSFLTSIREVEQYLANVVSIRRMMTRETSERGGFRVARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNTLDLMPLTYRWSSRFVF
LDAEEARGRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FEEDAIRLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPVAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQVFA
FDKGGSMLPLTLGLDGDLYQIGGDIGPSANGEARTLAFCPLAELATDGDRAWAAEWIEMLVALQGVTITP
DYRNAISRQLALMAESRGRSLSDFVSGVQMREVKDALHHYTVDGPMGLLLDAEQDGLALGAFQCFEIEEL
MNMGERNLVPVLTYLFRRIERRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKREYYVVSPEGRRLFNM
ALGPVALSFVGATGKEDLKRIRTLHSEHGAAWPYPWLQQRGIAHAETLFSAE

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 176196..185888

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6L39_RS26320 (G6L39_026320) 171361..172329 + 969 WP_173993976 carbohydrate ABC transporter permease -
G6L39_RS26325 (G6L39_026325) 172330..173151 + 822 WP_272471098 carbohydrate ABC transporter permease -
G6L39_RS26330 (G6L39_026330) 173294..174172 + 879 WP_173993980 glycerophosphodiester phosphodiesterase family protein -
G6L39_RS26335 (G6L39_026335) 174214..175035 + 822 WP_173993982 inositol monophosphatase family protein -
G6L39_RS26340 (G6L39_026340) 175060..176106 + 1047 WP_173993983 aldose 1-epimerase family protein -
G6L39_RS26345 (G6L39_026345) 176196..177515 - 1320 WP_173993985 IncP-type conjugal transfer protein TrbI virB10
G6L39_RS26350 (G6L39_026350) 177527..178003 - 477 WP_173993987 conjugal transfer protein TrbH -
G6L39_RS26355 (G6L39_026355) 178003..178824 - 822 WP_244644145 P-type conjugative transfer protein TrbG virB9
G6L39_RS26360 (G6L39_026360) 178871..179548 - 678 WP_173993991 conjugal transfer protein TrbF virB8
G6L39_RS26365 (G6L39_026365) 179566..180753 - 1188 WP_173993993 P-type conjugative transfer protein TrbL virB6
G6L39_RS26370 (G6L39_026370) 180747..180974 - 228 WP_172690269 entry exclusion protein TrbK -
G6L39_RS26375 (G6L39_026375) 180971..181780 - 810 WP_172690270 P-type conjugative transfer protein TrbJ virB5
G6L39_RS26380 (G6L39_026380) 181752..184220 - 2469 WP_173993995 conjugal transfer protein TrbE virb4
G6L39_RS26385 (G6L39_026385) 184231..184530 - 300 WP_173993997 conjugal transfer protein TrbD virB3
G6L39_RS26390 (G6L39_026390) 184523..184927 - 405 WP_173993999 conjugal transfer pilin TrbC virB2
G6L39_RS26395 (G6L39_026395) 184917..185888 - 972 WP_173994001 P-type conjugative transfer ATPase TrbB virB11
G6L39_RS26400 (G6L39_026400) 185885..186520 - 636 WP_173994003 acyl-homoserine-lactone synthase -

Host bacterium

ID   22395 GenBank   NZ_CP116686
Plasmid name   pAt2788b Incompatibility group   -
Plasmid size   186886 bp Coordinate of oriT [Strand]   97660..97702 [+]
Host baterium   Agrobacterium fabrum strain 2788

Cargo genes

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