Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121741
Name   oriT_pAt2 in_silico
Organism   Agrobacterium tumefaciens strain cl001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048577 (179086..179124 [+], 39 nt)
oriT length   39 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 39 nt

>oriT_pAt2
GGATCCGAAGGGCGCAATTATACGTCGCTGATGCGACGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13721 GenBank   WP_333723780
Name   traA_FY131_RS28000_pAt2 insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 122002.57 Da        Isoelectric Point: 9.3614

>WP_333723780.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPADAPEWLQSLIADR
SVAGASEAFWNKVEDFEKRSDAQLAKDVTIALPIELSAEQNIELVRDFVARHITAHGMVADWVFHDAPGN
PHIHLMTTLRPLTEDGFGSKKVVVTGPDGSVLRNDAGKIVYELWAGGLEDFNAFRDGWFSCQNRHLTLAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIERKAESVEEKAALERLELQEERRAENARRIQRNPEIVIDL
ITREKSVFDERDVAKILHRYIDHAGLFQSLKARILQSPDALRLDRERLDFTTGVRAPAKYTTRELIRLEA
EMANRAIWLLQRSSHGVRQPVLEATFARHERLSGEQKAAIEHVTGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYHVVGGALAGKAAEGLEKEAGIVSRTLSSWELHWDQGRGQLDEKTVFVLDEAGMVSSRQMALFVE
TVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGHLSKAITAYQ
SNGKMIGSELKADAVTNLIADWNREYAPTKSTLILAHLRRDVRMLNELARAKLIERGIIEQGSPFKTADG
NRSFSAGEQIVFLKNEGSLGVKNGMLGKVVEAASGRLVAVIGEGEHLRKVIVEQRFYNNVDHGYATTVHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGVYYGHRSFAKAGGLVEILSRRNSKETTLDYARGSIY
HQALRFAEGRGLHIVNVARTVARDRLEWTLRQKQKLVDLAGRLAAVGARLGFATSTANTIPTTAKEDKPM
VAGITTFPKSIDQAVEDKLASDPALKKQWEEVSMRFHHVYAQPESAFKAVDVDAMLSDPATAAKTLSHIT
AEPEAFGSLKGKAGVFASRADKSDRDRALKNVTPLADSISDYLRQRGDAERRNHAEELAVRRQVALEIPA
LSSNAKSVLERVRDAIDRNDLPSGLEFALADKMVKAELEGFAKAVTERFGERTFLSFAAKDANGEAFQRV
TSGMNAAQKSEVQQAWNTMRTVQQLSAHERSVTALKQTEALRQTKFQGLTLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(691-735)

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

(858-954)

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   16035 GenBank   WP_333723668
Name   traG_FY131_RS27985_pAt2 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 69249.15 Da        Isoelectric Point: 9.4654

>WP_333723668.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MKANKIVLVILPGAMMVATMFAMTGIETWLAGFGKSEAAKLAVGRVGVAAPYLAAAALGLILLFATAGSA
SIRAAGVGAAIGSAAVILTACLREGVRLAALSAQVPAGESALSYLDPSTMIGAAAALMSGCFALRVAMVG
NAAFARTAPKRIIGKRALHGEADWMNLAEAGRLLPDSGGIVVGERYRVDRDGVAGVSFRADSSETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVAPMVSKHREEAGRRVRILD
PRKPATGFNALDWVGQYGGTKEEDIASVASWIMSDSGRASGVRDDFFRASGLQLLTAIIADVCLSGHTPK
EKQTLRQVRENLSEPEPKLRQRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYA
ALVSGSTFRTEDIASRKTDVFINIDLKTLETHAGLARVVIGSFLNAIYNRDGAMEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQLRENYGGRDASSKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSLQSRGSSRTRSKQLAARPLIQQHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRKDMTACVE
RGRFGRREAPADEQ

  Protein domains


Predicted by InterproScan.

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

(163-630)

  Protein structure



No available structure.



ID   16036 GenBank   WP_333723684
Name   t4cp2_FY131_RS28080_pAt2 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91757.62 Da        Isoelectric Point: 5.9703

>WP_333723684.1 conjugal transfer protein TrbE [Agrobacterium tumefaciens]
MAALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
TGWMIQVEAIRVPTVDYPTPGQCHFPDPVTRAIDAERRTHFGREQGHFESKHAIILTYRPLESKKTALAK
YVYSDEASRKKSYADTVLFMFRNAIREIEQYLANTLSIARMQTREVRERGGERVARYDDLMQFVRFCITG
ESHPVRLPEVPMYLDWLVTAELEHGLTPKVESRFLAVVAIDGLPAESWPGILNNLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVIL
FDEEREGLREKAEAIRRLVQAEGFGARVETLNATDAFLGSLPGNWYANIREPLINTSNLADLVPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEFAQIFA
FDKGNSLLPLTLAAGGDHYEIGNDQNGEGRALAFCPLFDLSTDGDRAWATEWVEMLVALQGVTITPDHRN
AISRQIGLMATAPGKSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLRAFQCFEIEQLMNMG
ERNLVPVLTYLFHRIEKRLDGSPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSGAIPKREYYVATPDGRRLFDMSLGP
VALSFVGASGKEDLKLIRALKAEHGQDWPTHWLQSRGVHDATSHFNVQ

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 184252..197130

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FY131_RS28005 (FY131_27795) 182545..183075 + 531 WP_333723671 conjugative transfer signal peptidase TraF -
FY131_RS28010 (FY131_27800) 183065..184237 + 1173 WP_333723672 conjugal transfer protein TraB -
FY131_RS28015 (FY131_27805) 184252..184860 + 609 WP_333723673 TraH family protein virB1
FY131_RS28020 (FY131_27810) 184909..185286 - 378 WP_333723674 DUF5615 family PIN-like protein -
FY131_RS28025 (FY131_27815) 185291..185910 - 620 Protein_174 DUF433 domain-containing protein -
FY131_RS28030 (FY131_27820) 186030..186248 - 219 WP_333723675 helix-turn-helix domain-containing protein -
FY131_RS28035 (FY131_27825) 186387..186707 + 321 WP_333723676 transcriptional repressor TraM -
FY131_RS28040 (FY131_27830) 186709..187410 - 702 WP_333723677 autoinducer binding domain-containing protein -
FY131_RS28045 (FY131_27835) 187632..188930 - 1299 WP_333723678 IncP-type conjugal transfer protein TrbI virB10
FY131_RS28050 (FY131_27840) 188944..189381 - 438 WP_333723679 conjugal transfer protein TrbH -
FY131_RS28055 (FY131_27845) 189385..190196 - 812 Protein_180 P-type conjugative transfer protein TrbG -
FY131_RS28060 (FY131_27850) 190213..190875 - 663 WP_333723680 conjugal transfer protein TrbF virB8
FY131_RS28065 (FY131_27855) 190897..192075 - 1179 WP_333723681 P-type conjugative transfer protein TrbL virB6
FY131_RS28070 (FY131_27860) 192069..192272 - 204 WP_333723682 entry exclusion protein TrbK -
FY131_RS28075 (FY131_27865) 192269..193072 - 804 WP_333723683 P-type conjugative transfer protein TrbJ virB5
FY131_RS28080 (FY131_27870) 193044..195500 - 2457 WP_333723684 conjugal transfer protein TrbE virb4
FY131_RS28085 (FY131_27875) 195511..195795 - 285 WP_333723685 conjugal transfer protein TrbD virB3
FY131_RS28090 (FY131_27880) 195792..196169 - 378 WP_333723686 TrbC/VirB2 family protein virB2
FY131_RS28095 (FY131_27885) 196159..197130 - 972 WP_333723687 P-type conjugative transfer ATPase TrbB virB11
FY131_RS28100 (FY131_27890) 197133..197759 - 627 WP_333723688 acyl-homoserine-lactone synthase TraI -

Host bacterium

ID   22168 GenBank   NZ_CP048577
Plasmid name   pAt2 Incompatibility group   -
Plasmid size   198129 bp Coordinate of oriT [Strand]   179086..179124 [+]
Host baterium   Agrobacterium tumefaciens strain cl001

Cargo genes

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