Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103875
Name   oriT_pAt1D1108b in_silico
Organism   Agrobacterium tumefaciens strain 1D1108
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP032924 (164434..164470 [+], 37 nt)
oriT length   37 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: 37 nt

>oriT_pAt1D1108b
GGATCCAAGGGCGCAATTATACGTCGCTGATGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2878 GenBank   WP_121557926
Name   traA_At1D1108_RS26795_pAt1D1108b insolico UniProt ID   _
Length   1210 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1210 a.a.        Molecular weight: 133878.37 Da        Isoelectric Point: 8.0929

>WP_121557926.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPVNAPDWLRAMVADL
SVSGASEAFWNKVESFEKRSDAQLAKDVTIALPIELSAVQNIALVRDFVERHITAFGMIADWVLHDAPGN
PHIHLMTTLRPLTEDGFGAKKVAVLGQDGKAQRNDAGKIVYELWAGGAADFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIALEPTIHVGVGATAIERKADEAGETASSAAVKLERIELQEERREENARRIQRDPG
LVLDLITREKSVFDERDIAKVLHRYIDDPTLFRDLMARVLQHPDALRLDSERISFSTGARSPAKYTTHDL
IRIEAEMANRALWLGRQHIHRVASRVFTQAFERHDRLSDEQKSAIERIAGKTRIAAVVGRAGAGKTTMMK
AAREVWEAAGYRVVGAALAGKAAEGLEKEAGIASRTLSAWELRWDQGRDRLDDKTVLVLDEAGMVSSRQM
ARFVEEATRSGAKLVLVGDPDQLQPIEAGAAFRAISERIGYAELETIYRQREQWMRDASLDLARGNVSAA
LVAYESQGMVRTGWTRDDAISTLIAEWDREYDLTKTSLILAHRRRDVRMLNELARSKLVERGLVEAGHAF
KTEDGLRQFSAGDQIVFLKNEGSLGVKNGMLARVIEAQPGRIVAEVGDGDDRRQVVVEQRFYANVDHGYA
TTVHKSQGATVDRVKVLASSTLDRHLTYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPDNR
ASYFVTLGFADGEERTVWGVDLARAMAAADASIGDRIGLQHDGSERVTLPDGTEADRNTWKVVAVEELAV
ARLHERLSRDGSKETTLDYQNASSYRAALRFADARGLHLMNVGRTLLRDRLQWTVRQKDKLANLVSRLAA
AGSRLGLRYNAAGEARAREASETRNQTNSVIQEDRKPMVAGITSFAKSIEKSVEDKVSADPALKSQWQEV
SARFHLVYSDPQAAFNAVNVDAMVANSETAKSTLTAISRQPESFGPLKGKTGLFAGKADAQARETAIVNA
PALARDLDGYLQKRAEAERRYEAEERAVRLKMSIDVPALSDAARQTLEKVRDAIDRNDLPSGLEYALADK
MVKAELEGFAKAVSERFGERSFLPLAAKEADGKVFEKLSAGMAPAQKADLQSAWKTLRTVQQLSAHERTV
TALKQTETMRQAKTTGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(966-1062)

AAA domain (AAA_30)

(387-573)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   2720 GenBank   WP_121557925
Name   traG_At1D1108_RS26780_pAt1D1108b insolico UniProt ID   _
Length   652 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 652 a.a.        Molecular weight: 70594.38 Da        Isoelectric Point: 9.3591

>WP_121557925.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTTTRVVLVIMPVVLMATICLIFPGIENWLAAFGKSEQARLTLGRIGLAAPYVFAAALGVIFLFAAQGSR
SIKAAGWGVASGTLCVLAIAFIREATRLAGFIGQLEAGRTLLSYSDPSTVVGSGAAAVAGAFALRVAVKG
NAAFARSEPKRMRGKRALHGEADWMKMTEAEKLFSGTGGMIIGEKYRVDRDSVAALAFRSGDPTTWGNGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTVPTALKWGGTLVVLDPSNEVAPMVSEHRRKAGRRVVVLD
PKNSTSGFNVLDWIGRHGGTKEEDIAAVASWIMSDSGRATGVRDDFFRASGLQLLTAMIADVCLSGHTAE
RDQTLRQVRANLSEPEPKLRARLQEIYDNSESDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYGNYG
ALVSGSSFTTDALADGKTDVFINIDLKTLETHAGLARVIIGSFLNAIYNRDGAMEGRALFLLDEVARLGY
MRILETARDAGRKYGISLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGTTT
VEIDQVSRSFQSRGSSRTRSKQLASRPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRADMKCSVG
ENRFQKARDVADTEQQAADRNE

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   2721 GenBank   WP_121557939
Name   t4cp2_At1D1108_RS26875_pAt1D1108b insolico UniProt ID   _
Length   811 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 811 a.a.        Molecular weight: 91346.89 Da        Isoelectric Point: 5.7137

>WP_121557939.1 conjugal transfer protein TrbE [Agrobacterium tumefaciens]
MVALRTFRSTGPSFADLVPYAGLVDNGILLLKDGSLMSGWYFAGPDSESATDFERNELSRQINAILSRLG
SGWMIQVEAVRVPTTEYPSAERSHFPDTVTALIDDERRRHFEREQGHFESRQALILTYRPPERRRSGLTR
YIYSDSESRTASYADTVLDTFRRSIREIEQYLGNVVSVQRMQTREVRERGGERIARYDELFQFIRFAITG
ENHPVRLPEIPMYLDWLTTAELEHGLTPRVENRFLGVIAIDGLPAESWPGILNSLNLMPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSIDQDAMSMVAETEDAIAEASSQLVAYGYYTPVIVL
FDESREVLQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLVPLNSVWS
GSPTVTCPFYPPDAPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFCRYGEAQIFA
FDKGNSMLPLTLASGGDHYEIGGDAGEGAHLAFCPLSELLTEGDRAWASEWIETLISLQGVTVAPEHRNA
ISRQIGLMASAPGRSLSDFVSGVQLREIKDALHHYTVDGPMGLLLDAESDGLTLGRFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLDGRPSLIILDEAWLMLGHPVFRNKIREWLKVLRKANCAVILATQSISDAERS
GIIDVLKESCPTKICLPNGAARETGTREFYERIGFNERQIEIVATAIPKREYYVTSPDGRRLFDMALGPV
TLSFVGASGKSDLARIRALQSIHGKEWPRQWLIERGINHDV

  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: 161870..182931

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
At1D1108_RS26750 (At1D1108_51730) 157385..157990 + 606 WP_121557920 arginase family protein -
At1D1108_RS26755 (At1D1108_51740) 158030..158764 - 735 WP_121557921 IS21-like element helper ATPase IstB -
At1D1108_RS26760 (At1D1108_51750) 158772..160265 - 1494 Protein_145 IS21 family transposase -
At1D1108_RS28080 (At1D1108_51760) 160439..160612 + 174 WP_162995352 hypothetical protein -
At1D1108_RS26765 (At1D1108_51770) 160653..161165 - 513 WP_337587077 thermonuclease family protein -
At1D1108_RS26770 161176..161442 - 267 WP_121557960 WGR domain-containing protein -
At1D1108_RS26775 (At1D1108_51780) 161656..161853 - 198 WP_121557924 hypothetical protein -
At1D1108_RS26780 (At1D1108_51790) 161870..163828 - 1959 WP_121557925 Ti-type conjugative transfer system protein TraG virb4
At1D1108_RS26785 (At1D1108_51800) 163815..164030 - 216 WP_052821066 type IV conjugative transfer system coupling protein TraD -
At1D1108_RS26790 (At1D1108_51810) 164035..164298 - 264 WP_121557961 TraC family protein -
At1D1108_RS26795 (At1D1108_51820) 164546..168178 + 3633 WP_121557926 Ti-type conjugative transfer relaxase TraA -
At1D1108_RS26800 (At1D1108_51830) 168235..168741 + 507 WP_233283755 conjugative transfer signal peptidase TraF -
At1D1108_RS26805 (At1D1108_51840) 168731..169897 + 1167 WP_121557928 conjugal transfer protein TraB -
At1D1108_RS26810 (At1D1108_51850) 169911..170525 + 615 WP_121557929 TraH family protein -
At1D1108_RS26815 (At1D1108_51860) 170560..171180 - 621 WP_121557930 hypothetical protein -
At1D1108_RS26820 (At1D1108_51870) 171177..171356 - 180 WP_052821072 hypothetical protein -
At1D1108_RS26825 (At1D1108_51880) 171707..172411 + 705 WP_121557931 transcriptional regulator TraR -
At1D1108_RS26830 (At1D1108_51890) 172422..172721 - 300 WP_121557932 transcriptional repressor TraM -
At1D1108_RS26835 (At1D1108_51900) 173067..173378 + 312 WP_121557933 hypothetical protein -
At1D1108_RS26840 (At1D1108_51910) 173385..174677 - 1293 WP_121557934 IncP-type conjugal transfer protein TrbI virB10
At1D1108_RS26845 (At1D1108_51920) 174693..175139 - 447 WP_233283745 conjugal transfer protein TrbH -
At1D1108_RS26850 (At1D1108_51930) 175143..175973 - 831 WP_121557935 P-type conjugative transfer protein TrbG virB9
At1D1108_RS26855 (At1D1108_51940) 175988..176650 - 663 WP_112671253 conjugal transfer protein TrbF virB8
At1D1108_RS26860 (At1D1108_51950) 176672..177850 - 1179 WP_121557936 P-type conjugative transfer protein TrbL virB6
At1D1108_RS26865 (At1D1108_51960) 177844..178047 - 204 WP_121557937 entry exclusion protein TrbK -
At1D1108_RS26870 (At1D1108_51970) 178044..178853 - 810 WP_121557938 P-type conjugative transfer protein TrbJ virB5
At1D1108_RS26875 (At1D1108_51980) 178846..181281 - 2436 WP_121557939 conjugal transfer protein TrbE virb4
At1D1108_RS26880 (At1D1108_51990) 181292..181591 - 300 WP_121557940 conjugal transfer protein TrbD virB3
At1D1108_RS26885 (At1D1108_52000) 181584..181976 - 393 WP_121557941 TrbC/VirB2 family protein virB2
At1D1108_RS26890 (At1D1108_52010) 181966..182931 - 966 WP_121557963 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   4315 GenBank   NZ_CP032924
Plasmid name   pAt1D1108b Incompatibility group   -
Plasmid size   183311 bp Coordinate of oriT [Strand]   164434..164470 [+]
Host baterium   Agrobacterium tumefaciens strain 1D1108

Cargo genes

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