Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114025
Name   oriT_pDG3-1c in_silico
Organism   Agrobacterium salinitolerans strain DG3-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP074396 (37246..37290 [+], 45 nt)
oriT length   45 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: 45 nt

>oriT_pDG3-1c
GGTTCCAAGGGCGCAATTATACGTCGCTCACGCGACGCCTTGCGT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9011 GenBank   WP_217005269
Name   traA_KHC17_RS24880_pDG3-1c 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: 123627.05 Da        Isoelectric Point: 9.8722

>WP_217005269.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium salinitolerans]
MAIAHFSVSIVSRGDGRSAVLSAAYRHCARMEYEREARTIDYTRKQGLLHEEFVLPADAPKWARMLIADR
SIAGASEAFWNKVEAFEKRSDAQFAKDLTIALPVELTPEQNIALVREFVEKHILAKGMVADWVYHDNAGN
PHIHLMTTLRPLTVDGFGAKKVAVTGEDGQPLRNKAGKIVYELWAGGTDDFNAFRDAWFERLNHHLALNG
ISLRVDGRSYEKQGIDLEPTIHLGVGAKAIERKAEKQGVRPELERIELNDARRAENTRRILRRPEIVLDL
ITRERSVFDERDVAKVLHRYVDDPAVFQQLMLSIILNPQVLRLQRDTIDFATAKKVPARYSTREMIRLEA
TMAGQAMWLSGRETHDVDDKVLAATFARHARLSDEQKAAIERIAGSARIAAVVGRAGAGKTTMMKAAREA
WEVAGYRVVGGALAGKAAEGLEKEAGIASRTLASWELRWQQGRDTLDARTVFVMDEAGMVASKQMAGFIE
AVVRSGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREEWMRHASLDLARGNIEQGLLAYR
TRGHVVGESLKSEAVESLISAWNHDYDPAKSMLMLAHLRRDVRMLNMMAREKLVERGIIGEGHAFKTADG
TRQFDAGDQIVFLKNEGSLGVKNGMIGRVIEAAPNRMTVTVGEGDQRRQVTVESRFYNNVDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYFGRRSFEMNGGLAKVLSRRNAKETTLDYERGTLY
REALRFAENRGLHIVQVARTLLRDRLDWTLRQKSKLTDLANRLRALGERLGLQQSPPAQSAKEAKPMVAG
ITRFENSVADTVSERLDADPALKKQWEEVSIRFRYVFADPETAFQAMNFDAVLADKDAARQALKRLEAEP
ASIGPLRGKTGILASKTEREARRVAEINVPALRRDLERYLQMRQNAAQRLQADEQALRQRVSIDIPALSP
EARAVLERVRDAIDRNDLPAALAYALSNRETKLEIDGFNKAVTERFGERTLLTNAAREPSGKLFDKLSEG
MQPQEKERLKEAWPVMRTAQQLAAHERTTETLRQVEELRLAQRQTPVVKQ

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-566)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

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

(855-951)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   10444 GenBank   WP_217005262
Name   traG_KHC17_RS24865_pDG3-1c 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: 69017.99 Da        Isoelectric Point: 9.0882

>WP_217005262.1 Ti-type conjugative transfer system protein TraG [Agrobacterium salinitolerans]
MTVNRLLLATLPAAFMIATMLAISGIETWLSGFGASPQAKLMLGRIGLALPYAAAAAIGVITLFATAGAA
NIKTAGLSVLAGASLVCIAAIAREGWRLFALADRVPRGQSVFAYTDPSAMLGACAAVFTGIFALRVAIRG
NATFAKAAPRRISGKRAVHGEADWMKMGDAARLFPDAGGIVIGERYRVDKDSMAAMPFRAGDAQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVIDHRRKSGRNVIVLD
PATPAIGFNALDWIGRHGNTKEEDIVAVATWIMTDNARAASARDDFFRASAMQLLTALIADVCLSGHTNE
KDQTLRRVRSNLSEPEPKLRERLTRIYEQSESDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGDSFSTDDLAGGDADLFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGEIEGRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSTGMRGSSRSRSKQLSRRPLILPHEVLRMRADEQIVFTSGNPPLRCGRAIWFRRDDMKACVG
QNRFHREGE

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   10445 GenBank   WP_217005158
Name   t4cp2_KHC17_RS25170_pDG3-1c 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: 91445.13 Da        Isoelectric Point: 5.7989

>WP_217005158.1 conjugal transfer protein TrbE [Agrobacterium salinitolerans]
MVALKSFRHSGPSFADLVPYAGLVNNGVILLKDGSLMAGWYFGGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVPTDDYPADTDCHFPDPVTRAIDAERRAHFQKERGHFESRHALILTWRAPEARRSGLTR
YVYSDTASRSATYADKALESFLTSIREVEQYLANVVSIRRMMTRETSERGGSRVARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNALDLMPLTYRWSSRFVF
LDAEEARAKLERTRKKWQQKVRPFFDQLFQTQSRSADQDALTMVAETEDAIAEASSQLVAYGYYTPAIVI
FDEQQARLQEKCEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPTAPCPFYPPGSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYAGAQVFA
FDKGGSMLPLTLGLDGDHYQIGGDIGPSAEREGRALAFCPLAELSTDGDRAWAAEWIETLVALQGVTITP
DYRNAISRQIGLMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFEIEEL
MNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSIS
DAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATALPKREYYVVSPDGRRLFDM
ALGPVALSFVGASGKEDLKRIRALHSEHGAAWPCPWLQQRGIAHADTLFPAQ

  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: 93298..102997

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KHC17_RS25115 (KHC17_25115) 88554..89588 + 1035 WP_217005137 hydroxyacid dehydrogenase -
KHC17_RS25120 (KHC17_25120) 89585..90391 + 807 WP_217005139 sugar phosphate isomerase/epimerase -
KHC17_RS25125 (KHC17_25125) 90382..91629 + 1248 WP_217005141 glucarate dehydratase family protein -
KHC17_RS25130 (KHC17_25130) 91935..93194 + 1260 WP_217005144 MFS transporter -
KHC17_RS25135 (KHC17_25135) 93298..94626 - 1329 WP_217005146 IncP-type conjugal transfer protein TrbI virB10
KHC17_RS25140 (KHC17_25140) 94639..95100 - 462 WP_217005345 conjugal transfer protein TrbH -
KHC17_RS25145 (KHC17_25145) 95100..95954 - 855 WP_217005148 P-type conjugative transfer protein TrbG virB9
KHC17_RS25150 (KHC17_25150) 95972..96649 - 678 WP_217005150 conjugal transfer protein TrbF virB8
KHC17_RS25155 (KHC17_25155) 96667..97860 - 1194 WP_217005152 P-type conjugative transfer protein TrbL virB6
KHC17_RS25160 (KHC17_25160) 97854..98084 - 231 WP_217005154 entry exclusion protein TrbK -
KHC17_RS25165 (KHC17_25165) 98081..98890 - 810 WP_217005156 P-type conjugative transfer protein TrbJ virB5
KHC17_RS25170 (KHC17_25170) 98862..101330 - 2469 WP_217005158 conjugal transfer protein TrbE virb4
KHC17_RS25175 (KHC17_25175) 101340..101639 - 300 WP_217005161 conjugal transfer protein TrbD virB3
KHC17_RS25180 (KHC17_25180) 101632..102036 - 405 WP_217005163 conjugal transfer pilin TrbC virB2
KHC17_RS25185 (KHC17_25185) 102026..102997 - 972 WP_217005165 P-type conjugative transfer ATPase TrbB virB11
KHC17_RS30180 (KHC17_25190) 102994..103643 - 650 Protein_96 acyl-homoserine-lactone synthase TraI -
KHC17_RS25195 (KHC17_25195) 103990..105207 + 1218 WP_217005167 plasmid partitioning protein RepA -
KHC17_RS25200 (KHC17_25200) 105430..106443 + 1014 WP_160872130 plasmid partitioning protein RepB -
KHC17_RS25205 (KHC17_25205) 106653..107987 + 1335 WP_217005169 plasmid replication protein RepC -

Host bacterium

ID   14460 GenBank   NZ_CP074396
Plasmid name   pDG3-1c Incompatibility group   -
Plasmid size   141550 bp Coordinate of oriT [Strand]   37246..37290 [+]
Host baterium   Agrobacterium salinitolerans strain DG3-1

Cargo genes

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