Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103850
Name   oriT_pAt1D1609a in_silico
Organism   Agrobacterium tumefaciens strain 1D1609
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026927 (174361..174394 [+], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_pAt1D1609a
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2860 GenBank   WP_104680476
Name   traA_At1D1609_RS28140_pAt1D1609a insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 122851.83 Da        Isoelectric Point: 9.6481

>WP_104680476.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAVPHFSVSVVARGSGRSAVLSAAYRHCARMEFEREARTIDYTRKQGLLHEEFVIPADAPEWLHSMIADR
SVSGASEAFWNKVEDFEKRSDAQLAKDVTIALPIELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSVQDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIELEPTIHLGVGTKAIERKAEQSDHKSETSTSKLERIELQEQRRGENARRIQRRPE
IVLDLIMREKSVFDERDVAKVLYRYIDDAALFQSLMVRILQSSEALRLERERINFATGIRDPAKYTTREM
VRLEAEMANRAIWLSGSTSHGVREAVLQATFARHSRLSDEQRTAIEHVAGAARIAAVIGRAGAGKTTMME
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVARTLSSWELRWNQGRNQLDEKTVFVLDEAGMVSSRQM
ALVVETATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELESIYRQRQQWMRDASLDLARGNVGKA
VDAYRAHGQFRGLDLKAQAVESLIADWIHDYHPSKTSLILAHLRRDVRKLNEMARARLVERGIVADGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGEGEHRRQVTIEQRFYNNLDHGYA
TTIHKAQGVTIDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIQILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLMNVARTIAHDRLQWAVRQRSRLADLGARLAAIGAALGLVRGSTKHSIPDTI
KEAKPMVSGITTYPKSLDQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDTMLKDQSVAQS
TLARIASEPETFGVLKGKTGLLASRGDKQDREKALANVPALARNLERYLRERAEAELKHEREERAVRLKV
SVDIPALSTSAKQALERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTSG
KTFETVTAGMTAGQKAEVQSAWNSMRTVQQLGAHERTTEALKQAEVLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-740)

AAA domain (AAA_30)

(387-571)


  Protein structure



No available structure.




T4CP

ID   2692 GenBank   WP_104680473
Name   traG_At1D1609_RS28125_pAt1D1609a 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: 68965.05 Da        Isoelectric Point: 9.2464

>WP_104680473.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTINRIALVIVPTALMILTVIGMTGIEQWLAGFGKTEAARLAWGRAGIALPYVASAAIGVLLLFATAGAI
NIKQAGWGVLAGCCGTILIAAVRETMRLAAFTKALNANKSVFAYLDPATAIGAGAALMCACFALRIVLIG
NAAFARAEPRRIQGKRALHGEADWMKFTEAAKLFPDTGGIVIGERYRVDKDSVGARAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PRKSDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGRKFATSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIEGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQISRNSQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHRY

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   2693 GenBank   WP_104680492
Name   t4cp2_At1D1609_RS28225_pAt1D1609a insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91552.15 Da        Isoelectric Point: 5.5145

>WP_104680492.1 conjugal transfer protein TrbE [Agrobacterium tumefaciens]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDHCYFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFNNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCATG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDGDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRNLAFCPLSELRTDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIRWLETRGVHDAASLFK

  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: 179443..193511

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
At1D1609_RS28140 (At1D1609_54250) 174474..177800 + 3327 WP_104680476 Ti-type conjugative transfer relaxase TraA -
At1D1609_RS28145 177797..178330 + 534 Protein_177 conjugative transfer signal peptidase TraF -
At1D1609_RS28150 (At1D1609_54260) 178323..179426 + 1104 WP_233282735 conjugal transfer protein TraB -
At1D1609_RS28155 (At1D1609_54270) 179443..180057 + 615 WP_104680478 TraH family protein virB1
At1D1609_RS28160 (At1D1609_54280) 180097..180828 - 732 WP_104680479 hypothetical protein -
At1D1609_RS28165 (At1D1609_54290) 180818..181537 - 720 WP_104680480 hypothetical protein -
At1D1609_RS28170 (At1D1609_54300) 181534..182103 - 570 WP_104680481 hypothetical protein -
At1D1609_RS28175 (At1D1609_54310) 182191..182403 - 213 WP_104680482 helix-turn-helix transcriptional regulator -
At1D1609_RS28180 (At1D1609_54320) 182619..182942 + 324 WP_104680483 transcriptional repressor TraM -
At1D1609_RS28185 (At1D1609_54330) 182945..183649 - 705 WP_104680484 autoinducer binding domain-containing protein -
At1D1609_RS28190 (At1D1609_54340) 183997..185295 - 1299 WP_104680485 IncP-type conjugal transfer protein TrbI virB10
At1D1609_RS28195 (At1D1609_54350) 185307..185747 - 441 WP_104680486 conjugal transfer protein TrbH -
At1D1609_RS28200 (At1D1609_54360) 185751..186563 - 813 WP_104680487 P-type conjugative transfer protein TrbG virB9
At1D1609_RS28205 (At1D1609_54370) 186581..187243 - 663 WP_104680488 conjugal transfer protein TrbF virB8
At1D1609_RS28210 (At1D1609_54380) 187264..188445 - 1182 WP_104680489 P-type conjugative transfer protein TrbL virB6
At1D1609_RS28215 (At1D1609_54390) 188439..188639 - 201 WP_104680490 entry exclusion protein TrbK -
At1D1609_RS28220 (At1D1609_54400) 188636..189433 - 798 WP_104680491 P-type conjugative transfer protein TrbJ virB5
At1D1609_RS28225 (At1D1609_54410) 189411..191861 - 2451 WP_104680492 conjugal transfer protein TrbE virb4
At1D1609_RS28230 (At1D1609_54420) 191872..192171 - 300 WP_104680493 conjugal transfer protein TrbD virB3
At1D1609_RS28235 (At1D1609_54430) 192164..192544 - 381 WP_104680494 TrbC/VirB2 family protein virB2
At1D1609_RS28240 (At1D1609_54440) 192534..193511 - 978 WP_104680495 P-type conjugative transfer ATPase TrbB virB11
At1D1609_RS28245 (At1D1609_54450) 193522..194145 - 624 WP_104680496 acyl-homoserine-lactone synthase TraI -
At1D1609_RS28255 (At1D1609_54460) 194641..197616 + 2976 WP_104680305 Tn3 family transposase -
At1D1609_RS28260 (At1D1609_54470) 197636..198358 - 723 WP_104680498 AcvB/VirJ family lysyl-phosphatidylglycerol hydrolase -

Host bacterium

ID   4290 GenBank   NZ_CP026927
Plasmid name   pAt1D1609a Incompatibility group   -
Plasmid size   243381 bp Coordinate of oriT [Strand]   174361..174394 [+]
Host baterium   Agrobacterium tumefaciens strain 1D1609

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixB, fixA
Anti-CRISPR   -