Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102613
Name   oriT_FDAARGOS_618|unnamed1 in_silico
Organism   Agrobacterium pusense strain FDAARGOS_618
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JABRWM010000001 (89113..89156 [+], 44 nt)
oriT length   44 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: 44 nt

>oriT_FDAARGOS_618|unnamed1
GGATCCGAAGGGCGCAATTATACGTCGCTGATGCGACGCTCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1949 GenBank   WP_172891007
Name   traA_FOB26_RS00475_FDAARGOS_618|unnamed1 insolico UniProt ID   _
Length   1106 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1106 a.a.        Molecular weight: 122433.40 Da        Isoelectric Point: 9.5568

>WP_172891007.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium pusense]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPADAPEWLQSMIADR
SVSGASEAFWNKVEEFEKRSDAQLAKDVTIALPIELSIEQNIELVRDFVERHITAEGMVADWVFHDAPGN
PHIHLMTTLRPLTEDGFGSKKVAVAGPDGKALRNDSGKIVYELWAGGLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIDLTPTIHLGVGTKAIERKAARGNGPAGEKAALERLELQEERRAENARRIQRSPEI
VLDLITREKSVFDERDVAKILHRYVDDAGLFQILMVRILQSPETLRLDRERMDFATGGRAPTKYTTRELI
RLEAEMVNRAMWLSQRSSHGVRKPVLEATFAHHERLSDEQKVAIEHVAGVERIAAVIGRAGAGKTTMMKA
AREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWDQGRGQLDDKTVFVLDEAGMVSSRQMA
TFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGNVGKAL
AAYQSNGKMNGSELKANAVTNLISDWNREYDPAKSTLILAHLRRDVRMLNELARTKLIERGIIEQGFTFK
TADGVRSFAAGDQIVFLKNESSLGVKNGMLGKVMEAAPGRIVAVIGDGEHRAQVTVEQRFYNNVDHGYAT
TVHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGVYYGRRSFAKAGGLVEILSRRNSKETTLDYAG
GIIYRQALRFAEARGLHIVNVARTVARDRLEWTVRQKQKLVDLAGKLAAIGAKLGFATSTARTVPVAEKE
TKPMVAGITTFPKSIDQTVEDKLAADPALKKQWEEVSMRFIQVYAQPESAFKAVNVDAMLRDQAVAETTI
AKIASEPETFGALKGKTGLLASRSDKVDRDRALKNVTPLADSISDYLRQRGDAERRNHAEELAVRRQVAL
EIPALSSNAKSVLERVRDAIDRNDLPSGLEYALADKMVKAELEGFAKAVTERFGERTFLPLVAKDTTGEA
FQRVTSGMNAAQKSEVQQAWNTMRTVQQLSAHERSVTALKQAETLRQTKSQGLTLK

  Protein domains


Predicted by InterproScan.

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

(862-958)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-739)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(386-570)


  Protein structure



No available structure.




T4CP

ID   1576 GenBank   WP_112635354
Name   traG_FOB26_RS00460_FDAARGOS_618|unnamed1 insolico UniProt ID   _
Length   653 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 653 a.a.        Molecular weight: 70859.57 Da        Isoelectric Point: 7.9757

>WP_112635354.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium/Agrobacterium group]
MTANRVLLSIAPAIFMIAVATVLTGVEQWLSQMGKTEDTRLMLGRIGIATPYIAAAAIGLIWLFASAGSA
NIRFVGWSTAAGSAVAMIIAAAREGSRLTALADKVPANKSILAYLDPATMIGATVTLIVGCFALRVVVIG
NAAFARPEPKRISGKRALHGEADWMKLSEAERLFAEAGGIVIGERYRVDLDGASTRAFSADDQESWGDGG
KAPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSQHREGAGRRIRILD
PRQPNPGFNALDWIGKFGGTKEEDIASVASWIMSESGRASGVRDDFFRASGLQLLTAMIADVCLSGHTPP
EQQTLRQVRANLSEPEPKLRQRLQDIYDNSESNFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYA
ALVSGSAFSTDDIASGKTDVFINIDLKTLETHAGLARVIIGSFLNAIYNRDGAIEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSYQARGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRKDMESCVG
QNRFHRSSTSSNTSLEPPEADPQ

  Protein domains


Predicted by InterproScan.

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

(163-639)

  Protein structure



No available structure.



ID   1577 GenBank   WP_172891010
Name   t4cp2_FOB26_RS00545_FDAARGOS_618|unnamed1 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: 91742.48 Da        Isoelectric Point: 5.6954

>WP_172891010.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium/Agrobacterium group]
MVALKRFRTTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQISSILSRLG
TGWMIQVEAIRVPTVDYPTPDQCRFPDPVTRAIDAERRAHFGREQGHFESKHAIILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFRNAIREIEQYLSNTLSIARMKTREVRERGGERVARYDDLMQFVRFCITG
ESHPVRLPEVPMYLDWLATAELEHGLTPKVENRFLAVVAIDGLPAESWPGILNNLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIALASSQLVAYGYYTPVVIL
FDDDRDALQEKAEAIRRLVQAEGFGARVETLNATDAFLGSLPGNWYANVREPLINTSNLADLVPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEFAQIFA
FDKGNSLLPLTLAAGGDHYEIGNDQNGEGKALAFCPLFDLSTDGDRAWATEWIETLVALQGVTITPDHRN
AISRQIGLMATAPGKSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLRAFQCFEIEHLMNMG
ERNLVPVLTYLFHRIEKRLDGSPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSGAIPKREYYVATPDGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKAEYGQDWPTHWLESRGVPDATSHLNAQ

  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: 94278..106487

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FOB26_RS00480 (FOB26_00480) 92554..93114 + 561 WP_234909068 conjugative transfer signal peptidase TraF -
FOB26_RS00485 (FOB26_00485) 93104..94264 + 1161 WP_112635360 conjugal transfer protein TraB -
FOB26_RS00490 (FOB26_00490) 94278..94904 + 627 WP_113344519 TraH family protein virB1
FOB26_RS00495 (FOB26_00495) 95217..95432 - 216 WP_112635364 helix-turn-helix transcriptional regulator -
FOB26_RS00500 (FOB26_00500) 95634..95957 + 324 WP_112635366 transcriptional repressor TraM -
FOB26_RS00505 (FOB26_00505) 95954..96658 - 705 WP_112635368 autoinducer binding domain-containing protein -
FOB26_RS00510 (FOB26_00510) 96983..98284 - 1302 WP_112635370 IncP-type conjugal transfer protein TrbI virB10
FOB26_RS00515 (FOB26_00515) 98300..98737 - 438 WP_112635372 conjugal transfer protein TrbH -
FOB26_RS00520 (FOB26_00520) 98741..99553 - 813 WP_172891008 P-type conjugative transfer protein TrbG virB9
FOB26_RS00525 (FOB26_00525) 99570..100232 - 663 WP_112635384 conjugal transfer protein TrbF virB8
FOB26_RS00530 (FOB26_00530) 100254..101432 - 1179 WP_172891009 P-type conjugative transfer protein TrbL virB6
FOB26_RS00535 (FOB26_00535) 101437..101613 - 177 WP_112635388 entry exclusion protein TrbK -
FOB26_RS00540 (FOB26_00540) 101607..102410 - 804 WP_112635399 P-type conjugative transfer protein TrbJ virB5
FOB26_RS00545 (FOB26_00545) 102382..104838 - 2457 WP_172891010 conjugal transfer protein TrbE virb4
FOB26_RS00550 (FOB26_00550) 104848..105147 - 300 WP_172891011 conjugal transfer protein TrbD virB3
FOB26_RS00555 (FOB26_00555) 105140..105520 - 381 WP_112635405 TrbC/VirB2 family protein virB2
FOB26_RS00560 (FOB26_00560) 105510..106487 - 978 WP_112635407 P-type conjugative transfer ATPase TrbB virB11
FOB26_RS00565 (FOB26_00565) 106498..107124 - 627 WP_112635409 acyl-homoserine-lactone synthase TraI -
FOB26_RS00570 (FOB26_00570) 107499..108716 + 1218 WP_172891012 plasmid partitioning protein RepA -
FOB26_RS00575 (FOB26_00575) 108871..109878 + 1008 WP_112635411 plasmid partitioning protein RepB -
FOB26_RS00580 (FOB26_00580) 110069..111307 + 1239 WP_172891013 plasmid replication protein RepC -

Host bacterium

ID   3057 GenBank   NZ_JABRWM010000001
Plasmid name   FDAARGOS_618|unnamed1 Incompatibility group   -
Plasmid size   154534 bp Coordinate of oriT [Strand]   89113..89156 [+]
Host baterium   Agrobacterium pusense strain FDAARGOS_618

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   ncrA, ncrC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -