Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114581
Name   oriT_MA01|punnamed1 in_silico
Organism   Agrobacterium sp. MA01
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP045855 (88231..88274 [+], 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_MA01|punnamed1
GGATCCGAAGGGCGCAATTATACGTCGCTGATGCGACGCTCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9343 GenBank   WP_153763737
Name   traA_GH983_RS22435_MA01|punnamed1 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: 122426.18 Da        Isoelectric Point: 9.4958

>WP_153763737.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium sp. MA01]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKHGLLHEEFVISPDAPQWLQSMIADR
SVSGASEAFWNKVEEFERRSDAQLAKDVTIALPIELSVEQNIELVRDFVARHITAEGMVADWVFHDAPGN
PHIHLMTTLRPLTEDGFGSKKVAVTGPDGKALRNNSGKIVYELWAGGLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKAASGNGPAEEKAALERLELQEERRAENAQRIQRNPAI
VLDLITREKSVFDERDVAKVLHRYIDDVGLFQSLMARILQLPETLRLDRERVDFATGVRAPTKYTTRELI
RLESEMANRATWLSQRSSHGVGKTVLERTFAHHERLSDEQKVAIEHVVGVERIAAVIGRAGAGKTTMMKA
AREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWDQGRGQLDHKTVFVLDEAGMVSSRQMA
TFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGHVGKAL
AAYQSNGKMIGLELKADAVTNLIADWNRDYDPAKSTLILAHLRRDVRMLNELARMKLIERGIIEQGLVFK
TADGNRNFAAGDQIVFLKNEGSIGVKNGMLGKVLEATPGRLVAVIGEGEHQRHVTVEQSFYNNIDHGYAT
TVHKSQGATVDRVNVLASLSLDRHLTYVAMTRHREDLGVYYGRRSFAKAGGLVEILSRRNSKETTLDYAG
GSTYRQALRFAEAHGLHIINVARTVARDRLEWTVQQKQKLLDLAGRLAAIGAKLGFATSIANTVPTAAKE
TKPMVAGITTYPKSIDQAVEDKLAADPALKRQWEEVSMRFHHVYAQPESAFKAVDVDAMLRDQAAAAKTI
TKIASEPETFGALKGKTGLLASRADKVDRDRALKNVTPLADSISDYLRQRGDAERRNHAEELAVRRRVAL
DIPALSSNAKSVLERVRDAIDRNDLPSGLEYTLADKMVKAELEGFAKAVTERFGERTFLPLAAKDPNGEA
FLRVTSGMNTAQRSEVQQAWNTMRTVQQLSTHERSVTALKQAEALRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-739)

AAA domain (AAA_30)

(386-568)

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

(862-958)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   10838 GenBank   WP_153763736
Name   traG_GH983_RS22420_MA01|punnamed1 insolico UniProt ID   _
Length   634 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 634 a.a.        Molecular weight: 68299.99 Da        Isoelectric Point: 9.0918

>WP_153763736.1 Ti-type conjugative transfer system protein TraG [Agrobacterium sp. MA01]
MKVNRVVLFSLPVAMMVATVFTMTGMETWLSGFGQTEAAKIVLGRAGIAAPYVAAAALALVLLFATAGSA
SICAAGVGAAIGNAAVILIACVREGGRLAELSSQVPAGQSALSYLDPSTMIGAAAAFMSGCFAIRVAMVG
NAAFARATPTRITGKRALHGEADWMKLTEAEKLFPGSGGIVVGERYRVDRDSVAGVSFRADNGETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLVVLDPSNEVAPMVSKHREEAGRRVRILD
PRKPATGFNALDWVGQYGGTKEEDIASVASWIMSDSGRASGVRDDFFRASGLQLLTAIIADVCLSGHTPT
ERQTLRQVRENLSEPEPKLRQRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYA
AVVSGSTFRTDDIASGKTDVFINIDLKTLETHAGLARVVIGSFLNAIYNRDGAMEGRALFLLDEIARLGY
MRILETARDAGRKYGITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQSRGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNPPLRCGRAIWFRRKDMTTCVK
LSRF

  Protein domains


Predicted by InterproScan.

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

(163-629)

  Protein structure



No available structure.



ID   10839 GenBank   WP_153763743
Name   t4cp2_GH983_RS22515_MA01|punnamed1 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: 91830.54 Da        Isoelectric Point: 5.8553

>WP_153763743.1 conjugal transfer protein TrbE [Agrobacterium sp. MA01]
MAALKHFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
TGWMIQVEAIRVPTVDYPTPDQCHFPDPVTRAIDLERRAHFRREQGHFESKHAIILTYRPLESKKTALAK
YIYSDEESRKKSYADTVLSVFRNAIREIEQYLANTLSIARMQTREVRERGGERVARYDDLLQFVRFCITG
ESHPVRLPEVPMYLDWLATAELEHGLTPKVENRFLAVVAIDGLPAESWPGILNNLDLMPLTYRWSSRFIF
LDAEDARQKLERTRKKWQQKVRPFFDQLFQTQSRSADQDAMTMVAETEDAIAQASSQLVAYGYYTPVVIL
FDEERDALQEKAEAIRRLVQAEGFGARVETLNATDAFLGSLPGNWYANIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYDCAQIFA
FDKGNSLLPLTLAAGGDHYEIGNDQKGEERALAFCPLFDLSTDGDRAWATEWIETLVALQGVTITPDHRN
AISRQIGLMATAPGKSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLRAFQCFEIEQLMNLG
ERNLVPVLTYLFHRIEKRLDGSPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSGAIPKREYYVATPDGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKAEHGQEWPTHWLESRGVHDATSHLNVR

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 93410..106278

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GH983_RS22440 (GH983_22440) 91666..92232 + 567 WP_097143196 conjugative transfer signal peptidase TraF -
GH983_RS22445 (GH983_22445) 92222..93394 + 1173 WP_097143197 conjugal transfer protein TraB -
GH983_RS22450 (GH983_22450) 93410..94015 + 606 WP_153763738 TraH family protein virB1
GH983_RS22455 (GH983_22455) 94058..94435 - 378 WP_153763739 DUF5615 family PIN-like protein -
GH983_RS22460 (GH983_22460) 94440..95063 - 624 WP_153763740 DUF433 domain-containing protein -
GH983_RS22465 (GH983_22465) 95185..95403 - 219 WP_097143201 helix-turn-helix domain-containing protein -
GH983_RS22470 (GH983_22470) 95543..95863 + 321 WP_097143202 transcriptional repressor TraM -
GH983_RS22475 (GH983_22475) 95865..96566 - 702 WP_194842846 autoinducer binding domain-containing protein -
GH983_RS22480 (GH983_22480) 96744..98081 - 1338 WP_153763742 IncP-type conjugal transfer protein TrbI virB10
GH983_RS22485 (GH983_22485) 98096..98533 - 438 WP_097143205 conjugal transfer protein TrbH -
GH983_RS22490 (GH983_22490) 98537..99349 - 813 WP_097143206 P-type conjugative transfer protein TrbG virB9
GH983_RS22495 (GH983_22495) 99366..100028 - 663 WP_097143207 conjugal transfer protein TrbF virB8
GH983_RS22500 (GH983_22500) 100049..101227 - 1179 WP_097143208 P-type conjugative transfer protein TrbL virB6
GH983_RS22505 (GH983_22505) 101221..101421 - 201 WP_097143209 entry exclusion protein TrbK -
GH983_RS22510 (GH983_22510) 101418..102176 - 759 WP_246727636 P-type conjugative transfer protein TrbJ virB5
GH983_RS22515 (GH983_22515) 102193..104649 - 2457 WP_153763743 conjugal transfer protein TrbE virb4
GH983_RS22520 (GH983_22520) 104659..104943 - 285 WP_113426515 conjugal transfer protein TrbD virB3
GH983_RS22525 (GH983_22525) 104940..105317 - 378 WP_097143212 TrbC/VirB2 family protein virB2
GH983_RS22530 (GH983_22530) 105307..106278 - 972 WP_097143213 P-type conjugative transfer ATPase TrbB virB11
GH983_RS22535 (GH983_22535) 106281..106907 - 627 WP_097143214 acyl-homoserine-lactone synthase TraI -
GH983_RS22540 (GH983_22540) 107289..108488 + 1200 WP_084438685 plasmid partitioning protein RepA -
GH983_RS22545 (GH983_22545) 108581..109603 + 1023 WP_113426518 plasmid partitioning protein RepB -
GH983_RS22550 (GH983_22550) 109756..110994 + 1239 WP_097143216 plasmid replication protein RepC -

Host bacterium

ID   15016 GenBank   NZ_CP045855
Plasmid name   MA01|punnamed1 Incompatibility group   -
Plasmid size   132451 bp Coordinate of oriT [Strand]   88231..88274 [+]
Host baterium   Agrobacterium sp. MA01

Cargo genes

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