Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106915
Name   oriT_YW14|2 in_silico
Organism   Pseudorhizobium flavum strain YW14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LR723671 (131106..131144 [+], 39 nt)
oriT length   39 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: 39 nt

>oriT_YW14|2
GGATCCGAAGGGCGCAATTATACGTCGCTGATGCGACGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4572 GenBank   WP_077548313
Name   traA_GFD27_RS20390_YW14|2 insolico UniProt ID   _
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 122002.56 Da        Isoelectric Point: 9.6251

>WP_077548313.1 Ti-type conjugative transfer relaxase TraA [Pseudorhizobium flavum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVVPGDAPEWLQSLIADR
SVAGASEVFWNKVEDFEKRSDAQLAKDVTIALPIELSAEQNIDLVRDFVARHITAQGMVADWVFHDAPGN
PHIHLMTTLRPLTEEGFGSKKIAVTGPDGKPLRNDSGKIVYELWAGGIEDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIDLTPTIHLGVGTKAIERKTEGAEEKAALERLELQEERRAENARRIQRSPEMVLDV
ITREKSVFDERDVAKILHRYIDDAGLFQSLMARILQSPETLRLDRERLDFATGVRMPAKHTTRELIRLES
EMANRAIWLSQRSSHGVRKHVLEATFARHDRLSDEQKAAIEHVAGTERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELGWSQGRGKLNERTVFVLDEAGMVSSRQMATFVE
AVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGNIGKAVAAYQ
SNGKMIGSELKADAVANLISDWNRDYNPAKSTLILAHLRRDVRMLNELARATLMERGIIEQGFVFKTADG
NRNFAAGDQIVFLKNEGSIGVKNGMLGKVMEATPGRIVAVIGEGEHLRQVIVEQRFYNNVDHGYATTVHK
SQGATVDRVRVLASLSLDRHLIYVAMTRHREDLGVYYGRRSFAKAGGLVEILSRRNSKETTLDYAGGSIY
RQALRFAEARGLHIVNVARTVARDRLEWTARQKQKLVDLAGRLAVLGARLGFATSTASTIQTSAKEAKPM
VAGITTFSKSIDQAVEDKLASDPALKKQWEEVSMRFHHVYAQPEAAFNAANLDAMLSDPAAAAKTLSRIT
AEPEAFGSLKGKTGVFASRADKLDRDRALKNVTPLADSISDYLRQRGDAERRNYAEELAVRRQVALEIPA
LSSNARSVLERVRYAIDRNDLSSDLEYALADKLVKAELEGFAKAVTERFGERTFLPLAAKDTTGEAFQRV
TSGMNAAQKSEVQQAWNTMRTVQQLSAHERTATAFKQAETPRQTRSQGLTLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)

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

(858-954)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)


  Protein structure



No available structure.




T4CP

ID   4657 GenBank   WP_152338491
Name   traG_GFD27_RS20375_YW14|2 insolico UniProt ID   _
Length   650 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 650 a.a.        Molecular weight: 70652.89 Da        Isoelectric Point: 9.4766

>WP_152338491.1 Ti-type conjugative transfer system protein TraG [Pseudorhizobium flavum]
MKANRVVLFVLPVAVMIGTLFTMTGIETWLAGLGRTEVARLTLGRVGVAAPYMVAAALGLIFLFATAGSA
SIRAAGVGAAIGNAVVILMACLREGIRLAVLSPQVPAGKSALSYLDPSTMIGTAAALMSGCFAVRVAMAG
NAAFARATPKRIFGKRALHGEADWMTLAEAEKLFPTTGGIVVGERYRVDRDSVAGISFRADTTETWGAGG
KSPLLCFHGSFGSSHGIVFAGSGGLKTTSVTIPTALKWGGSLIVLDPSNEVAPMVSKHREEAGRRVRILD
PRKPATGFNALDWVGQYGGTKEEDIASVASWIMSDSGRVSGVRDDFFRASGLQLLTAIIADVCLSGHTPK
EQQTLRQVRSNLSEPEPKLRQRLQDIYDNSESDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQHYA
ALVSGSTFRTEDIASGKTDVFINIDLKTLETHAGLARVVIGSFLNAIYNRDGAMEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQSRGSSRTRSKQLAARPLVQPHEVLRMRADEQIVFTAGNPPLRCGRAIWFRRQDMKCCVQ
QNRFNEPKRTPSFEKEPSQE

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   4658 GenBank   WP_077548298
Name   t4cp2_GFD27_RS20470_YW14|2 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: 91866.71 Da        Isoelectric Point: 5.9710

>WP_077548298.1 conjugal transfer protein TrbE [Pseudorhizobium flavum]
MAALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
TGWMIQVEAIRVPTVDYPTPDQCHFPDLVTRAIDAERRTHFGREQGHFESKHAIILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFRNAIREIEQYLANTLSIARMQTREIRERGGERVARYDDLLQFVRFCITG
ESHPVRLPEVPMYLDWLATAELEHGLTPKVENRFLAVVAIDGLPAESWPGILNNLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVGETEDAIAQASSQLVAYGYYTPVVIL
FDGDRDALQEKAEAIRRLVQAEGFGARVETLNATDAFLGSLPGNWYANIREPLINTSNLADLVPLNSVWS
GNAVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEFAQIFA
FDKGNSLLPLTLAAGGDHYEIGNDQDGEGRALAFCPLFDLSTDGDRAWATEWIEMLVALQGVTITPDHRN
AISRQIGLMATAPGKSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLRAFQCFEIEQLMNMG
ERNLVPVLTYLFHRIEKRLDGSPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYKRIGFNERQIEIVSSAIPKREYYVATPDGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKAEHSQDWPTHWLELRGVHDATSHLRIQ

  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: 136263..149153

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GFD27_RS20395 (RFYW14_04125) 134565..135095 + 531 WP_077548312 conjugative transfer signal peptidase TraF -
GFD27_RS20400 (RFYW14_04126) 135085..136248 + 1164 WP_077548311 conjugal transfer protein TraB -
GFD27_RS20405 (RFYW14_04127) 136263..136871 + 609 WP_077548310 TraH family protein virB1
GFD27_RS20410 (RFYW14_04128) 136920..137297 - 378 WP_077548309 DUF5615 family PIN-like protein -
GFD27_RS20415 (RFYW14_04129) 137302..137925 - 624 WP_077548308 DUF433 domain-containing protein -
GFD27_RS20420 (RFYW14_04130) 138047..138265 - 219 WP_077548307 helix-turn-helix transcriptional regulator -
GFD27_RS20425 (RFYW14_04131) 138405..138725 + 321 WP_172977928 transcriptional repressor TraM -
GFD27_RS20430 (RFYW14_04132) 138727..139428 - 702 WP_235864267 autoinducer binding domain-containing protein -
GFD27_RS20435 (RFYW14_04133) 139649..140947 - 1299 WP_077548305 IncP-type conjugal transfer protein TrbI virB10
GFD27_RS20440 (RFYW14_04134) 140963..141400 - 438 WP_077548304 conjugal transfer protein TrbH -
GFD27_RS20445 (RFYW14_04135) 141404..142216 - 813 WP_077548303 P-type conjugative transfer protein TrbG virB9
GFD27_RS20450 (RFYW14_04136) 142233..142895 - 663 WP_077548302 conjugal transfer protein TrbF virB8
GFD27_RS20455 (RFYW14_04137) 142917..144095 - 1179 WP_077548301 P-type conjugative transfer protein TrbL virB6
GFD27_RS20460 (RFYW14_04138) 144089..144292 - 204 WP_077548300 entry exclusion protein TrbK -
GFD27_RS20465 (RFYW14_04139) 144289..145092 - 804 WP_077548299 P-type conjugative transfer protein TrbJ virB5
GFD27_RS20470 (RFYW14_04140) 145064..147520 - 2457 WP_077548298 conjugal transfer protein TrbE virb4
GFD27_RS20475 (RFYW14_04141) 147531..147815 - 285 WP_235864266 conjugal transfer protein TrbD virB3
GFD27_RS20480 (RFYW14_04142) 147812..148192 - 381 WP_077548296 TrbC/VirB2 family protein virB2
GFD27_RS20485 (RFYW14_04143) 148182..149153 - 972 WP_077548295 P-type conjugative transfer ATPase TrbB virB11
GFD27_RS20490 (RFYW14_04144) 149156..149782 - 627 WP_077548294 acyl-homoserine-lactone synthase TraI -
GFD27_RS20495 (RFYW14_04145) 150151..151338 + 1188 WP_077548293 plasmid partitioning protein RepA -
GFD27_RS20500 (RFYW14_04146) 151413..152399 + 987 WP_077548292 plasmid partitioning protein RepB -
GFD27_RS20505 (RFYW14_04147) 152554..153777 + 1224 WP_077548291 plasmid replication protein RepC -

Host bacterium

ID   7352 GenBank   NZ_LR723671
Plasmid name   YW14|2 Incompatibility group   -
Plasmid size   227935 bp Coordinate of oriT [Strand]   131106..131144 [+]
Host baterium   Pseudorhizobium flavum strain YW14

Cargo genes

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