Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103800
Name   oriT_SL42|unnamed2 in_silico
Organism   Rhizobium sp. SL42
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP063399 (115144..115187 [-], 44 nt)
oriT length   44 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 44 nt

>oriT_SL42|unnamed2
GGATCCGAAGGGCGCAATTATACGTCGCTGATGCGACACTCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2821 GenBank   WP_237371934
Name   traA_IM739_RS22840_SL42|unnamed2 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: 121733.48 Da        Isoelectric Point: 9.5267

>WP_237371934.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. SL42]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARAIDYRAKQGLLHEEFVIPSDAPEWLQSMIADR
SVSGASEAFWNKVEDFEKRSDAQLAKDVTIALPIELSPLQNIELVRDFVGRHITAEGMVADWVFHDAPGN
PHIHLMTTLRPLTEDGFGSKKVAVTGPDGQPLRNDAGKIVYKLWAGGLENFNAFRDGWFACQNRHLAIAG
LDVRVDGRSFEEQGIELTPTIHLGVGAKAVERKADGKGEAASLERLELQEERRAENVRRIQRNPELVLDL
ITREKSVFDERDVAKVLHRYIDDAGLFQSLMARILQNPETLRLDRERLDFVTGVRAPEKYTTRELIRLEA
EMANRAILLSQRSSHGVRKPVLEATFARHERLSDEQKAAIEHVAGGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELSWSQGRGMLDEKTVFVLDEAGMVSSRQMAMFVE
TVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDFARGHVGKAVAAYQ
SNGKMIGSELKADAVTNLIADWNREYDPARSTLILAHLRRDVRMLNELARAKLIERGIIEQGFVFKTADG
NRHFAAGDQIVFLKNEGAIGVKNGMLGKVVEAALGRIVAVIGEGEHLRQVIVEQRFYNNVDHGYATTVHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGVYYGHRSFAKAGGLVEILSRKNSKETTLDYAGGSIY
SQALRFAEARGLHIVNVARTVARDRLEWTARQKQKLVDLAGRLAVLGARLGFATSAASTIQTSAKEAKPM
VAGITTFPKSIDQAVEDKLASDPALKKQWEEVSMRFHHVYAQPEAAFKAANLDAMLSDPATAAKTLSRIT
AEPEAFGSLKGKTGVFANRADKLDRDRALKNVRPLADSISDYLRQRGDTERRSHAEELAVRRQVALEIPA
LSSNARSVLERVRDAIDRNDLPSGLEFALADKMVKAELEGFAKAVTERFGERTFLPLAAKDANGEAFQRV
TSGMNAAQKSEVQQAWNTMRTVQQLSAHERSVTALKQTEALRQTRSQGLTLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-565)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(858-954)


  Protein structure



No available structure.




T4CP

ID   2644 GenBank   WP_237371892
Name   t4cp2_IM739_RS22585_SL42|unnamed2 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: 92055.93 Da        Isoelectric Point: 6.3776

>WP_237371892.1 conjugal transfer protein TrbE [Rhizobium sp. SL42]
MAALKRFRTTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDAESATDLERNELSRQINVILSRLG
TGWMIQVEAVRVPTVDYPSPDQCHFPDPVTRAIDAERRSHFQRAQGHFESKHAIILTYRPLESKKTAFAK
YIYSDEESRKKSYADTVLFVFRNAIREIEQYLANTLSIARMQTREVRERGGERTARYDELFQFVRFCITG
ESHPVRLPEVPMYLDWLVTGELQHGLTPKLENRFLAVVAIDGLPAESWPGILNNLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVIL
FDKNREALQEKAEAIRRLLQAEGFGARVETLNATDAFLGSLPGNWYANIREPLINTSNLADLVPLNSVWS
GNPVNPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEFAQVFA
FDKGNSLLPLTLAAGGDHYEIGNDQSGEERALAFCPLFDLSTDGDRAWATGWLEMLVALQGVTITPDHRN
AISRQIGLMATAPGKSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLRAFQCFEIEQLMNMG
ERNLVPVLTYLFHRIEKRLDGSPSLILLDEAWLMLGHPVFRDKIREWLKVLRKTNCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNKRQIEIVSSAIPKREYYVATPDGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKTEHGQDWPAYWLESRGVHDATSHLNVR

  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.



ID   2645 GenBank   WP_237371937
Name   traG_IM739_RS22855_SL42|unnamed2 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: 68832.65 Da        Isoelectric Point: 8.2763

>WP_237371937.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. SL42]
MKANRIVLLILPVAMMIATVFVVTGIDTWLAGFGKTEAAKLGLGRAGVAAPYMAAAALGLIFLFAAAGSA
SIRAAGWGAATGNATIILTACAREGLRLAALSSQVPAGQSALSYLDPATMIGAAAALMSGCFAMRVAMVG
NAAFARAAPKRIVGKRALHGEADWMKLAEAERLFSQAGGIVIGERYRVDRDSVAGVSFRSENKETWGAGG
QSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGSLIVLDPSNEVAPMVSKHREDAGRRIRILD
PREPATGFNALDWVGQYGGTKEEDIASVASWIMSDSGRPTGVRDDFFRASALQLLTAIIADVCLSGHTPE
EQQTLRQVRVNLSEPEPKLRQRLQDIYDTSGSDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYA
ALVSGSTFQTDDIASGTTDVFINIDLKTLETHAGLVRVVIGSFLNAIYNRDGAMEGRALFLLDEVARLGY
MRILETARDAGRKYSITLTMIYQSIGQLRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQSRGSSRTRSKQLAARPLIQPHEVLCMRADEQIIFTAGNPPLRCGRAIWFRREDMKSCVD
ANLFMKAGA

  Protein domains


Predicted by InterproScan.

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

(163-632)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 61254..70753

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IM739_RS22550 (IM739_22535) 56256..57470 - 1215 WP_237371885 plasmid replication protein RepC -
IM739_RS22555 (IM739_22540) 57627..58625 - 999 WP_237371886 plasmid partitioning protein RepB -
IM739_RS22560 (IM739_22545) 58622..59857 - 1236 WP_237371887 plasmid partitioning protein RepA -
IM739_RS22565 (IM739_22550) 60625..61251 + 627 WP_237371888 acyl-homoserine-lactone synthase -
IM739_RS22570 (IM739_22555) 61254..62225 + 972 WP_237371889 P-type conjugative transfer ATPase TrbB virB11
IM739_RS22575 (IM739_22560) 62215..62589 + 375 WP_237371890 TrbC/VirB2 family protein virB2
IM739_RS22580 (IM739_22565) 62589..62873 + 285 WP_237371891 conjugal transfer protein TrbD virB3
IM739_RS22585 (IM739_22570) 62884..65340 + 2457 WP_237371892 conjugal transfer protein TrbE virb4
IM739_RS22590 (IM739_22575) 65312..66115 + 804 WP_237371893 P-type conjugative transfer protein TrbJ virB5
IM739_RS22595 (IM739_22580) 66112..66315 + 204 WP_237371894 entry exclusion protein TrbK -
IM739_RS22600 (IM739_22585) 66309..67487 + 1179 WP_237371895 P-type conjugative transfer protein TrbL virB6
IM739_RS22605 (IM739_22590) 67509..68171 + 663 WP_237371896 conjugal transfer protein TrbF virB8
IM739_RS22610 (IM739_22595) 68188..69000 + 813 WP_237371897 P-type conjugative transfer protein TrbG virB9
IM739_RS22615 (IM739_22600) 69004..69441 + 438 WP_237371898 conjugal transfer protein TrbH -
IM739_RS22620 (IM739_22605) 69455..70753 + 1299 WP_237371899 IncP-type conjugal transfer protein TrbI virB10
IM739_RS22625 (IM739_22610) 70991..72232 + 1242 WP_237371900 glycosyltransferase -
IM739_RS22630 (IM739_22615) 72413..72886 - 474 WP_237371901 isoprenylcysteine carboxylmethyltransferase family protein -
IM739_RS22635 (IM739_22620) 72923..73302 - 380 Protein_63 antibiotic biosynthesis monooxygenase family protein -
IM739_RS22640 (IM739_22625) 73358..74251 - 894 WP_237371902 NAD(P)/FAD-dependent oxidoreductase -
IM739_RS22645 (IM739_22630) 74469..75116 + 648 WP_237371903 TetR/AcrR family transcriptional regulator -

Host bacterium

ID   4240 GenBank   NZ_CP063399
Plasmid name   SL42|unnamed2 Incompatibility group   -
Plasmid size   351829 bp Coordinate of oriT [Strand]   115144..115187 [-]
Host baterium   Rhizobium sp. SL42

Cargo genes

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