Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119136
Name   oriT_pSfreGR64b in_silico
Organism   Sinorhizobium fredii GR64
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137018 (412206..412240 [+], 35 nt)
oriT length   35 nt
IRs (inverted repeats)      20..25, 30..35  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 35 nt

>oriT_pSfreGR64b
ATCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12099 GenBank   WP_018097561
Name   traA_SFGR64A_RS32030_pSfreGR64b insolico UniProt ID   _
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 121913.25 Da        Isoelectric Point: 10.1251

>WP_018097561.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Sinorhizobium]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMAFEREARTIDYTRKQGLLHEEFVVPADAPDWLRAMIADQ
SVSGASEAFWNKVEGFEKRADAQLAKDITIALPIELSTEQNIVLIRDFIDRHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTDDGFGAKKIAVLGPDGSPIRNDSGKIVYDLWGGSAPDFNAFRDGWFACQNKHLSLAG
LDIRVDGRSFEKQGIELTPTIHLGVGAKAIERKSAEADRHISLERLELQEERRAENARRIQRRPEVVLDL
ITREKSVFDERDVAKILHRYFADAGRFHSLMARILQSPETLRLERERIDFASGLRAPAKYTTRELIRLEA
EMADRANWLSLQSSHGVRDAVLEAIFARHTRLSEEQKAAIAHVVAGERVAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGILSRTLSSWELRWSEGRDLIDDKTVFVLDEAGMVSSRQMALFVE
TATKAGAKLVLIGDPQQLQPIEAGAAFRAIADRIGYAELGTIYRQREQWMRDASLELARGNVGKAVEAYR
AHGHVSGSELKTEAMQALITDWNRDYDPTRTSLILAHLRRDVRMLNEMARAMLVERGIVDKGFAFRTEDG
SRQFATGDQIVFLKNEGALGVKNGMLAKVVDAAPGRIVAEVAEAEHRRQVTVESRFYNSVDLGYATTIHK
SQGATVDRVKVLASLSLDRHLAYVALTRHREDLAIYYGRRSFAKAGGLIPILSRKNAKETTLDYANGRLY
RQALHFARARGFHLVSVARTLVRDRLEWTVRQKSRFADLGARLSAIAGKLGLSAAAVGTSQPRTVKELKP
MVSGITTFAKSLEQAVEDKLSADPGLMKQWQEVSARFHLVYAQPEVAFKAANVDAMLKDEAAAKTTISMI
GSEPKIFGALKGKTGILASRADKQTRDTAGANAPALARNLERYLRQRTVAARKYEIEERALRLKVAVHIP
ALSPAAKQTLERVRDAIVRNDLQAGLEYALADKMVKAELEGFGRAVSERFGERTFLPLAAKDTDGQAFQS
VTNGMSEAQKAELRSAWNSMRTVQQLAAHERTTEALKQAATMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(859-955)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-736)

AAA domain (AAA_30)

(382-567)


  Protein structure



No available structure.




T4CP

ID   14171 GenBank   WP_018097558
Name   traG_SFGR64A_RS32015_pSfreGR64b insolico UniProt ID   _
Length   658 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 658 a.a.        Molecular weight: 71252.39 Da        Isoelectric Point: 9.5837

>WP_018097558.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Sinorhizobium]
MTRILLFLAPCALMILAGIGMTGIEQWLSAFGKTDAARQMLGRAGIALPHFVVSLVGISFLFASASSMRI
RATGWGVVAGATGTLLIAAIREAMRLSAFAEQVPVGKSIVNYLDPATAIGATIALMSALFGLRVAIGGNV
ALARAEPKRIYGKRALHGEADWMKLSRAGTLFPESGGIVIGERYRVDRDSVAGQSFRADSAETWGSGGTS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVSNHRGSANRDVFVLDPK
QSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRGAALQLLTALMADICLSGHTKEID
QTLRQVRKNLSEPEPKLRQRLQSIYENSDSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGTTFTTSDLAGGKTDVFINVDLKTLETHSGLARVIIGSFLNAIYNRNGAMQGRALFVLDEVARLGYMR
ILETARDAGRKYGIMLTMIYQSIGQMRETYGGREAASKWFESASWISFAAINDPETAEYISRRCGTTTVE
IDQVSRSFQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKGCVGKN
RFSEAEKHAASLPDRPTRSATSKVDPER

  Protein domains


Predicted by InterproScan.

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

(161-634)

  Protein structure



No available structure.



ID   14172 GenBank   WP_028004178
Name   t4cp2_SFGR64A_RS32245_pSfreGR64b 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: 91580.27 Da        Isoelectric Point: 5.7694

>WP_028004178.1 MULTISPECIES: conjugal transfer protein TrbE [Sinorhizobium]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESASALERNELSRQINAILSRLG
SGWMIQVEAIRIPTIDYPSENRCHFPDPVTRAIDAERRTHFAREQGHFESKHALILTYRPLESTKTALSN
YIYSDEESRKKSYADTVLFMFKNAVREIEQYLANTLSIRRMETREVSERGGTRLARYDELLQFIRFCVTG
ENHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLMPHTYRWSSRFIF
LDAEEARQTLERTRKKWQQKVRPFFDQLFQTESRSVDQDAVTMVAETEDAIAQASSQLVAYGYYTPVIVL
FDEDSDALQEKAESIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTCNLADLIPLNSVWS
GNPVAPCPFYPANSPPLIQVSSGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYAGAQIFA
FDKGNSLLPLTLAVDGDHYEIGGDNDGEGRVLAFCPLSDLDSDADRAWAAEWIEMLVALQGVRVTPDHRN
AISRQIGLMASAPGRSLSDFLSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLSLGLFQTFEIERVMNMG
ERNLVPVLTCLFHRIEKRLDGSPSLIILDEAWLMLGHPVFRAKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGGAREPGTREFYERLGFNDRQIEIVAGATVKREYYVATPEGRRLFDMALGP
VALSFVGASGKDDLKRVRALKSEHGREWPIHWLKTRGVHDAARLLNFD

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 449740..459249

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SFGR64A_RS32185 (SFGR64A_32180) 445395..446447 - 1053 WP_050577805 thymidylate synthase -
SFGR64A_RS32190 (SFGR64A_32185) 446783..447757 - 975 Protein_407 RHE_PE00001 family protein -
SFGR64A_RS32195 (SFGR64A_32190) 448083..448295 - 213 WP_018097600 helix-turn-helix domain-containing protein -
SFGR64A_RS32200 (SFGR64A_32195) 448503..448826 + 324 WP_028004187 transcriptional repressor TraM -
SFGR64A_RS32205 (SFGR64A_32200) 448830..449534 - 705 WP_028004186 autoinducer binding domain-containing protein -
SFGR64A_RS32210 (SFGR64A_32205) 449740..451041 - 1302 WP_028004185 IncP-type conjugal transfer protein TrbI virB10
SFGR64A_RS32215 (SFGR64A_32210) 451054..451491 - 438 WP_028004184 conjugal transfer protein TrbH -
SFGR64A_RS32220 (SFGR64A_32215) 451494..452306 - 813 WP_028004183 P-type conjugative transfer protein TrbG virB9
SFGR64A_RS32225 (SFGR64A_32220) 452324..452986 - 663 WP_028004182 conjugal transfer protein TrbF virB8
SFGR64A_RS32230 (SFGR64A_32225) 453011..454186 - 1176 WP_028004181 P-type conjugative transfer protein TrbL virB6
SFGR64A_RS32235 (SFGR64A_32230) 454180..454380 - 201 WP_028004180 entry exclusion protein TrbK -
SFGR64A_RS32240 (SFGR64A_32235) 454377..455171 - 795 WP_028004179 P-type conjugative transfer protein TrbJ virB5
SFGR64A_RS32245 (SFGR64A_32240) 455143..457599 - 2457 WP_028004178 conjugal transfer protein TrbE virb4
SFGR64A_RS32250 (SFGR64A_32245) 457610..457909 - 300 WP_040961869 conjugal transfer protein TrbD virB3
SFGR64A_RS32255 (SFGR64A_32250) 457902..458282 - 381 WP_028004176 TrbC/VirB2 family protein virB2
SFGR64A_RS32260 (SFGR64A_32255) 458272..459249 - 978 WP_028004175 P-type conjugative transfer ATPase TrbB virB11
SFGR64A_RS32265 (SFGR64A_32260) 459261..459881 - 621 WP_028004174 acyl-homoserine-lactone synthase -
SFGR64A_RS32270 (SFGR64A_32265) 460255..461472 + 1218 WP_028004173 plasmid partitioning protein RepA -
SFGR64A_RS32275 (SFGR64A_32270) 461469..462506 + 1038 WP_192817398 plasmid partitioning protein RepB -
SFGR64A_RS32280 (SFGR64A_32275) 462742..463992 + 1251 WP_080604313 plasmid replication protein RepC -

Host bacterium

ID   19567 GenBank   NZ_CP137018
Plasmid name   pSfreGR64b Incompatibility group   -
Plasmid size   463992 bp Coordinate of oriT [Strand]   412206..412240 [+]
Host baterium   Sinorhizobium fredii GR64

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD, nodM, fixN, fixO, fixG, mLTONO_5203, nifX, nifN, nifE, nifK, nifD, nifH, nodA, nifQ, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, nodH, nodJ, nodI, nodS, nodC, nodB
Anti-CRISPR   -