Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101146
Name   oriT_pSM81_Rh15 in_silico
Organism   Rhizobium ruizarguesonis strain SM81
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIMG01000006 (124509..124550 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      22..27, 31..36  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 42 nt

>oriT_pSM81_Rh15
GGCTCCAAGGGCGCAATTATACGTCGCGATGCGACGCGTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1143 GenBank   WP_130825053
Name   traA_ELH29_RS34065_pSM81_Rh15 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123283.69 Da        Isoelectric Point: 9.7679

>WP_130825053.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPAGAPSWVRSLTADR
SVAGASEAFWNKVEAFEKRADAQLARDLTIALPLELSAEQNIALVRDFVEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLSEDGFGSKKVPVIGDDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRVDGRSYEKQGIELEPTIHLGEGAKAIERKAEQQGVRPELERIELNEQRRSENARRILKNPLIVLDL
ITREKSVFDERDVAKVVHRYIDDPAVFQQLMIRIILNPDVLRLQRDSVDFATGNKQPARYSTRAMIRLEA
TMARQARWLSAKETQAVSEAVLGATFLRHERLSDEQKAAIERITGPHRIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIESRTLASWELRWNRGRDVLDDKTIFVMDEAGMVASKQMAGFVD
TVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALSAYG
ANVKITGERLKAEAVERLIAAWNQDYDQSKTTLILAHLRRDVRVLNVMAREKLVERGVVGEGKIFKTADG
ERRFDAGDQIVFLKNEGSLGLKNGMIGHVVEAQPNRIVAVVGEGDYRRQVIVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFSFNGGLAKVLSRKNAKETTLDYERGQLY
REALRFAENRGLHIVQVARTLVRDQLDWTLRQKARLVDLGQRLAAFAARLGLAQSLNIQTMKEAAPMVEG
IKTFSGSAADTVGDKLGADPTLKRQWEEVSARFSYVFADPETAFRAMNFDVVLVDKQAAKLILQKLEGEP
ASIGPLRGKTGILATKSERESRRVAEVNVPPLKRDLEQYLRMRETATMRHQADEQALRQRVSIEIPALSP
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNRAVTERFGERTLLSNAAQEPSGTLYEKLSEG
MKPEQKEQLKQAWPVMRTAQQLGAHERTIQSLRQAEEQRLTQRQAPVLKQ

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(855-951)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

AAA domain (AAA_30)

(382-566)


  Protein structure



No available structure.




T4CP

ID   708 GenBank   WP_130821130
Name   t4cp2_ELH29_RS33620_pSM81_Rh15 insolico UniProt ID   _
Length   826 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 826 a.a.        Molecular weight: 92474.43 Da        Isoelectric Point: 5.9517

>WP_130821130.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKPFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVATEDYPTDQASHFPDPVTRAIDAERRSHFQKERGHYESRHALILTWRPPEPRRSGLTR
YVYSDIGSRSATYADKALETFLTSIREVEQYIANVVSIRRMTTRETSERGGYRMARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNTLDRMPLTYRWSSRFVF
LDAEEARARLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FDEDHHRLQENCEAIRRLVQAEGFGARIETLNATDAFIGSLPGVSYANIREPLINTRNLADLIPLNSIWS
GSPVAPCPFYPPASPPLMQVATGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYAEAQVFA
FDKGGSMLPLTLGLAGNHYNIGGEQPDRAEEGRAGEARGLSFCPLAELAADGDLAWASEWIEMLVALQGV
TVTPDYRNAISRQLALMAKSRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGAFQCFE
IEELMNMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPAFRDKIREWLKVLRKANCAVVLAT
QSISDAERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKRDYYVVSPEGRR
LFDMALGPVALSFVGASGKEDLKRIRALHLEHGANWPLHWLQQRGIAHAETLLPIE

  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.



ID   709 GenBank   WP_130821159
Name   traG_ELH29_RS34050_pSM81_Rh15 insolico UniProt ID   _
Length   636 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 636 a.a.        Molecular weight: 68350.39 Da        Isoelectric Point: 9.4956

>WP_130821159.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTANRLLLAILPAAIMIAAMVITSGMEHRLAALGTNAQAKLMLGRAGLALPYVVVAAIGGMALSAANGSA
NIKAVGLSVIVGNGMAIAVAILRETIRLTGFAANIPAEQSVLTYIDPATMLGTIAAFVSGVFALRVALRG
NAAFATASPKRIGGRRAVHGGADWMKLPDAAKLFPEHGGIVIGERYRVDRDSVAAMPFRADEAQSWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVSEHRRQAGRKVIVLD
PTATDVGFNALDWIGRHGNTKEEDIVAVATWIMTDNARMASARDDFFRASAMQLLTALIADVCLSGHTDA
KDQTLRRVRANLSEPEPQLRARLTKIYEGSASDFVKENVAVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGNSFSTDDLADGETDIFIALDLKVLEAHPGLARVVIGSFLNAIYNRNGDVKGRTLFLLDEVARLGY
LRILETARDAGRKYAITLAMIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLSRRPLILPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACVG
DNRFQR

  Protein domains


Predicted by InterproScan.

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

(163-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 22590..32277

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH29_RS33570 (ELH29_33565) 19267..20331 + 1065 WP_130821138 aldo/keto reductase -
ELH29_RS33575 (ELH29_33570) 20446..21624 + 1179 WP_245502936 LacI family DNA-binding transcriptional regulator -
ELH29_RS33580 (ELH29_33575) 21666..22442 + 777 WP_130821137 SDR family NAD(P)-dependent oxidoreductase -
ELH29_RS33585 (ELH29_33580) 22590..23906 - 1317 WP_130825051 IncP-type conjugal transfer protein TrbI virB10
ELH29_RS33590 (ELH29_33585) 23914..24390 - 477 WP_130821135 conjugal transfer protein TrbH -
ELH29_RS33595 (ELH29_33590) 24390..25241 - 852 WP_130821194 P-type conjugative transfer protein TrbG virB9
ELH29_RS33600 (ELH29_33595) 25259..25921 - 663 WP_130821134 conjugal transfer protein TrbF virB8
ELH29_RS33605 (ELH29_33600) 25939..27129 - 1191 WP_130821133 P-type conjugative transfer protein TrbL virB6
ELH29_RS33610 (ELH29_33605) 27123..27350 - 228 WP_130821132 entry exclusion protein TrbK -
ELH29_RS33615 (ELH29_33610) 27347..28156 - 810 WP_130821131 P-type conjugative transfer protein TrbJ virB5
ELH29_RS33620 (ELH29_33615) 28128..30608 - 2481 WP_130821130 conjugal transfer protein TrbE virb4
ELH29_RS33625 (ELH29_33620) 30620..30919 - 300 WP_130821129 conjugal transfer protein TrbD virB3
ELH29_RS33630 (ELH29_33625) 30912..31316 - 405 WP_130821128 conjugal transfer pilin TrbC virB2
ELH29_RS33635 (ELH29_33630) 31306..32277 - 972 WP_130821127 P-type conjugative transfer ATPase TrbB virB11
ELH29_RS33640 (ELH29_33635) 32274..32912 - 639 WP_130821126 acyl-homoserine-lactone synthase TraI -
ELH29_RS33645 (ELH29_33640) 33290..34480 + 1191 WP_130821125 plasmid partitioning protein RepA -
ELH29_RS33650 (ELH29_33645) 34565..35560 + 996 WP_130821124 plasmid partitioning protein RepB -
ELH29_RS33655 (ELH29_33650) 35717..36961 + 1245 WP_130821123 plasmid replication protein RepC -

Host bacterium

ID   1590 GenBank   NZ_SIMG01000006
Plasmid name   pSM81_Rh15 Incompatibility group   -
Plasmid size   131951 bp Coordinate of oriT [Strand]   124509..124550 [+]
Host baterium   Rhizobium ruizarguesonis strain SM81

Cargo genes

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