Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101167
Name   oriT_pSM153A_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM153A
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPX01000005 (473282..473322 [+], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pSM153A_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1164 GenBank   WP_130676458
Name   traA_ELI24_RS31210_pSM153A_Rh04 insolico UniProt ID   _
Length   1107 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1107 a.a.        Molecular weight: 122847.98 Da        Isoelectric Point: 10.2104

>WP_130676458.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPTGAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDAQLAKDLTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKIAVASPDGNPMRNDAGKIVYELWAGSADDFNAVRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIDRKAEQANARTSAWSPKLERVELQQDRRAENARRIQRRPD
IVLDLITREKSVFDDRDVGKILHRYIDDAALFQNLMMRILQSPQALRLERDRIDFATGVRTPAKYTMREM
IKLEAEMVNRAIWLSDRASHGVREAALEVTFARHARLSDEQRTAIERVAGGERIAAVMGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNRIDARTVFVLDEAGMVSSRQM
AHFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRAQWMRDASLDLARGNVGKA
VDAYRAHGQVRGLDLKAQAVENLIADWNHDYDPSKSSLILAHLRRDVRMLNDMARAKLVERGIVADGFAF
KSEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRLVVALGEGDHRRVVTIEQRFYNKLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLVPILARRNAKETTLDYE
KSSFYGQALRFAEARGLHLMNVARTLARDRLEWTVRQKQKLADLGARLAAIGVKLGRAANAKTSPNLNAK
ESKPMVSGISTFSKSIDQSVEDKLAADPGLKKQWEDVSARFHLVYAQPESAFKAANVEAMLKDQAIAKTT
LAKLAGEPERFGALRGKTGVFANRGDKQDRERAIANVPALARNLERYLRQRAEVERKHETEERAVRRQVS
VDIPALSASAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELDGFAKAVSERFGERTFLGIASKDPSGE
TFKSVTAGMNPAQKAEVEIAWNSMRSIQQLSAHEKTTEALKQAETLRQTRSQGFSLK

  Protein domains


Predicted by InterproScan.

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

(863-959)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-740)

AAA domain (AAA_30)

(387-572)

MobA/MobL family (MobA_MobL)

(17-243)


  Protein structure



No available structure.




T4CP

ID   749 GenBank   WP_130676457
Name   traG_ELI24_RS31195_pSM153A_Rh04 insolico UniProt ID   _
Length   655 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 655 a.a.        Molecular weight: 70988.75 Da        Isoelectric Point: 8.3224

>WP_130676457.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTANKIALFSVPIALMILVTIGMTGTEQWFSEFGKTETGRLILGRTGIALPYIASAATGIIFLFASAGST
NIKLAGWGVVGGSSATVVIAALRETVRLAAIFDHFPAVRSALSYADPATMIGAGAALMSAGFALRVALVG
NAAFARSEPRRIRGRRALHGEAEWMKSTEAGKLFPDTGGIVIGERYRVDKDIAAMQSFRADSVETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVLLDPSNEVAPMVIGHRTNAGRDVHILD
PRTPDTGFNALDWIGLHGRTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDRTEE
DDQTLRQVRKNLSEPEPKLRARLQSIYDNSRSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSESTFSTNDISAGNADVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
ENRFHSPASGDESAMDPETTMKLRG

  Protein domains


Predicted by InterproScan.

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

(164-638)

  Protein structure



No available structure.



ID   750 GenBank   WP_130676472
Name   t4cp2_ELI24_RS31395_pSM153A_Rh04 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 91568.08 Da        Isoelectric Point: 6.2529

>WP_130676472.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVSLRAFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEVSRQINAILSRLG
SGWMIQVEAVRLATVDYASAGKSHFPDRVTQAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YIYSDEDSRKQSYADTVLFIFRNAIREVEQYLANIISIRRMLTRETVERGGARVAHYDELLQFIRFCVTG
ENHPVRVPDIPMYLDWIATAELRHGLAPKVENRFLGVVAIDGLPSESWPGILNSLDAMPLGYRWSSRFIF
LDAEEARVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDALSMVAETEDAIAQASSQLVAYGYYTPVVVL
FESDSERLNEKTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GNPRAPCPFYSPDSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLACGGDHYEIGGDEDTGLSFCPLSELSSEGDRAWASEWIESLVGMQGITITPDHRNAIS
RQIGLMDGASGRSISDFVSGVQMREIKDALRHYTVDGPMGQLLDAETDGLALGLFQTFEIEQVMNMGERN
LVPVLTYLFRRIEKRLTGAPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREPGTRDFYERIGFNERQIEIVATAIPKREYYVASPEGRRLFDMALGPLTL
SFVGASSKDDLKHIRALHGEHGPQWPLHWLQKRGIKDAASLLKDA

  Protein domains


Predicted by InterproScan.

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 503055..512524

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI24_RS31335 (ELI24_31350) 498519..498725 + 207 WP_080642907 hypothetical protein -
ELI24_RS31340 (ELI24_31355) 498845..498997 - 153 Protein_464 aminoglycoside phosphotransferase -
ELI24_RS31345 (ELI24_31360) 499049..501010 - 1962 WP_130676469 elongation factor G -
ELI24_RS31350 (ELI24_31370) 501850..502053 - 204 Protein_466 IS6 family transposase -
ELI24_RS31355 (ELI24_31375) 502319..503029 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELI24_RS31360 (ELI24_31380) 503055..504335 - 1281 WP_130676470 IncP-type conjugal transfer protein TrbI virB10
ELI24_RS31365 (ELI24_31385) 504350..504778 - 429 WP_018068569 conjugal transfer protein TrbH -
ELI24_RS31370 (ELI24_31390) 504781..505602 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELI24_RS31375 (ELI24_31395) 505619..506281 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELI24_RS31380 (ELI24_31400) 506302..507450 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELI24_RS31385 (ELI24_31405) 507477..507674 - 198 WP_130674182 entry exclusion protein TrbK -
ELI24_RS31390 (ELI24_31410) 507671..508471 - 801 WP_130676471 P-type conjugative transfer protein TrbJ virB5
ELI24_RS31395 (ELI24_31415) 508443..510890 - 2448 WP_130676472 conjugal transfer protein TrbE virb4
ELI24_RS31400 (ELI24_31420) 510900..511199 - 300 WP_130676473 conjugal transfer protein TrbD virB3
ELI24_RS31405 (ELI24_31425) 511189..511569 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELI24_RS31410 (ELI24_31430) 511559..512524 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELI24_RS31415 (ELI24_31435) 512538..513164 - 627 WP_018068560 acyl-homoserine-lactone synthase TraI -
ELI24_RS31420 (ELI24_31440) 513529..514746 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELI24_RS31425 (ELI24_31445) 514731..515771 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELI24_RS31430 (ELI24_31450) 516010..517275 + 1266 WP_130676474 plasmid replication protein RepC -

Host bacterium

ID   1611 GenBank   NZ_SIPX01000005
Plasmid name   pSM153A_Rh04 Incompatibility group   -
Plasmid size   529374 bp Coordinate of oriT [Strand]   473282..473322 [+]
Host baterium   Rhizobium ruizarguesonis strain SM153A

Cargo genes

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