Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101184
Name   oriT_pSM82_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM82
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIMH01000005 (22720..22760 [+], 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_pSM82_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1181 GenBank   WP_130726230
Name   traA_ELH30_RS33305_pSM82_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: 122845.94 Da        Isoelectric Point: 10.2104

>WP_130726230.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPTGAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDAQLAKDLTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGAKKIAVASPDGNPMRNDAGKIVYELWAGSADDFNAVRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIDRKAEQANARTSAWSPKLERVELQQDRRAENARRIQRRPD
IVLDLITREKSVFDDRDVGKILHRYIDDAALFQNLMMRILQSPQALRLERDRIDFATGVRTPAKYTTREM
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)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-740)

AAA domain (AAA_30)

(387-572)


  Protein structure



No available structure.




T4CP

ID   780 GenBank   WP_024323836
Name   traG_ELH30_RS33290_pSM82_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: 71050.85 Da        Isoelectric Point: 8.7825

>WP_024323836.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTANKIALFSVPIALMILVTIGMTGTEQWFSEFGKTETGRLILGRTGIALPYIASAATGIIFLFASAGST
NIKLAGWGVVGGSSATVVIAALRETVRLAAIFDHFPAVRSALSYADPATMIGAGAALMSAGFALRVALVG
NAAFARSEPRRIRGRRALHGEAEWMKSTEAGKLFPDTGGIVIGERYRVDKDIAAKQSFRADSVETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVLLDPSNEVAPMVIGHRTNAGRDVHILD
PRTPDTGFNALDWIGLHGRTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDRTEE
DDQTLRQVRKNLSEPEPKLRARLQSIYDNSRSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSESTFSTNDISAGNADVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
ENRFHSPARGDESAMDPETPMKLRG

  Protein domains


Predicted by InterproScan.

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

(164-637)

  Protein structure



No available structure.



ID   781 GenBank   WP_024323902
Name   t4cp2_ELH30_RS33495_pSM82_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: 91549.04 Da        Isoelectric Point: 6.2219

>WP_024323902.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVSLRAFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEVSRQINAILSRLG
SGWMIQVEAVRLATVDYASAGKSHFPDRVTQAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YIYSDEDSRKQSYADTVLFIFRNAIREVEQYLANIISIRRMLTRETVERGGARVAHYDELLQFIRFCVTG
ENHPVRVPDIPMYLDWIATAELRHGLAPKVENRFLGVVAIDGLPSESWPGILNSLDAMPLGYRWSSRFIF
LDAEEARVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDALSMVAETEDAIAQASSQLVAYGYYTPVVVL
FESDSERLNEKTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GNPRAPCPFYSPDSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLACGGDHYEIGGDEDTGLSFCPLSELSSEGDRAWASEWIESLVGMQGITITPDHRNAIS
RQIGLMDGASGRSISDFVSGVQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQTFEIEQVMNMGERN
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: 52475..61868

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH30_RS33435 (ELH30_33440) 47939..48145 + 207 WP_080642907 hypothetical protein -
ELH30_RS33440 (ELH30_33445) 48265..48417 - 153 Protein_42 aminoglycoside phosphotransferase -
ELH30_RS33445 (ELH30_33450) 48469..50430 - 1962 WP_130726237 elongation factor G -
ELH30_RS33450 (ELH30_33455) 51270..51473 - 204 Protein_44 IS6 family transposase -
ELH30_RS33455 (ELH30_33460) 51739..52449 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELH30_RS33460 (ELH30_33465) 52475..53755 - 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH30_RS33465 (ELH30_33470) 53770..54198 - 429 WP_018068569 conjugal transfer protein TrbH -
ELH30_RS33470 (ELH30_33475) 54201..55022 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH30_RS33475 (ELH30_33480) 55039..55701 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH30_RS33480 (ELH30_33485) 55722..56794 - 1073 Protein_50 P-type conjugative transfer protein TrbL -
ELH30_RS33485 (ELH30_33490) 56821..57018 - 198 WP_130726238 entry exclusion protein TrbK -
ELH30_RS33490 (ELH30_33495) 57015..57815 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH30_RS33495 (ELH30_33500) 57787..60234 - 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH30_RS33500 (ELH30_33505) 60244..60543 - 300 WP_130726239 conjugal transfer protein TrbD virB3
ELH30_RS33505 (ELH30_33510) 60533..60913 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH30_RS33510 (ELH30_33515) 60903..61868 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH30_RS33515 (ELH30_33520) 61882..62508 - 627 WP_018068560 acyl-homoserine-lactone synthase TraI -
ELH30_RS33520 (ELH30_33525) 62873..64090 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELH30_RS33525 (ELH30_33530) 64075..65115 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELH30_RS33530 (ELH30_33535) 65354..66619 + 1266 WP_130676474 plasmid replication protein RepC -

Host bacterium

ID   1628 GenBank   NZ_SIMH01000005
Plasmid name   pSM82_Rh04 Incompatibility group   -
Plasmid size   203410 bp Coordinate of oriT [Strand]   22720..22760 [+]
Host baterium   Rhizobium ruizarguesonis strain SM82

Cargo genes

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