Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101189
Name   oriT_pSM167_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM167
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQW01000005 (17139..17179 [+], 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_pSM167_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1186 GenBank   WP_130726230
Name   traA_ELI49_RS30485_pSM167_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   790 GenBank   WP_024323836
Name   traG_ELI49_RS30470_pSM167_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   791 GenBank   WP_024323902
Name   t4cp2_ELI49_RS30680_pSM167_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: 48261..57730

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI49_RS30620 (ELI49_30630) 43725..43931 + 207 WP_080642907 hypothetical protein -
ELI49_RS30625 (ELI49_30635) 44051..44203 - 153 Protein_44 aminoglycoside phosphotransferase -
ELI49_RS30630 (ELI49_30640) 44255..46216 - 1962 WP_130726237 elongation factor G -
ELI49_RS30635 (ELI49_30645) 47056..47259 - 204 Protein_46 IS6 family transposase -
ELI49_RS30640 (ELI49_30650) 47525..48235 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELI49_RS30645 (ELI49_30655) 48261..49541 - 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELI49_RS30650 (ELI49_30660) 49556..49984 - 429 WP_018068569 conjugal transfer protein TrbH -
ELI49_RS30655 (ELI49_30665) 49987..50808 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELI49_RS30660 (ELI49_30670) 50825..51487 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELI49_RS30665 (ELI49_30675) 51508..52656 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELI49_RS30670 (ELI49_30680) 52683..52880 - 198 WP_130726238 entry exclusion protein TrbK -
ELI49_RS30675 (ELI49_30685) 52877..53677 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELI49_RS30680 (ELI49_30690) 53649..56096 - 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELI49_RS30685 (ELI49_30695) 56106..56405 - 300 WP_130726239 conjugal transfer protein TrbD virB3
ELI49_RS30690 (ELI49_30700) 56395..56775 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELI49_RS30695 (ELI49_30705) 56765..57730 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELI49_RS30700 (ELI49_30710) 57744..58370 - 627 WP_018068560 acyl-homoserine-lactone synthase TraI -
ELI49_RS30705 (ELI49_30715) 58735..59952 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELI49_RS30710 (ELI49_30720) 59937..60977 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELI49_RS30715 (ELI49_30725) 61216..62481 + 1266 WP_130676474 plasmid replication protein RepC -

Host bacterium

ID   1633 GenBank   NZ_SIQW01000005
Plasmid name   pSM167_Rh04 Incompatibility group   -
Plasmid size   68189 bp Coordinate of oriT [Strand]   17139..17179 [+]
Host baterium   Rhizobium ruizarguesonis strain SM167

Cargo genes

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