Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101158
Name   oriT_pSM113_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM113
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SINM01000005 (104326..104366 [-], 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_pSM113_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1155 GenBank   WP_130816657
Name   traA_ELH61_RS28780_pSM113_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: 122891.97 Da        Isoelectric Point: 10.1838

>WP_130816657.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPTGAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDSQLAKDLTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGAKKIAVASPDGNPMRNDAGKIVYELWAGSADDFNAVRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIDRKAEQANARTSAWSPKLERVELQQDRRAENARRIQRRPD
IVLDLITREKSVFDDRDVGKILHRYIDDAALFQNLMMRILQSPQALRLERDRIDFATGVRTPAKYTTREM
IKLEAEMVNRAIWLSDRASHGVREAALEVTFARHARLSDEQRTAIERVAGGERIAAVMGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNRIDARTVFVLDEAGMVSSRQM
AHFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRAQWMRDASLDLARGNVGKA
VDAYRAHGQVRGLDLKAQAVENLIADWNHDYDPSKSSLILAHLRRDVRMLNDMARAKLVERGIVADGFAF
KSEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRLVVALGEGDHRRVVTIEQRFYNKLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLVPILARRNAKETTLDYE
KSSFYGQALRFAEARGLHLMNVARTLARDRLEWTVRQKQKLADLGARLAAIGVKLGRAANAKTSPNLNAK
ESKPMVSGISTFSKSIDQSVEDKLAADPGLKKQWEDVSARFHLVYAQPESAFKAANVEAMLKDQAIAKTT
LAKLAGEPERFGALRGKTGVFANWGDKQDRERAIANVPALARNLERYLRQRAEVERKHETEERAVRRQVS
VDIPALSASAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELDGFAKAVSERFGERTFLGIASKDPSGE
TFKSVTAGMNPAQKAEVEIAWNSMRSIQQLSAHEKTTEALKQAETLRQTRSQGFSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-740)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-572)

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

(863-959)


  Protein structure



No available structure.




T4CP

ID   731 GenBank   WP_024323902
Name   t4cp2_ELH61_RS28590_pSM113_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.



ID   732 GenBank   WP_024323836
Name   traG_ELH61_RS28795_pSM113_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 65139..74608

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH61_RS28555 (ELH61_28555) 60388..61653 - 1266 WP_130676474 plasmid replication protein RepC -
ELH61_RS28560 (ELH61_28560) 61892..62932 - 1041 WP_027689819 plasmid partitioning protein RepB -
ELH61_RS28565 (ELH61_28565) 62917..64134 - 1218 WP_075225817 plasmid partitioning protein RepA -
ELH61_RS28570 (ELH61_28570) 64499..65125 + 627 WP_130674180 acyl-homoserine-lactone synthase TraI -
ELH61_RS28575 (ELH61_28575) 65139..66104 + 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH61_RS28580 (ELH61_28580) 66094..66474 + 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH61_RS28585 (ELH61_28585) 66464..66763 + 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH61_RS28590 (ELH61_28590) 66773..69220 + 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH61_RS28595 (ELH61_28595) 69192..69992 + 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH61_RS28600 (ELH61_28600) 70034..70186 + 153 WP_245278470 DUF2749 domain-containing protein -
ELH61_RS28605 (ELH61_28605) 70213..71361 + 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH61_RS28610 (ELH61_28610) 71382..72044 + 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH61_RS28615 (ELH61_28615) 72061..72882 + 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH61_RS28620 (ELH61_28620) 72885..73313 + 429 WP_018068569 conjugal transfer protein TrbH -
ELH61_RS28625 (ELH61_28625) 73328..74608 + 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH61_RS28630 (ELH61_28630) 74634..75344 - 711 WP_024323909 autoinducer binding domain-containing protein -
ELH61_RS28635 (ELH61_28635) 75610..75813 + 204 Protein_77 IS6 family transposase -
ELH61_RS28640 (ELH61_28640) 76653..78614 + 1962 WP_130720409 elongation factor G -
ELH61_RS28645 (ELH61_28645) 78666..78818 + 153 Protein_79 aminoglycoside phosphotransferase -
ELH61_RS28650 (ELH61_28650) 78938..79144 - 207 WP_080642907 hypothetical protein -

Host bacterium

ID   1602 GenBank   NZ_SINM01000005
Plasmid name   pSM113_Rh04 Incompatibility group   -
Plasmid size   132690 bp Coordinate of oriT [Strand]   104326..104366 [-]
Host baterium   Rhizobium ruizarguesonis strain SM113

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifT, nodJ, nodI, nodA, nodD
Anti-CRISPR   -