Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101161
Name   oriT_pSM92_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM92
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIMR01000005 (27986..28026 [+], 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_pSM92_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1158 GenBank   WP_130674195
Name   traA_ELH40_RS35175_pSM92_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: 122861.94 Da        Isoelectric Point: 10.2104

>WP_130674195.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPTGAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDSQLAKDLTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDVPGN
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)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-740)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-572)


  Protein structure



No available structure.




T4CP

ID   737 GenBank   WP_024323836
Name   traG_ELH40_RS35160_pSM92_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   738 GenBank   WP_024323902
Name   t4cp2_ELH40_RS35365_pSM92_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: 57743..67212

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH40_RS35305 (ELH40_35310) 53208..53414 + 207 WP_080642907 hypothetical protein -
ELH40_RS35310 (ELH40_35315) 53534..53686 - 153 Protein_54 aminoglycoside phosphotransferase -
ELH40_RS35315 (ELH40_35320) 53738..55699 - 1962 WP_130720409 elongation factor G -
ELH40_RS35320 (ELH40_35325) 56539..56742 - 204 Protein_56 IS6 family transposase -
ELH40_RS35325 (ELH40_35330) 57008..57604 + 597 WP_245497758 autoinducer binding domain-containing protein -
ELH40_RS40740 57583..57717 + 135 WP_245497759 helix-turn-helix transcriptional regulator -
ELH40_RS35330 (ELH40_35335) 57743..59023 - 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH40_RS35335 (ELH40_35340) 59038..59466 - 429 WP_018068569 conjugal transfer protein TrbH -
ELH40_RS35340 (ELH40_35345) 59469..60290 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH40_RS35345 (ELH40_35350) 60307..60969 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH40_RS35350 (ELH40_35355) 60990..62138 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH40_RS35355 (ELH40_35360) 62165..62362 - 198 WP_130674182 entry exclusion protein TrbK -
ELH40_RS35360 (ELH40_35365) 62359..63159 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH40_RS35365 (ELH40_35370) 63131..65578 - 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH40_RS35370 (ELH40_35375) 65588..65887 - 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH40_RS35375 (ELH40_35380) 65877..66257 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH40_RS35380 (ELH40_35385) 66247..67212 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH40_RS35385 (ELH40_35390) 67226..67852 - 627 WP_130674180 acyl-homoserine-lactone synthase TraI -
ELH40_RS35390 (ELH40_35395) 68217..69434 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELH40_RS35395 (ELH40_35400) 69419..70459 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELH40_RS35400 (ELH40_35405) 70698..71963 + 1266 WP_130676474 plasmid replication protein RepC -

Host bacterium

ID   1605 GenBank   NZ_SIMR01000005
Plasmid name   pSM92_Rh04 Incompatibility group   -
Plasmid size   78448 bp Coordinate of oriT [Strand]   27986..28026 [+]
Host baterium   Rhizobium ruizarguesonis strain SM92

Cargo genes

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