Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102557
Name   oriT_pSM27_Rh04 in_silico
Organism   Rhizobium leguminosarum strain SM27
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKL01000005 (57676..57716 [-], 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_pSM27_Rh04
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1908 GenBank   WP_130801322
Name   traA_ELG82_RS32300_pSM27_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: 122944.16 Da        Isoelectric Point: 10.2420

>WP_130801322.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPVWAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDAQLAKDVTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKIAVASPDGNPMRNGDGKIVYELWAGSADDFNAIRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIDRKAEQANARTSAWSPKLERVELQEDRRAENARRMQRRPE
IVLDLITREKSVFDERDVAKILHRYIDDAALFQNLMVRILQSPEALRLQRDRIDFATATRTPAKYTTREM
IRLEAEMVNRAIWLSGRASHGVREAVLEVTFARHARLSDEQRTAIERVAGGERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKQAGIQSRTLSSWELRWNQGRNQIDARTVFVLDEAGMVSSRQM
AHFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRTQWMRDASLDLARGNVGKA
VDDYRAHGHVRGLDLKAQAVENLIADWNHDYDPSKSSLILAHLRRDVRMLNDMARAKLVDRGIVVDGFAF
TTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRLVVALGEGDHRRLVTIEQRFYNKLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILARRKAKETTLDYE
KSSLYGQALRFAEARGLHLMNVARTVARDRLEWTVRQKQKLADLGARLAAIGVKLGRAASAKTSPNPNAK
ESKPMVSGISTFPKSIDQSVEDKLAADPGLKKQWEDVSTRFHLVYAQPESAFKAVNVEAMLKDQAIAKTT
LAKLAGEPERFGALRGKTGVFANRGDKQDRERAIANVPALARNLERYLRQRAEVERKHEREERAVRRQVS
VDIPALSASAKQTLERVRDAIDRNDLSAGLEYALADKMVKAELDGFAKAVSERFGERTFLGIASKDPSGV
TFKSVTAGMNPAQKAEVQIAWNSMRSIQQLSADEKTSEALKQAETLRQARSQGLSLK

  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   1524 GenBank   WP_130801259
Name   t4cp2_ELG82_RS32065_pSM27_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: 91388.01 Da        Isoelectric Point: 6.1930

>WP_130801259.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVSLRAFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEVSRQINAILSRLG
SGWMIQVEAVRLATVDYASAGKSHFPDRVTLAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YIYSDEDSRKQSYADTVLFIFRNAIREVEQYLANIISIRRMLTRETAERGGVRVAHYDELLQFIRFCVTG
ENHPVRVPDIPMYLDWIATAELRHGLAPKVENRFLGVVAIDGLPSESWPGILNSLDAMPLGYRWSSRFIF
LDAEEARVRLERTRKKWLQKVRPFFDQLFQTQSRSVDQDAISMVAETEDAIAQASSQLVAYGYYTPVVVL
FDNDAERLNEKTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GNPQAPCPFYPPGSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLACGGDHYEIGGDEDAGLSFCPLSELSSDGDRAWASEWIESLVAMQGITITPDHRNAIS
RQIGLMDGAPGRSISDFVSGIQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQTFEIEQVMNMGERN
LVPVLTYLFRRIEKRLTGAPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREAGTRDFYERIGFNERQIEIVATAIPKREYYVASPEGRRLFDMALGPLAL
SFVGASSKDDLKHIRALHGEHGPEWPLHWLHKRGIKDAASLLKDA

  Protein domains


Predicted by InterproScan.

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

(191-400)

  Protein structure



No available structure.



ID   1525 GenBank   WP_130801328
Name   traG_ELG82_RS32315_pSM27_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: 71008.84 Da        Isoelectric Point: 9.0366

>WP_130801328.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTANKIALVSVPIALMILVTIGMTGIERWFSEFGKTETARLTLGRTGIALPYIASAATGIIFLFASAGST
NIKLAGWGVVGGSSATIVIAALRETVRLAAIFDHFPAVRSALSYADPATMIGAGAALTSAGFALRVARLG
NVAFARSEPRRIRGRRALHGEAEWMKSTEAGKLFPDTGGIVIGERYRVDQDMTAKQSFRPDSVETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVLLDPSNEVAPMVIGHRTNAGRDVHILD
PRTCDTGFNALDWIGLHGRTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGRTEE
GDQTLRQVRKNLSEPEPKLRARLQSIYDNSRSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSESTFSTNDISAGNADVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
ENRFHSPASGDESAMDPETPMKLRG

  Protein domains


Predicted by InterproScan.

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

(164-638)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12763..22142

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG82_RS32030 (ELG82_32035) 8012..9277 - 1266 WP_130801245 plasmid replication protein RepC -
ELG82_RS32035 (ELG82_32040) 9516..10556 - 1041 WP_130801247 plasmid partitioning protein RepB -
ELG82_RS32040 (ELG82_32045) 10541..11758 - 1218 WP_130801249 plasmid partitioning protein RepA -
ELG82_RS32045 (ELG82_32050) 12123..12749 + 627 WP_130801251 acyl-homoserine-lactone synthase TraI -
ELG82_RS32050 (ELG82_32055) 12763..13728 + 966 WP_130801253 P-type conjugative transfer ATPase TrbB virB11
ELG82_RS32055 (ELG82_32060) 13718..14098 + 381 WP_130801255 TrbC/VirB2 family protein virB2
ELG82_RS32060 (ELG82_32065) 14088..14387 + 300 WP_130801257 conjugal transfer protein TrbD virB3
ELG82_RS32065 (ELG82_32070) 14397..16844 + 2448 WP_130801259 conjugal transfer protein TrbE virb4
ELG82_RS32070 (ELG82_32075) 16816..17616 + 801 WP_130801261 P-type conjugative transfer protein TrbJ virB5
ELG82_RS32075 (ELG82_32080) 17748..18896 + 1149 WP_130801330 P-type conjugative transfer protein TrbL virB6
ELG82_RS32080 (ELG82_32085) 18916..19578 + 663 WP_130801263 conjugal transfer protein TrbF virB8
ELG82_RS32085 (ELG82_32090) 19595..20416 + 822 WP_130801265 P-type conjugative transfer protein TrbG virB9
ELG82_RS32090 (ELG82_32095) 20419..20847 + 429 WP_130801267 conjugal transfer protein TrbH -
ELG82_RS32095 (ELG82_32100) 20862..22142 + 1281 WP_130801269 IncP-type conjugal transfer protein TrbI virB10
ELG82_RS32100 (ELG82_32105) 22168..22878 - 711 WP_130801270 autoinducer binding domain-containing protein -
ELG82_RS32105 (ELG82_32110) 23137..23343 + 207 Protein_23 IS6 family transposase -
ELG82_RS32110 (ELG82_32115) 24031..25992 + 1962 WP_130801271 elongation factor G -
ELG82_RS32115 (ELG82_32120) 26406..26825 + 420 WP_245505619 lysophospholipase -

Host bacterium

ID   3001 GenBank   NZ_SIKL01000005
Plasmid name   pSM27_Rh04 Incompatibility group   -
Plasmid size   62563 bp Coordinate of oriT [Strand]   57676..57716 [-]
Host baterium   Rhizobium leguminosarum strain SM27

Cargo genes

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