Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102542
Name   oriT_pSM15_Rh04 in_silico
Organism   Rhizobium leguminosarum strain SM15
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKB01000005 (4848..4888 [+], 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_pSM15_Rh04
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1893 GenBank   WP_130801322
Name   traA_ELG72_RS33805_pSM15_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   1499 GenBank   WP_130801328
Name   traG_ELG72_RS33790_pSM15_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.



ID   1500 GenBank   WP_130801259
Name   t4cp2_ELG72_RS34040_pSM15_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40423..49802

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG72_RS33990 (ELG72_33990) 35740..36159 - 420 WP_245505619 lysophospholipase -
ELG72_RS33995 (ELG72_33995) 36573..38534 - 1962 WP_130805246 elongation factor G -
ELG72_RS34000 (ELG72_34000) 39222..39428 - 207 Protein_43 IS6 family transposase -
ELG72_RS34005 (ELG72_34005) 39687..40397 + 711 WP_130801270 autoinducer binding domain-containing protein -
ELG72_RS34010 (ELG72_34010) 40423..41703 - 1281 WP_130801269 IncP-type conjugal transfer protein TrbI virB10
ELG72_RS34015 (ELG72_34015) 41718..42146 - 429 WP_130801267 conjugal transfer protein TrbH -
ELG72_RS34020 (ELG72_34020) 42149..42970 - 822 WP_130801265 P-type conjugative transfer protein TrbG virB9
ELG72_RS34025 (ELG72_34025) 42987..43649 - 663 WP_130801263 conjugal transfer protein TrbF virB8
ELG72_RS34030 (ELG72_34030) 43669..44817 - 1149 WP_130801330 P-type conjugative transfer protein TrbL virB6
ELG72_RS34035 (ELG72_34035) 44949..45749 - 801 WP_130805247 P-type conjugative transfer protein TrbJ virB5
ELG72_RS34040 (ELG72_34040) 45721..48168 - 2448 WP_130801259 conjugal transfer protein TrbE virb4
ELG72_RS34045 (ELG72_34045) 48178..48477 - 300 WP_130801257 conjugal transfer protein TrbD virB3
ELG72_RS34050 (ELG72_34050) 48467..48847 - 381 WP_130801255 TrbC/VirB2 family protein virB2
ELG72_RS34055 (ELG72_34055) 48837..49802 - 966 WP_130801253 P-type conjugative transfer ATPase TrbB virB11
ELG72_RS34060 (ELG72_34060) 49816..50442 - 627 WP_130801251 acyl-homoserine-lactone synthase TraI -
ELG72_RS34065 (ELG72_34065) 50807..52024 + 1218 WP_130801249 plasmid partitioning protein RepA -
ELG72_RS34070 (ELG72_34070) 52009..53049 + 1041 WP_130801247 plasmid partitioning protein RepB -
ELG72_RS34075 (ELG72_34075) 53288..54553 + 1266 WP_130801245 plasmid replication protein RepC -

Host bacterium

ID   2986 GenBank   NZ_SIKB01000005
Plasmid name   pSM15_Rh04 Incompatibility group   -
Plasmid size   60810 bp Coordinate of oriT [Strand]   4848..4888 [+]
Host baterium   Rhizobium leguminosarum strain SM15

Cargo genes

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