Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101170
Name   oriT_pSM88_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM88
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIMN01000005 (70079..70119 [-], 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_pSM88_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1167 GenBank   WP_130674195
Name   traA_ELH36_RS37030_pSM88_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   755 GenBank   WP_024323902
Name   t4cp2_ELH36_RS36840_pSM88_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   756 GenBank   WP_024323836
Name   traG_ELH36_RS37045_pSM88_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: 30870..40339

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH36_RS36805 (ELH36_36805) 26119..27384 - 1266 WP_130674179 plasmid replication protein RepC -
ELH36_RS36810 (ELH36_36810) 27623..28663 - 1041 WP_027689819 plasmid partitioning protein RepB -
ELH36_RS36815 (ELH36_36815) 28648..29865 - 1218 WP_075225817 plasmid partitioning protein RepA -
ELH36_RS36820 (ELH36_36820) 30230..30856 + 627 WP_130674180 acyl-homoserine-lactone synthase TraI -
ELH36_RS36825 (ELH36_36825) 30870..31835 + 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH36_RS36830 (ELH36_36830) 31825..32205 + 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH36_RS36835 (ELH36_36835) 32195..32494 + 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH36_RS36840 (ELH36_36840) 32504..34951 + 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH36_RS36845 (ELH36_36845) 34923..35723 + 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH36_RS36850 (ELH36_36850) 35765..35917 + 153 WP_245278470 DUF2749 domain-containing protein -
ELH36_RS36855 (ELH36_36855) 35944..37092 + 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH36_RS36860 (ELH36_36860) 37113..37775 + 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH36_RS36865 (ELH36_36865) 37792..38613 + 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH36_RS36870 (ELH36_36870) 38616..39044 + 429 WP_018068569 conjugal transfer protein TrbH -
ELH36_RS36875 (ELH36_36875) 39059..40339 + 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH36_RS36880 (ELH36_36880) 40365..41075 - 711 WP_024323909 autoinducer binding domain-containing protein -
ELH36_RS36885 (ELH36_36885) 41341..41544 + 204 Protein_45 IS6 family transposase -
ELH36_RS36890 (ELH36_36890) 42384..44345 + 1962 WP_130674184 elongation factor G -
ELH36_RS36895 (ELH36_36895) 44397..44549 + 153 Protein_47 aminoglycoside phosphotransferase -
ELH36_RS36900 (ELH36_36900) 44669..44875 - 207 WP_080642907 hypothetical protein -

Host bacterium

ID   1614 GenBank   NZ_SIMN01000005
Plasmid name   pSM88_Rh04 Incompatibility group   -
Plasmid size   88520 bp Coordinate of oriT [Strand]   70079..70119 [-]
Host baterium   Rhizobium ruizarguesonis strain SM88

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodA, nodD
Anti-CRISPR   -