Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101180
Name   oriT_pSM120_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM120
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SINT01000005 (23486..23526 [+], 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_pSM120_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1177 GenBank   WP_130674195
Name   traA_ELH68_RS33305_pSM120_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   773 GenBank   WP_024323836
Name   traG_ELH68_RS33290_pSM120_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   774 GenBank   WP_024323902
Name   t4cp2_ELH68_RS33495_pSM120_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: 53244..62713

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH68_RS33435 (ELH68_33430) 48708..48914 + 207 WP_080642907 hypothetical protein -
ELH68_RS33440 (ELH68_33435) 49034..49186 - 153 Protein_45 aminoglycoside phosphotransferase -
ELH68_RS33445 (ELH68_33440) 49238..51199 - 1962 WP_130720409 elongation factor G -
ELH68_RS33450 (ELH68_33445) 52039..52242 - 204 Protein_47 IS6 family transposase -
ELH68_RS33455 (ELH68_33450) 52508..53218 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELH68_RS33460 (ELH68_33455) 53244..54524 - 1281 WP_130720410 IncP-type conjugal transfer protein TrbI virB10
ELH68_RS33465 (ELH68_33460) 54539..54967 - 429 WP_018068569 conjugal transfer protein TrbH -
ELH68_RS33470 (ELH68_33465) 54970..55791 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH68_RS33475 (ELH68_33470) 55808..56470 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH68_RS33480 (ELH68_33475) 56491..57639 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH68_RS33485 (ELH68_33480) 57666..57863 - 198 WP_130674182 entry exclusion protein TrbK -
ELH68_RS33490 (ELH68_33485) 57860..58660 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH68_RS33495 (ELH68_33490) 58632..61079 - 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH68_RS33500 (ELH68_33495) 61089..61388 - 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH68_RS33505 (ELH68_33500) 61378..61758 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH68_RS33510 (ELH68_33505) 61748..62713 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH68_RS33515 (ELH68_33510) 62727..63353 - 627 WP_130674180 acyl-homoserine-lactone synthase TraI -
ELH68_RS33520 (ELH68_33515) 63718..64935 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELH68_RS33525 (ELH68_33520) 64920..65960 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELH68_RS33530 (ELH68_33525) 66199..67464 + 1266 WP_130676474 plasmid replication protein RepC -

Host bacterium

ID   1624 GenBank   NZ_SINT01000005
Plasmid name   pSM120_Rh04 Incompatibility group   -
Plasmid size   124533 bp Coordinate of oriT [Strand]   23486..23526 [+]
Host baterium   Rhizobium ruizarguesonis strain SM120

Cargo genes

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