Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101195
Name   oriT_pSM119_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM119
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SINS01000005 (39492..39532 [+], 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_pSM119_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1191 GenBank   WP_130674195
Name   traA_ELH67_RS35415_pSM119_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   798 GenBank   WP_024323836
Name   traG_ELH67_RS35400_pSM119_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   799 GenBank   WP_024323902
Name   t4cp2_ELH67_RS35605_pSM119_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: 69272..78741

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH67_RS35545 (ELH67_35545) 64736..64942 + 207 WP_080642907 hypothetical protein -
ELH67_RS35550 (ELH67_35550) 65062..65214 - 153 Protein_72 aminoglycoside phosphotransferase -
ELH67_RS35555 (ELH67_35555) 65266..67227 - 1962 WP_130674184 elongation factor G -
ELH67_RS35560 (ELH67_35560) 68067..68270 - 204 Protein_74 IS6 family transposase -
ELH67_RS35565 (ELH67_35565) 68536..69246 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELH67_RS35570 (ELH67_35570) 69272..70552 - 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH67_RS35575 (ELH67_35575) 70567..70995 - 429 WP_018068569 conjugal transfer protein TrbH -
ELH67_RS35580 (ELH67_35580) 70998..71819 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH67_RS35585 (ELH67_35585) 71836..72498 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH67_RS35590 (ELH67_35590) 72519..73667 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH67_RS35595 (ELH67_35595) 73694..73891 - 198 WP_130674182 entry exclusion protein TrbK -
ELH67_RS35600 (ELH67_35600) 73888..74688 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH67_RS35605 (ELH67_35605) 74660..77107 - 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH67_RS35610 (ELH67_35610) 77117..77416 - 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH67_RS35615 (ELH67_35615) 77406..77786 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH67_RS35620 (ELH67_35620) 77776..78741 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH67_RS35625 (ELH67_35625) 78755..79381 - 627 WP_130674180 acyl-homoserine-lactone synthase TraI -
ELH67_RS35630 (ELH67_35630) 79746..80963 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELH67_RS35635 (ELH67_35635) 80948..81988 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELH67_RS35640 (ELH67_35640) 82227..83492 + 1266 WP_130674179 plasmid replication protein RepC -

Host bacterium

ID   1639 GenBank   NZ_SINS01000005
Plasmid name   pSM119_Rh04 Incompatibility group   -
Plasmid size   350606 bp Coordinate of oriT [Strand]   39492..39532 [+]
Host baterium   Rhizobium ruizarguesonis strain SM119

Cargo genes

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