Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101166
Name   oriT_pSM95_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM95
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIMU01000005 (28297..28337 [+], 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_pSM95_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1163 GenBank   WP_130827351
Name   traA_ELH43_RS34420_pSM95_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: 122851.92 Da        Isoelectric Point: 10.1570

>WP_130827351.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPTGAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDAQLAKDLNIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGAKKIAVASPDGNPMRNDAGKIVYELWAGSADDFNAVRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIDRKAEQANARTSAWSPKLERVELQQDRRAENARRIQRRPD
IVLDLITREKSVFDDRDVGKILHRYIDDAALFQNLMMRILQSPQALRLERDRIDFATGVRTPAKYTTREM
IKLEAEMVNRAIWLSDRASHGVREAALEVTFARHARLSDEQRTAIERVAGGERIAAVMGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAVEGLEKEAGIQSRTLSSWELRWNQGRNRIDARTVFVLDEAGMVSSRQM
AHFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRAQWMRDASLDLARGNVGKA
VDAYRAHGQVRGLDLKAQAVENLFADWNHDYDPSKSSLILAHLRRDVRMLNDMARAKLVERGIVADGFAF
KSEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRLVVALGEGDHRRVVTIEQRFYNKLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRCSFAKSGGPVPILARRNAKETTLDYE
KSSFYGQALRFAEARGLHLMNVARTLARDRLEWTVRQKQKLADLGARLAAIGVKLGRAANAKTSPNLNAK
ESKPMVSGISTFSKSIDQSVEDKLAADPGLKKQWEDVSARFHLVYAQPESAFKAANVEAMLKDQAIAKTT
LAKLAGEPERFGALRGKTGVFANRGDKQDRERAIANVPALARNLERYLRQRAEVERKHETEERAVRRQVS
VDIPALSASAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELDGFAKAVSERFGERTFLGIASKDPSGE
TFKSVTAGMNPAQKAEVEIAWNSMRSIQQLSAHEKTTEALKQAETLRQTRSQGFSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(694-740)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(863-959)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-572)


  Protein structure



No available structure.




T4CP

ID   747 GenBank   WP_130827350
Name   traG_ELH43_RS34405_pSM95_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: 70992.82 Da        Isoelectric Point: 8.9896

>WP_130827350.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTANKIALFSVPIALMILVTIGMTGTEQWFSEFGKTETGRLILGRTGIALPYIASAATGIIFLFASAGST
NIKLAGWGVVGGSSATVVIAALRETVRLAAIFDHFPAVRSALSYADPATMIGAGAALMSAGFALRVALVG
NAAFARSEPRRIRGRRALHGEAEWMKSTEAGKLFPDTGGIVIGERYRVDKDIAAKQSFRADSVETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVLLDPSNEVAPMVIGHRTNAGRDVHILD
PRTPDTGFNALDWIGLHGRTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDRTEE
DDQTLRQVRKNLSEPEPKLRARLQSIYDNSRSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSESTFSTNDISAGNADVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VAIDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
ENRFHSPARGDESAMDPETPMKLRG

  Protein domains


Predicted by InterproScan.

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

(164-637)

  Protein structure



No available structure.



ID   748 GenBank   WP_130773523
Name   t4cp2_ELH43_RS34620_pSM95_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: 91522.01 Da        Isoelectric Point: 6.2219

>WP_130773523.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVSLRAFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEVSRQINAILSRLG
SGWMIQVEAVRLATVDYASAGKSHFPDRVTQAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YIYSDEDSRKQSYADTVLFIFRNAIREVEQYLANIISIRRMLTRETVERGGARVAHYDELLQFIRFCVTG
ENHPVRVPDIPMYLDWIATAELRHGLAPKVENRFLGVVAIDGLPSESWPGILNSLDAMPLGYRWSSRFIF
LDAEEARVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDALSMVAETEDAIAQASSQLVAYGYYTPVVVL
FESDSERLNEKTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GNPRAPCPFYSPDSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLACGGDHYEIGGDEDTGLSFCPLSELSSEGDRAWASEWIESLVGMQGITITPDHRNAIS
RQIGLMDGASGRSISDFVSGVQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQTFEIEQVMNMGERN
LVPVLTYLFRRIEKRLTGAPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPSGAAREPGTRDFYERIGFNERQIEIVATAIPKREYYVASPEGRRLFDMALGPLTL
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: 58059..67528

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH43_RS34550 (ELH43_34555) 53266..53469 + 204 WP_130773519 hypothetical protein -
ELH43_RS34555 (ELH43_34560) 53524..53730 + 207 WP_080642907 hypothetical protein -
ELH43_RS34560 (ELH43_34565) 53850..54002 - 153 Protein_56 aminoglycoside phosphotransferase -
ELH43_RS34565 (ELH43_34570) 54054..56015 - 1962 WP_130773521 elongation factor G -
ELH43_RS34575 (ELH43_34580) 56854..57057 - 204 Protein_58 IS6 family transposase -
ELH43_RS34580 (ELH43_34585) 57323..58033 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELH43_RS34585 (ELH43_34590) 58059..59339 - 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH43_RS34590 (ELH43_34595) 59354..59782 - 429 WP_018068569 conjugal transfer protein TrbH -
ELH43_RS34595 (ELH43_34600) 59785..60606 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH43_RS34600 (ELH43_34605) 60623..61285 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH43_RS34605 (ELH43_34610) 61306..62454 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH43_RS34610 (ELH43_34615) 62481..62678 - 198 WP_130726238 entry exclusion protein TrbK -
ELH43_RS34615 (ELH43_34620) 62675..63475 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH43_RS34620 (ELH43_34625) 63447..65894 - 2448 WP_130773523 conjugal transfer protein TrbE virb4
ELH43_RS34625 (ELH43_34630) 65904..66203 - 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH43_RS34630 (ELH43_34635) 66193..66573 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH43_RS34635 (ELH43_34640) 66563..67528 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH43_RS34640 (ELH43_34645) 67542..68168 - 627 WP_018068560 acyl-homoserine-lactone synthase TraI -
ELH43_RS34645 (ELH43_34650) 68533..69750 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELH43_RS34650 (ELH43_34655) 69735..70775 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELH43_RS34655 (ELH43_34660) 71014..72279 + 1266 WP_130773525 plasmid replication protein RepC -

Host bacterium

ID   1610 GenBank   NZ_SIMU01000005
Plasmid name   pSM95_Rh04 Incompatibility group   -
Plasmid size   91549 bp Coordinate of oriT [Strand]   28297..28337 [+]
Host baterium   Rhizobium ruizarguesonis strain SM95

Cargo genes

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