Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101197
Name   oriT_pSM112_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM112
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SINL01000004 (21672..21712 [+], 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_pSM112_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1193 GenBank   WP_130674195
Name   traA_ELH60_RS36575_pSM112_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   802 GenBank   WP_024323836
Name   traG_ELH60_RS36560_pSM112_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   803 GenBank   WP_024323902
Name   t4cp2_ELH60_RS36765_pSM112_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: 51452..60921

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH60_RS36705 (ELH60_36700) 46916..47122 + 207 WP_080642907 hypothetical protein -
ELH60_RS36710 (ELH60_36705) 47242..47394 - 153 Protein_42 aminoglycoside phosphotransferase -
ELH60_RS36715 (ELH60_36710) 47446..49407 - 1962 WP_130674184 elongation factor G -
ELH60_RS36720 (ELH60_36715) 50247..50450 - 204 Protein_44 IS6 family transposase -
ELH60_RS36725 (ELH60_36720) 50716..51426 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELH60_RS36730 (ELH60_36725) 51452..52732 - 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH60_RS36735 (ELH60_36730) 52747..53175 - 429 WP_018068569 conjugal transfer protein TrbH -
ELH60_RS36740 (ELH60_36735) 53178..53999 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH60_RS36745 (ELH60_36740) 54016..54678 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH60_RS36750 (ELH60_36745) 54699..55847 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH60_RS36755 (ELH60_36750) 55874..56071 - 198 WP_130674182 entry exclusion protein TrbK -
ELH60_RS36760 (ELH60_36755) 56068..56868 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH60_RS36765 (ELH60_36760) 56840..59287 - 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH60_RS36770 (ELH60_36765) 59297..59596 - 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH60_RS36775 (ELH60_36770) 59586..59966 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH60_RS36780 (ELH60_36775) 59956..60921 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH60_RS36785 (ELH60_36780) 60935..61561 - 627 WP_130674180 acyl-homoserine-lactone synthase TraI -
ELH60_RS36790 (ELH60_36785) 61926..63143 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELH60_RS36795 (ELH60_36790) 63128..64168 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELH60_RS36800 (ELH60_36795) 64407..65672 + 1266 WP_130674179 plasmid replication protein RepC -

Host bacterium

ID   1641 GenBank   NZ_SINL01000004
Plasmid name   pSM112_Rh04 Incompatibility group   -
Plasmid size   137764 bp Coordinate of oriT [Strand]   21672..21712 [+]
Host baterium   Rhizobium ruizarguesonis strain SM112

Cargo genes

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