Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101187
Name   oriT_pSM109_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM109
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SINI01000005 (28346..28386 [+], 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_pSM109_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1184 GenBank   WP_130674195
Name   traA_ELH57_RS35905_pSM109_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   786 GenBank   WP_024323836
Name   traG_ELH57_RS35890_pSM109_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   787 GenBank   WP_024323902
Name   t4cp2_ELH57_RS36095_pSM109_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: 58104..67573

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH57_RS36035 (ELH57_36030) 53568..53774 + 207 WP_080642907 hypothetical protein -
ELH57_RS36040 (ELH57_36035) 53894..54046 - 153 Protein_53 aminoglycoside phosphotransferase -
ELH57_RS36045 (ELH57_36040) 54098..56059 - 1962 WP_130720409 elongation factor G -
ELH57_RS36050 (ELH57_36045) 56899..57102 - 204 Protein_55 IS6 family transposase -
ELH57_RS36055 (ELH57_36050) 57368..58078 + 711 WP_024323909 autoinducer binding domain-containing protein -
ELH57_RS36060 (ELH57_36055) 58104..59384 - 1281 WP_130674183 IncP-type conjugal transfer protein TrbI virB10
ELH57_RS36065 (ELH57_36060) 59399..59827 - 429 WP_018068569 conjugal transfer protein TrbH -
ELH57_RS36070 (ELH57_36065) 59830..60651 - 822 WP_018068568 P-type conjugative transfer protein TrbG virB9
ELH57_RS36075 (ELH57_36070) 60668..61330 - 663 WP_024323906 conjugal transfer protein TrbF virB8
ELH57_RS36080 (ELH57_36075) 61351..62499 - 1149 WP_050574296 P-type conjugative transfer protein TrbL virB6
ELH57_RS36085 (ELH57_36080) 62526..62723 - 198 WP_130674182 entry exclusion protein TrbK -
ELH57_RS36090 (ELH57_36085) 62720..63520 - 801 WP_130674181 P-type conjugative transfer protein TrbJ virB5
ELH57_RS36095 (ELH57_36090) 63492..65939 - 2448 WP_024323902 conjugal transfer protein TrbE virb4
ELH57_RS36100 (ELH57_36095) 65949..66248 - 300 WP_024323901 conjugal transfer protein TrbD virB3
ELH57_RS36105 (ELH57_36100) 66238..66618 - 381 WP_018068562 TrbC/VirB2 family protein virB2
ELH57_RS36110 (ELH57_36105) 66608..67573 - 966 WP_024323900 P-type conjugative transfer ATPase TrbB virB11
ELH57_RS36115 (ELH57_36110) 67587..68213 - 627 WP_130674180 acyl-homoserine-lactone synthase TraI -
ELH57_RS36120 (ELH57_36115) 68578..69795 + 1218 WP_075225817 plasmid partitioning protein RepA -
ELH57_RS36125 (ELH57_36120) 69780..70820 + 1041 WP_027689819 plasmid partitioning protein RepB -
ELH57_RS36130 (ELH57_36125) 71059..72324 + 1266 WP_130676474 plasmid replication protein RepC -

Host bacterium

ID   1631 GenBank   NZ_SINI01000005
Plasmid name   pSM109_Rh04 Incompatibility group   -
Plasmid size   100244 bp Coordinate of oriT [Strand]   28346..28386 [+]
Host baterium   Rhizobium ruizarguesonis strain SM109

Cargo genes

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