Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101165
Name   oriT_pSM107_Rh22 in_silico
Organism   Rhizobium ruizarguesonis strain SM107
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SING01000006 (7826..7869 [-], 44 nt)
oriT length   44 nt
IRs (inverted repeats)      21..27, 32..38  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 44 nt

>oriT_pSM107_Rh22
GGATCCAAGGGCGCAATTATACGTCGCTGATGCGACGTGCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1162 GenBank   WP_130773809
Name   traA_ELH55_RS33975_pSM107_Rh22 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123584.35 Da        Isoelectric Point: 9.7853

>WP_130773809.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAIAHFSASIVSRGGGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPADAPKWVRALIADR
SVSGAVEAFWNKVEVFEKRSDAQLARDLTIALPLELTPEQNIALVRDFAEKHILAKGMVADWVYHDNPGN
PHIHLMTTLRPLTEDGFGSKKVAVVGEDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLVLGG
IDLRIDGRSYEKQGIKLEPTIHLGVGAKAIERKAQERGVRPELERIELNEERRSENTRRILNNPAIVLDL
ITREKSVFDERDIAKVLHRYVDDPAVFQQLMLRIILNPEVLRLQRDTIEFATGEKLPARYSTRAMIRLEA
TMVRQALWLSNRDGHAVSEAALDATFRRHERLSQEQKAAIERIAGPARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIQSRTLASWELRWSRGRDVLDNKTVFVMDEAGMVASKQMAGFVD
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALTAYD
ANVRITETRLKAEAVERLIGDWNHDYDQTKTTLILAHLRRDVRMLNIMAREKLVERGIVGEGHAFKTADG
IRQFDAGDQIVFLKNETSLGVKNGMIAHVVEAAANRIVAVVGGGDQRRQVIVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGRRSFAFNGGLAKVLSRRQAKETTLDYEPGKLY
REALRYAENRGLNIVQVARTLLRDQLDWTLRQKTKLVDLGQRLAVFAERLGLHHPPKTQTMKEAAPMVAG
IKIFSGSVADTVEQKLDTDPALRKQWEEVSTRFAYVFADPETAFRAINFDAVLVDKETAKLALQTLTTAP
ASIGPLKGKTGILASKTEREERRVADLNVPALKRDLEQYLRMRETAVQRLQADEQGLRQRVSIDIPALSQ
AAHVVLERVRDAIDRNDLPAAMAYALSNRETKLEIDGFNQAVTERFGERTLITNAAREPSGKLFDKLSEG
MQPEQKERLTEAWPIMRASQQLAAHERTVQTLRQAEDLRLAPRQTPVMKQ

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-736)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-568)

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

(855-951)


  Protein structure



No available structure.




T4CP

ID   745 GenBank   WP_130773811
Name   traG_ELH55_RS33990_pSM107_Rh22 insolico UniProt ID   _
Length   656 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 656 a.a.        Molecular weight: 70349.49 Da        Isoelectric Point: 9.5383

>WP_130773811.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTASKVFLAIVPATTMIVVVVFMPGIEHWLAAFGKTPQAKLILGRIGLALPYATAAAIGTIFLFAANGAA
GIKAAGWGVVSGNGVAILIALLREGVRLAGIAGDVPKGQSVLGYADPATMLGASTAILAGVFALRVAMMG
NAAFAKGSPRRIGGKRAVHGEADWMKIQEAAKLFPDPGGIVVGERYRVDRDSVAAVSFRSGDPSTWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTVPTALKWGGGLVVLDPSSEVAPMVSEHRRKAGRKVIILD
PSASGIGFNALDWIGRHGSTKEEDIVAVAIWIMTDNPRSASARDDFFRASAMQLLTALIADVCLSGHTDE
EDQTLRRVRKNLSEPEPQLRARLTKIYEQSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGDSFSTDDLADGGTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGDVKGRALFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSIGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQINRSSGIKGSSRSRSRQLSRRPLILPHEVLRMRSDEQIVFTSGNPPLRCGRAIWFRRKDMSASVG
ENRFHKPITEGVKSYKAAPTTDTEAT

  Protein domains


Predicted by InterproScan.

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

(163-635)

  Protein structure



No available structure.



ID   746 GenBank   WP_130773865
Name   t4cp2_ELH55_RS34335_pSM107_Rh22 insolico UniProt ID   _
Length   821 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 821 a.a.        Molecular weight: 91780.57 Da        Isoelectric Point: 5.4896

>WP_130773865.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKSFRHPGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWIIQVEAIRVPTGDYPAEAESYFPDPVTRAIDDERRAHFQTERGHFESRHALILTWRPPEPRRSGLTR
YIYSDAASRSATYADKALENFLTSIREVEQYLANVVSIRRMMTRETSERGGFRVARYDELFQFIRFCVTG
ENHPVRLPDIPMYLDWLVTAELQHGLTPMVENRFLGVVAIDGLPAESWPGILNTLDRMPLTYRWSSRFVF
LDSEEARARLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMLMVAETEDAIAEASSQLVAYGYYTPVIVI
FEEDAVRLQEKCEAIRQLIQAEGFGARIETLNATDAYLGSLPGVSYANIREPLINTRNLADLIPLNSVWS
GSPTAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYADAQVFA
FDKGGSMLPLTFGLNGDHYQIGGDIGPSTSGEKALAFCPLAELSTDGDRAWASEWIEMLVALQGVTITPD
YRNAISRQLALMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLALGALQCFEIEELM
NMGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISD
AERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKREYYVVSPEGRRLFNMA
LGPVALSFVGATGKEDLKQIRNLHSEHGAAWPLHWLQQRGITHAETLFPAE

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 92763..102450

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELH55_RS34300 (ELH55_34300) 88147..89361 - 1215 WP_130773859 plasmid replication protein RepC -
ELH55_RS34305 (ELH55_34305) 89516..90502 - 987 WP_130773860 plasmid partitioning protein RepB -
ELH55_RS34310 (ELH55_34310) 90577..91764 - 1188 WP_130773861 plasmid partitioning protein RepA -
ELH55_RS34315 (ELH55_34315) 92131..92766 + 636 WP_130773862 acyl-homoserine-lactone synthase -
ELH55_RS34320 (ELH55_34320) 92763..93734 + 972 WP_130773863 P-type conjugative transfer ATPase TrbB virB11
ELH55_RS34325 (ELH55_34325) 93724..94128 + 405 WP_130773864 conjugal transfer pilin TrbC virB2
ELH55_RS34330 (ELH55_34330) 94121..94420 + 300 WP_033184404 conjugal transfer protein TrbD virB3
ELH55_RS34335 (ELH55_34335) 94422..96887 + 2466 WP_130773865 conjugal transfer protein TrbE virb4
ELH55_RS34340 (ELH55_34340) 96859..97668 + 810 WP_130773866 P-type conjugative transfer protein TrbJ virB5
ELH55_RS34345 (ELH55_34345) 97665..97892 + 228 WP_130773867 entry exclusion protein TrbK -
ELH55_RS34350 (ELH55_34350) 97886..99076 + 1191 WP_130773868 P-type conjugative transfer protein TrbL virB6
ELH55_RS34355 (ELH55_34355) 99094..99771 + 678 WP_130773869 conjugal transfer protein TrbF virB8
ELH55_RS34360 (ELH55_34360) 99789..100640 + 852 WP_130773870 P-type conjugative transfer protein TrbG virB9
ELH55_RS34365 (ELH55_34365) 100640..101116 + 477 WP_130773871 conjugal transfer protein TrbH -
ELH55_RS34370 (ELH55_34370) 101128..102450 + 1323 WP_130773872 IncP-type conjugal transfer protein TrbI virB10
ELH55_RS34375 (ELH55_34375) 102580..103680 - 1101 WP_130773873 LacI family DNA-binding transcriptional regulator -
ELH55_RS34380 (ELH55_34380) 103826..104848 + 1023 WP_130773874 SIS domain-containing protein -
ELH55_RS34385 (ELH55_34385) 104859..105677 + 819 WP_130773875 PfkB family carbohydrate kinase -
ELH55_RS34390 (ELH55_34390) 105995..107056 + 1062 WP_130773876 ABC transporter substrate-binding protein -

Host bacterium

ID   1609 GenBank   NZ_SING01000006
Plasmid name   pSM107_Rh22 Incompatibility group   -
Plasmid size   115807 bp Coordinate of oriT [Strand]   7826..7869 [-]
Host baterium   Rhizobium ruizarguesonis strain SM107

Cargo genes

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