Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102558
Name   oriT_pSM36_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM36
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKR01000006 (195011..195051 [-], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pSM36_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1909 GenBank   WP_130784879
Name   traA_ELG88_RS36045_pSM36_Rh07 insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 122892.96 Da        Isoelectric Point: 9.7033

>WP_130784879.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVCSMIADR
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKIALLGPDGKPVRNDAGKLVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKTQASAPKLERIELQGERRSENARRIERRPE
IVLDLITREKSVFDERDVAKVLYRYIDDAALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTRDM
VRLEAEMANRAIWLSGRASHGVREEVLQTTFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLESAPGRIVAEVGDGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRIHWAVRQKQNLADLGARLAAISTALGLARGSNKHSIPNTI
KGAKPMVSGITTFPKSLDHAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAVFKAINVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGVLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTADQKAEVQSAWNSMRTVQQLGSHERTTEALKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)


  Protein structure



No available structure.




T4CP

ID   1526 GenBank   WP_130788633
Name   t4cp2_ELG88_RS35960_pSM36_Rh07 insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91673.41 Da        Isoelectric Point: 5.7027

>WP_130788633.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALVLTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMSMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNAPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATSEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLETRGVHDAASLLKYV

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.



ID   1527 GenBank   WP_128409206
Name   traG_ELG88_RS36060_pSM36_Rh07 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 69653.97 Da        Isoelectric Point: 9.3813

>WP_128409206.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSSFMKTVPADKTVLAFLDPATSIGASAALLCACFALRVALIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDVGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGRAGRDVFLLD
PRKPDIGFNVLDWVGRFGGTKEEDIASIASWIMSDSGGVRGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPRPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 175594..197628

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG88_RS35920 (ELG88_35935) 171124..172146 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG88_RS35925 (ELG88_35940) 172143..173357 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG88_RS38715 174269..174481 - 213 WP_245458276 hypothetical protein -
ELG88_RS35940 (ELG88_35955) 174959..175597 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG88_RS35945 (ELG88_35960) 175594..176571 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG88_RS35950 (ELG88_35965) 176561..176944 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG88_RS35955 (ELG88_35970) 176937..177236 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG88_RS35960 (ELG88_35975) 177247..179703 + 2457 WP_130788633 conjugal transfer protein TrbE virb4
ELG88_RS35965 (ELG88_35980) 179675..180478 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG88_RS35970 (ELG88_35985) 180475..180675 + 201 WP_128408800 entry exclusion protein TrbK -
ELG88_RS35975 (ELG88_35990) 180669..181850 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG88_RS35980 (ELG88_35995) 181871..182533 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG88_RS35985 (ELG88_36000) 182567..183364 + 798 WP_130788634 P-type conjugative transfer protein TrbG virB9
ELG88_RS35990 (ELG88_36005) 183368..183808 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG88_RS35995 (ELG88_36010) 183820..185118 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG88_RS36000 (ELG88_36015) 185427..186131 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG88_RS36005 (ELG88_36020) 186116..186457 - 342 WP_128408807 transcriptional repressor TraM -
ELG88_RS36010 (ELG88_36025) 186683..186925 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG88_RS36015 (ELG88_36030) 187039..187671 + 633 WP_128408809 DUF433 domain-containing protein -
ELG88_RS36020 (ELG88_36035) 187668..188042 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG88_RS36025 (ELG88_36040) 188399..189114 + 716 Protein_189 Crp/Fnr family transcriptional regulator -
ELG88_RS36030 (ELG88_36045) 189259..189879 - 621 WP_128408811 TraH family protein virB1
ELG88_RS36035 (ELG88_36050) 189897..191063 - 1167 WP_130788635 conjugal transfer protein TraB -
ELG88_RS36040 (ELG88_36055) 191053..191565 - 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG88_RS36045 (ELG88_36060) 191613..194939 - 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG88_RS36050 (ELG88_36065) 195194..195487 + 294 WP_128409207 conjugal transfer protein TraC -
ELG88_RS36055 (ELG88_36070) 195492..195707 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG88_RS36060 (ELG88_36075) 195694..197628 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG88_RS36070 (ELG88_36085) 198068..198370 + 303 Protein_197 thermonuclease family protein -
ELG88_RS36075 (ELG88_36090) 198440..199519 + 1080 WP_130784880 IS630 family transposase -
ELG88_RS36080 (ELG88_36095) 199516..199665 + 150 Protein_199 thermonuclease family protein -
ELG88_RS36085 (ELG88_36100) 199897..200211 - 315 WP_128408836 hypothetical protein -
ELG88_RS39000 (ELG88_36105) 200655..200963 + 309 WP_130784881 WGR domain-containing protein -
ELG88_RS38725 201132..201275 + 144 WP_245488070 hypothetical protein -
ELG88_RS38055 201497..201658 - 162 WP_018516739 hypothetical protein -
ELG88_RS36100 (ELG88_36115) 201959..202270 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   3002 GenBank   NZ_SIKR01000006
Plasmid name   pSM36_Rh07 Incompatibility group   -
Plasmid size   261797 bp Coordinate of oriT [Strand]   195011..195051 [-]
Host baterium   Rhizobium leguminosarum strain SM36

Cargo genes

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