Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102571
Name   oriT_pSM30_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM30
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKM01000005 (66750..66790 [+], 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_pSM30_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1920 GenBank   WP_130784879
Name   traA_ELG83_RS35435_pSM30_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   1542 GenBank   WP_128409206
Name   traG_ELG83_RS35420_pSM30_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.



ID   1543 GenBank   WP_130788633
Name   t4cp2_ELG83_RS35520_pSM30_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 64173..86205

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG83_RS35380 (ELG83_35375) 59531..59842 + 312 WP_127431460 DUF736 domain-containing protein -
ELG83_RS36900 60143..60304 + 162 WP_018516739 hypothetical protein -
ELG83_RS37435 60526..60669 - 144 WP_245488070 hypothetical protein -
ELG83_RS37730 (ELG83_35385) 60838..61146 - 309 WP_130784881 WGR domain-containing protein -
ELG83_RS35395 (ELG83_35390) 61590..61904 + 315 WP_128408836 hypothetical protein -
ELG83_RS35400 (ELG83_35395) 62136..62285 - 150 Protein_65 thermonuclease family protein -
ELG83_RS35405 (ELG83_35400) 62282..63361 - 1080 WP_130784880 IS630 family transposase -
ELG83_RS35410 (ELG83_35405) 63431..63733 - 303 Protein_67 thermonuclease family protein -
ELG83_RS35420 (ELG83_35415) 64173..66107 - 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG83_RS35425 (ELG83_35420) 66094..66309 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG83_RS35430 (ELG83_35425) 66314..66607 - 294 WP_128409207 conjugal transfer protein TraC -
ELG83_RS35435 (ELG83_35430) 66862..70188 + 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG83_RS35440 (ELG83_35435) 70236..70748 + 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG83_RS35445 (ELG83_35440) 70738..71904 + 1167 WP_128408812 conjugal transfer protein TraB -
ELG83_RS35450 (ELG83_35445) 71922..72542 + 621 WP_128408811 TraH family protein virB1
ELG83_RS35455 (ELG83_35450) 72687..73402 - 716 Protein_75 Crp/Fnr family transcriptional regulator -
ELG83_RS35460 (ELG83_35455) 73759..74133 - 375 WP_128408810 DUF5615 family PIN-like protein -
ELG83_RS35465 (ELG83_35460) 74130..74762 - 633 WP_128408809 DUF433 domain-containing protein -
ELG83_RS35470 (ELG83_35465) 74876..75118 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG83_RS35475 (ELG83_35470) 75344..75685 + 342 WP_128408807 transcriptional repressor TraM -
ELG83_RS35480 (ELG83_35475) 75670..76374 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELG83_RS35485 (ELG83_35480) 76683..77981 - 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG83_RS35490 (ELG83_35485) 77993..78433 - 441 WP_128408804 conjugal transfer protein TrbH -
ELG83_RS35495 (ELG83_35490) 78437..79248 - 812 Protein_83 P-type conjugative transfer protein TrbG -
ELG83_RS35500 (ELG83_35495) 79266..79928 - 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG83_RS35505 (ELG83_35500) 79949..81130 - 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG83_RS35510 (ELG83_35505) 81124..81324 - 201 WP_128408800 entry exclusion protein TrbK -
ELG83_RS35515 (ELG83_35510) 81321..82124 - 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG83_RS35520 (ELG83_35515) 82096..84552 - 2457 WP_130788633 conjugal transfer protein TrbE virb4
ELG83_RS35525 (ELG83_35520) 84563..84862 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG83_RS35530 (ELG83_35525) 84855..85238 - 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG83_RS35535 (ELG83_35530) 85228..86205 - 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG83_RS35540 (ELG83_35535) 86202..86840 - 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG83_RS37445 87318..87530 + 213 WP_245458276 hypothetical protein -
ELG83_RS35555 (ELG83_35550) 88442..89656 + 1215 WP_130784921 plasmid partitioning protein RepA -
ELG83_RS35560 (ELG83_35555) 89653..90675 + 1023 WP_128408794 plasmid partitioning protein RepB -

Host bacterium

ID   3015 GenBank   NZ_SIKM01000005
Plasmid name   pSM30_Rh07 Incompatibility group   -
Plasmid size   133771 bp Coordinate of oriT [Strand]   66750..66790 [+]
Host baterium   Rhizobium leguminosarum strain SM30

Cargo genes

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