Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102548
Name   oriT_pSM40_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM40
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKV01000005 (67684..67724 [+], 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_pSM40_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1899 GenBank   WP_130784879
Name   traA_ELG92_RS35070_pSM40_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   1508 GenBank   WP_128409206
Name   traG_ELG92_RS35055_pSM40_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   1509 GenBank   WP_130794975
Name   t4cp2_ELG92_RS35155_pSM40_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: 91703.43 Da        Isoelectric Point: 5.7027

>WP_130794975.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTLAIDAERRAHFAREQGHFESKHALVLTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLSVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
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: 65107..87140

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG92_RS35015 (ELG92_35030) 60465..60776 + 312 WP_127431460 DUF736 domain-containing protein -
ELG92_RS37745 61077..61238 + 162 WP_018516739 hypothetical protein -
ELG92_RS38290 61460..61603 - 144 WP_245488070 hypothetical protein -
ELG92_RS38610 (ELG92_35040) 61772..62080 - 309 WP_130784881 WGR domain-containing protein -
ELG92_RS35030 (ELG92_35045) 62524..62838 + 315 WP_128408836 hypothetical protein -
ELG92_RS35035 (ELG92_35050) 63070..63219 - 150 Protein_65 thermonuclease family protein -
ELG92_RS35040 (ELG92_35055) 63216..64295 - 1080 WP_130784880 IS630 family transposase -
ELG92_RS35045 (ELG92_35060) 64365..64667 - 303 Protein_67 thermonuclease family protein -
ELG92_RS35055 (ELG92_35070) 65107..67041 - 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG92_RS35060 (ELG92_35075) 67028..67243 - 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG92_RS35065 (ELG92_35080) 67248..67541 - 294 WP_128409207 conjugal transfer protein TraC -
ELG92_RS35070 (ELG92_35085) 67796..71122 + 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG92_RS35075 (ELG92_35090) 71170..71682 + 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG92_RS35080 (ELG92_35095) 71672..72838 + 1167 WP_128408812 conjugal transfer protein TraB -
ELG92_RS35085 (ELG92_35100) 72856..73476 + 621 WP_128408811 TraH family protein virB1
ELG92_RS35090 (ELG92_35105) 73621..74336 - 716 Protein_75 Crp/Fnr family transcriptional regulator -
ELG92_RS35095 (ELG92_35110) 74693..75067 - 375 WP_128408810 DUF5615 family PIN-like protein -
ELG92_RS35100 (ELG92_35115) 75064..75696 - 633 WP_128408809 DUF433 domain-containing protein -
ELG92_RS35105 (ELG92_35120) 75810..76052 - 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG92_RS35110 (ELG92_35125) 76278..76619 + 342 WP_128408807 transcriptional repressor TraM -
ELG92_RS35115 (ELG92_35130) 76604..77308 - 705 WP_128408806 autoinducer binding domain-containing protein -
ELG92_RS35120 (ELG92_35135) 77617..78915 - 1299 WP_130794973 IncP-type conjugal transfer protein TrbI virB10
ELG92_RS35125 (ELG92_35140) 78927..79367 - 441 WP_128408804 conjugal transfer protein TrbH -
ELG92_RS35130 (ELG92_35145) 79371..80183 - 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG92_RS35135 (ELG92_35150) 80201..80863 - 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG92_RS35140 (ELG92_35155) 80884..82065 - 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG92_RS35145 (ELG92_35160) 82059..82259 - 201 WP_128408800 entry exclusion protein TrbK -
ELG92_RS35150 (ELG92_35165) 82256..83059 - 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG92_RS35155 (ELG92_35170) 83031..85487 - 2457 WP_130794975 conjugal transfer protein TrbE virb4
ELG92_RS35160 (ELG92_35175) 85498..85797 - 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG92_RS35165 (ELG92_35180) 85790..86173 - 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG92_RS35170 (ELG92_35185) 86163..87140 - 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG92_RS35175 (ELG92_35190) 87137..87775 - 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG92_RS38300 88253..88465 + 213 WP_245458276 hypothetical protein -
ELG92_RS35185 (ELG92_35200) 88565..90676 - 2112 WP_130790737 recombinase family protein -
ELG92_RS35190 (ELG92_35205) 90969..91430 - 462 WP_024323550 helix-turn-helix domain-containing protein -

Host bacterium

ID   2992 GenBank   NZ_SIKV01000005
Plasmid name   pSM40_Rh07 Incompatibility group   -
Plasmid size   431811 bp Coordinate of oriT [Strand]   67684..67724 [+]
Host baterium   Rhizobium leguminosarum strain SM40

Cargo genes

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