Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101154
Name   oriT_pSM158_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM158
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQJ01000006 (29274..29314 [-], 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_pSM158_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1151 GenBank   WP_130692296
Name   traA_ELI36_RS29995_pSM158_Rh07 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: 122959.16 Da        Isoelectric Point: 9.4990

>WP_130692296.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADS
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
VRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRVGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAAGGIIAEIGEGEHRQVTIEQRFYNNLDHGYAT
TIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYEK
SALCRQAFRFAEARGLHLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGKALGLVRGSNKHSIPDTIK
EARPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAAFKAINVDAMVEDQSVAQST
LARIAGEPESFGALKGKTGVLASRGDKHDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKVS
VDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDGK
TFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-739)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)

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

(863-959)


  Protein structure



No available structure.




T4CP

ID   723 GenBank   WP_130692276
Name   t4cp2_ELI36_RS29910_pSM158_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: 91738.38 Da        Isoelectric Point: 5.7923

>WP_130692276.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNEQSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLIPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMSMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPISPCPFYPPNAPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQIGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAMPKREYYVATSEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLKYV

  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   724 GenBank   WP_130692298
Name   traG_ELI36_RS30010_pSM158_Rh07 insolico UniProt ID   _
Length   643 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 643 a.a.        Molecular weight: 69483.71 Da        Isoelectric Point: 9.1051

>WP_130692298.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSAFMTVPADKTVWAFLDPATSIGASAALLCACFALRVALIGN
AAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGGK
SPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLDP
RKPDIGFNVLDWVGRFGGTKEEDIASIASWIMSDSGGVRGVRDDFFRASALQLLTALIADVCLSGHTDEK
DQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAA
LVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGYM
RIIETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTV
EIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGT
NRFHMVGDTPRPA

  Protein domains


Predicted by InterproScan.

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

(162-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9861..31888

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI36_RS29870 (ELI36_29875) 5391..6413 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELI36_RS29875 (ELI36_29880) 6410..7624 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELI36_RS29880 (ELI36_29885) 8241..8495 - 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELI36_RS39675 8536..8748 - 213 WP_245458276 hypothetical protein -
ELI36_RS29890 (ELI36_29895) 9226..9864 + 639 WP_130692272 acyl-homoserine-lactone synthase -
ELI36_RS29895 (ELI36_29900) 9861..10838 + 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELI36_RS29900 (ELI36_29905) 10828..11211 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELI36_RS29905 (ELI36_29910) 11204..11503 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI36_RS29910 (ELI36_29915) 11514..13970 + 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELI36_RS29915 (ELI36_29920) 13942..14745 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELI36_RS29920 (ELI36_29925) 14742..14942 + 201 WP_128408800 entry exclusion protein TrbK -
ELI36_RS29925 (ELI36_29930) 14936..16117 + 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELI36_RS29930 (ELI36_29935) 16138..16800 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELI36_RS29935 (ELI36_29940) 16818..17630 + 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELI36_RS29940 (ELI36_29945) 17634..18074 + 441 WP_130692284 conjugal transfer protein TrbH -
ELI36_RS29945 (ELI36_29950) 18086..19384 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELI36_RS29950 (ELI36_29955) 19693..20397 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELI36_RS29955 (ELI36_29960) 20382..20723 - 342 WP_128408807 transcriptional repressor TraM -
ELI36_RS29960 (ELI36_29965) 20949..21191 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELI36_RS29965 (ELI36_29970) 21305..21937 + 633 WP_128408809 DUF433 domain-containing protein -
ELI36_RS29970 (ELI36_29975) 21934..22308 + 375 WP_130692288 DUF5615 family PIN-like protein -
ELI36_RS29975 (ELI36_29980) 22665..23380 + 716 Protein_25 Crp/Fnr family transcriptional regulator -
ELI36_RS29980 (ELI36_29985) 23525..24145 - 621 WP_130692290 TraH family protein virB1
ELI36_RS29985 (ELI36_29990) 24163..25329 - 1167 WP_130692292 conjugal transfer protein TraB -
ELI36_RS29990 (ELI36_29995) 25319..25882 - 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELI36_RS29995 (ELI36_30000) 25879..29202 - 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELI36_RS30000 (ELI36_30005) 29457..29750 + 294 WP_128409207 conjugal transfer protein TraC -
ELI36_RS30005 (ELI36_30010) 29755..29970 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELI36_RS30010 (ELI36_30015) 29957..31888 + 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELI36_RS30015 (ELI36_30020) 32326..32775 + 450 WP_130692300 thermonuclease family protein -

Host bacterium

ID   1598 GenBank   NZ_SIQJ01000006
Plasmid name   pSM158_Rh07 Incompatibility group   -
Plasmid size   32810 bp Coordinate of oriT [Strand]   29274..29314 [-]
Host baterium   Rhizobium ruizarguesonis strain SM158

Cargo genes

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