Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101155
Name   oriT_pSM143_Rh07 in_silico
Organism   Rhizobium ruizarguesonis strain SM143
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIOZ01000007 (29375..29415 [-], 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_pSM143_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1152 GenBank   WP_130692296
Name   traA_ELI00_RS33040_pSM143_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   725 GenBank   WP_130692276
Name   t4cp2_ELI00_RS32955_pSM143_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   726 GenBank   WP_130692298
Name   traG_ELI00_RS33055_pSM143_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: 9962..31989

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI00_RS32915 (ELI00_32915) 5492..6514 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELI00_RS32920 (ELI00_32920) 6511..7725 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELI00_RS32925 (ELI00_32925) 8342..8596 - 255 WP_130692270 IS66 family insertion sequence element accessory protein TnpB -
ELI00_RS39965 8637..8849 - 213 WP_245458276 hypothetical protein -
ELI00_RS32935 (ELI00_32935) 9327..9965 + 639 WP_130692272 acyl-homoserine-lactone synthase -
ELI00_RS32940 (ELI00_32940) 9962..10939 + 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELI00_RS32945 (ELI00_32945) 10929..11312 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELI00_RS32950 (ELI00_32950) 11305..11604 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI00_RS32955 (ELI00_32955) 11615..14071 + 2457 WP_130692276 conjugal transfer protein TrbE virb4
ELI00_RS32960 (ELI00_32960) 14043..14846 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELI00_RS32965 (ELI00_32965) 14843..15043 + 201 WP_128408800 entry exclusion protein TrbK -
ELI00_RS32970 (ELI00_32970) 15037..16218 + 1182 WP_130692278 P-type conjugative transfer protein TrbL virB6
ELI00_RS32975 (ELI00_32975) 16239..16901 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELI00_RS32980 (ELI00_32980) 16919..17731 + 813 WP_130692282 P-type conjugative transfer protein TrbG virB9
ELI00_RS32985 (ELI00_32985) 17735..18175 + 441 WP_130692284 conjugal transfer protein TrbH -
ELI00_RS32990 (ELI00_32990) 18187..19485 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELI00_RS32995 (ELI00_32995) 19794..20498 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELI00_RS33000 (ELI00_33000) 20483..20824 - 342 WP_128408807 transcriptional repressor TraM -
ELI00_RS33005 (ELI00_33005) 21050..21292 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELI00_RS33010 (ELI00_33010) 21406..22038 + 633 WP_128408809 DUF433 domain-containing protein -
ELI00_RS33015 (ELI00_33015) 22035..22409 + 375 WP_130692288 DUF5615 family PIN-like protein -
ELI00_RS33020 (ELI00_33020) 22766..23481 + 716 Protein_25 Crp/Fnr family transcriptional regulator -
ELI00_RS33025 (ELI00_33025) 23626..24246 - 621 WP_130692290 TraH family protein virB1
ELI00_RS33030 (ELI00_33030) 24264..25430 - 1167 WP_130692292 conjugal transfer protein TraB -
ELI00_RS33035 (ELI00_33035) 25420..25983 - 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELI00_RS33040 (ELI00_33040) 25980..29303 - 3324 WP_130692296 Ti-type conjugative transfer relaxase TraA -
ELI00_RS33045 (ELI00_33045) 29558..29851 + 294 WP_128409207 conjugal transfer protein TraC -
ELI00_RS33050 (ELI00_33050) 29856..30071 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELI00_RS33055 (ELI00_33055) 30058..31989 + 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELI00_RS33060 (ELI00_33060) 32427..32876 + 450 WP_130692300 thermonuclease family protein -
ELI00_RS33065 (ELI00_33065) 33118..33432 - 315 WP_130692302 hypothetical protein -
ELI00_RS33070 (ELI00_33070) 34213..35706 + 1494 WP_130764305 group II intron reverse transcriptase/maturase -
ELI00_RS33075 (ELI00_33075) 36058..36366 + 309 WP_063473655 WGR domain-containing protein -
ELI00_RS39325 36434..36607 - 174 WP_165403408 hypothetical protein -

Host bacterium

ID   1599 GenBank   NZ_SIOZ01000007
Plasmid name   pSM143_Rh07 Incompatibility group   -
Plasmid size   62178 bp Coordinate of oriT [Strand]   29375..29415 [-]
Host baterium   Rhizobium ruizarguesonis strain SM143

Cargo genes

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