Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101186
Name   oriT_pSM166B_Rh08 in_silico
Organism   Rhizobium ruizarguesonis strain SM166B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQV01000006 (238411..238444 [-], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_pSM166B_Rh08
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1183 GenBank   WP_130657460
Name   traA_ELI48_RS32340_pSM166B_Rh08 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: 122987.83 Da        Isoelectric Point: 9.6219

>WP_130657460.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKFVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKVEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQGPEALRLERERINFATGSRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLEATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWEIRWNQSRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDAALDLARGNVGKA
VDAYRGYGHVRGLDLKAQAVESLIADWNHGYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLGKVVEASRNRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYD
KASFYGQALRFAEARGFHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSFPDTI
KEAKPMVSGITTFPQTLDQAVEDKLAADPGLKKQWEDVSTRFQLVYATPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPESFGAIKGKTGLLASRGDKQDREKAIANVPALARNLERYLRERAEAELKHETEERAVRLKV
SVDIPALSSAAKQTLERVRDVIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTDGQKAEVQSTWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(686-740)

AAA domain (AAA_30)

(387-572)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   784 GenBank   WP_065276635
Name   t4cp2_ELI48_RS32250_pSM166B_Rh08 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91588.38 Da        Isoelectric Point: 5.9977

>WP_065276635.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKPFRVTGPSFADLVPYAGLIDDGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSKDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNALRELEQYFANSLSIRRMETRETFERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETQDAIAQASSRLVAYGYYTPVVVL
FDIDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRTLKSEHGHDWPIHWLETRGVHDAASLFK

  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   785 GenBank   WP_130657461
Name   traG_ELI48_RS32355_pSM166B_Rh08 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: 69518.76 Da        Isoelectric Point: 8.9386

>WP_130657461.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALAVMPAALMILVVIGMTGIEQWLSGFGKTEAARLAWGRTGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTETLNADKSVLAYLDPATAIGAGVALMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRIDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLD
PRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDGGGVRGVRDDFFRASALQLLTALIADVCLSGHTDG
HDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFATNDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKVRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMVGDTPKPA

  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: 218141..233275

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI48_RS32215 (ELI48_32215) 213468..214682 - 1215 WP_065276629 plasmid replication protein RepC -
ELI48_RS32220 (ELI48_32220) 214872..215909 - 1038 WP_130657451 plasmid partitioning protein RepB -
ELI48_RS32225 (ELI48_32225) 215906..217129 - 1224 WP_065276670 plasmid partitioning protein RepA -
ELI48_RS32230 (ELI48_32230) 217506..218144 + 639 WP_130660092 acyl-homoserine-lactone synthase -
ELI48_RS32235 (ELI48_32235) 218141..219118 + 978 WP_065276632 P-type conjugative transfer ATPase TrbB virB11
ELI48_RS32240 (ELI48_32240) 219108..219491 + 384 WP_065276633 TrbC/VirB2 family protein virB2
ELI48_RS32245 (ELI48_32245) 219484..219783 + 300 WP_130654279 conjugal transfer protein TrbD virB3
ELI48_RS32250 (ELI48_32250) 219794..222244 + 2451 WP_065276635 conjugal transfer protein TrbE virb4
ELI48_RS32255 (ELI48_32255) 222222..223019 + 798 WP_130657453 P-type conjugative transfer protein TrbJ virB5
ELI48_RS32260 (ELI48_32260) 223016..223216 + 201 WP_130676499 entry exclusion protein TrbK -
ELI48_RS32265 (ELI48_32265) 223210..224391 + 1182 WP_065276638 P-type conjugative transfer protein TrbL virB6
ELI48_RS32270 (ELI48_32270) 224412..225074 + 663 WP_130676500 conjugal transfer protein TrbF virB8
ELI48_RS32275 (ELI48_32275) 225092..225904 + 813 WP_065276640 P-type conjugative transfer protein TrbG virB9
ELI48_RS32280 (ELI48_32280) 225908..226342 + 435 WP_130657454 conjugal transfer protein TrbH -
ELI48_RS32285 (ELI48_32285) 226354..227652 + 1299 WP_130660093 IncP-type conjugal transfer protein TrbI virB10
ELI48_RS32290 (ELI48_32290) 227963..228667 + 705 WP_130654288 autoinducer binding domain-containing protein -
ELI48_RS32295 (ELI48_32295) 228671..228994 - 324 WP_130654289 transcriptional repressor TraM -
ELI48_RS32300 (ELI48_32300) 229218..229460 + 243 WP_130654290 helix-turn-helix transcriptional regulator -
ELI48_RS39965 (ELI48_32305) 229563..229994 + 432 Protein_217 hypothetical protein -
ELI48_RS32310 (ELI48_32310) 230085..230702 + 618 WP_130654291 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI48_RS32315 (ELI48_32315) 230695..231172 + 478 Protein_219 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI48_RS32320 (ELI48_32320) 231169..232533 + 1365 Protein_220 IS66 family transposase -
ELI48_RS32325 (ELI48_32325) 232658..233275 - 618 WP_130657457 TraH family protein virB1
ELI48_RS32330 (ELI48_32330) 233292..234455 - 1164 WP_130657458 conjugal transfer protein TraB -
ELI48_RS32335 (ELI48_32335) 234445..235008 - 564 WP_130657459 conjugative transfer signal peptidase TraF -

Host bacterium

ID   1630 GenBank   NZ_SIQV01000006
Plasmid name   pSM166B_Rh08 Incompatibility group   -
Plasmid size   266786 bp Coordinate of oriT [Strand]   238411..238444 [-]
Host baterium   Rhizobium ruizarguesonis strain SM166B

Cargo genes

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