Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102543
Name   oriT_pSM15_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM15
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKB01000006 (195037..195077 [-], 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_pSM15_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1894 GenBank   WP_130784879
Name   traA_ELG72_RS35085_pSM15_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   1501 GenBank   WP_128409206
Name   traG_ELG72_RS35100_pSM15_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 175621..197654

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG72_RS34960 (ELG72_34960) 171151..172173 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG72_RS34965 (ELG72_34965) 172170..173384 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG72_RS39300 174296..174508 - 213 WP_245458276 hypothetical protein -
ELG72_RS34980 (ELG72_34980) 174986..175624 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG72_RS34985 (ELG72_34985) 175621..176598 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG72_RS34990 (ELG72_34990) 176588..176971 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG72_RS34995 (ELG72_34995) 176964..177263 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG72_RS35000 (ELG72_35000) 177274..179730 + 2457 Protein_176 conjugal transfer protein TrbE -
ELG72_RS35005 (ELG72_35005) 179702..180505 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG72_RS35010 (ELG72_35010) 180502..180702 + 201 WP_128408800 entry exclusion protein TrbK -
ELG72_RS35015 (ELG72_35015) 180696..181877 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG72_RS35020 (ELG72_35020) 181898..182560 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG72_RS35025 (ELG72_35025) 182578..183390 + 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG72_RS35030 (ELG72_35030) 183394..183834 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG72_RS35035 (ELG72_35035) 183846..185144 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG72_RS35040 (ELG72_35040) 185453..186157 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG72_RS35045 (ELG72_35045) 186142..186483 - 342 WP_128408807 transcriptional repressor TraM -
ELG72_RS35050 (ELG72_35050) 186709..186951 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG72_RS35055 (ELG72_35055) 187065..187697 + 633 WP_128408809 DUF433 domain-containing protein -
ELG72_RS35060 (ELG72_35060) 187694..188068 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG72_RS35065 (ELG72_35065) 188425..189140 + 716 Protein_189 Crp/Fnr family transcriptional regulator -
ELG72_RS35070 (ELG72_35070) 189285..189905 - 621 WP_128408811 TraH family protein virB1
ELG72_RS35075 (ELG72_35075) 189923..191089 - 1167 WP_128408812 conjugal transfer protein TraB -
ELG72_RS35080 (ELG72_35080) 191079..191591 - 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG72_RS35085 (ELG72_35085) 191639..194965 - 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG72_RS35090 (ELG72_35090) 195220..195513 + 294 WP_128409207 conjugal transfer protein TraC -
ELG72_RS35095 (ELG72_35095) 195518..195733 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG72_RS35100 (ELG72_35100) 195720..197654 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG72_RS35110 (ELG72_35110) 198094..198396 + 303 Protein_197 thermonuclease family protein -
ELG72_RS35115 (ELG72_35115) 198466..199545 + 1080 WP_130784880 IS630 family transposase -
ELG72_RS35120 (ELG72_35120) 199542..199691 + 150 Protein_199 thermonuclease family protein -
ELG72_RS35125 (ELG72_35125) 199923..200237 - 315 WP_128408836 hypothetical protein -
ELG72_RS39630 (ELG72_35130) 200681..200989 + 309 WP_130784881 WGR domain-containing protein -
ELG72_RS39310 201158..201301 + 144 WP_245488070 hypothetical protein -
ELG72_RS38685 201523..201684 - 162 WP_018516739 hypothetical protein -
ELG72_RS35140 (ELG72_35140) 201985..202296 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   2987 GenBank   NZ_SIKB01000006
Plasmid name   pSM15_Rh07 Incompatibility group   -
Plasmid size   263562 bp Coordinate of oriT [Strand]   195037..195077 [-]
Host baterium   Rhizobium leguminosarum strain SM15

Cargo genes

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