Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102556
Name   oriT_pSM39_Rh01_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM39
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIKU01000002 (1081307..1081347 [-], 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_pSM39_Rh01_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1907 GenBank   WP_130784879
Name   traA_ELG91_RS29510_pSM39_Rh01_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   1522 GenBank   WP_041937055
Name   t4cp2_ELG91_RS26885_pSM39_Rh01_Rh07 insolico UniProt ID   _
Length   561 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 561 a.a.        Molecular weight: 61077.14 Da        Isoelectric Point: 7.0403

>WP_041937055.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Rhizobium]
MIHASQIKIAFANMMHMAARDPLWAIVAFISFPLRYARSFLKGAVGYVIVIVTVYFGIDYLRRVILGSSR
GDVIWHIGDWIFMLFAVVLLIRFLSEPLITHFATASDADTHGSARFAGRREIAPLTKAEGGLLIGRANNS
GRLLRYSGPAHLLTMAPTRSGKGVGTIIPNLLTADRSIICIDPKGENAKIAGEAREKFGPVHILDPFGVT
GGPSAAFNPMDGVDKDSVDVAEDVSTLADALVFDEPGLSGDAHWNEEAKALIAGLLLHVIASQSDDRRTL
TTLRHLLTLAPEAFRAVLDAMQDSDAVNGLVARAANRHLGKSDREASGVLSAAQRHTHFLDSPRMTEVLS
RSDFRFGDLKADKATVFLVLPPDRLAAYSRWLRLLVAQSLTEMARTAPSPHPSAPPVLYLLDEFAALGHL
APIERAMGLMAGYGVQLWPIVQDIHQLRATYRQRAGTFLSNAGVLQVFGVNDHDSARLVSDLLGQETVVF
NTAARALDSEKSGLSFAEQHVGRPLLTPDEVRNMHAETELLFIAGQRPIVATKLRYYADPEFSGLFTASQ
I

  Protein domains


Predicted by InterproScan.

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

(140-552)

  Protein structure



No available structure.



ID   1523 GenBank   WP_128409206
Name   traG_ELG91_RS29525_pSM39_Rh01_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: 1061892..1083924

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELG91_RS29385 (ELG91_29390) 1057422..1058444 - 1023 WP_128408794 plasmid partitioning protein RepB -
ELG91_RS29390 (ELG91_29395) 1058441..1059655 - 1215 WP_130784921 plasmid partitioning protein RepA -
ELG91_RS37475 1060567..1060779 - 213 WP_245458276 hypothetical protein -
ELG91_RS29405 (ELG91_29410) 1061257..1061895 + 639 WP_063473646 acyl-homoserine-lactone synthase -
ELG91_RS29410 (ELG91_29415) 1061892..1062869 + 978 WP_130784875 P-type conjugative transfer ATPase TrbB virB11
ELG91_RS29415 (ELG91_29420) 1062859..1063242 + 384 WP_128408797 TrbC/VirB2 family protein virB2
ELG91_RS29420 (ELG91_29425) 1063235..1063534 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELG91_RS29425 (ELG91_29430) 1063545..1066000 + 2456 Protein_986 conjugal transfer protein TrbE -
ELG91_RS29430 (ELG91_29435) 1065972..1066775 + 804 WP_128408799 P-type conjugative transfer protein TrbJ virB5
ELG91_RS29435 (ELG91_29440) 1066772..1066972 + 201 WP_128408800 entry exclusion protein TrbK -
ELG91_RS29440 (ELG91_29445) 1066966..1068147 + 1182 WP_130784876 P-type conjugative transfer protein TrbL virB6
ELG91_RS29445 (ELG91_29450) 1068168..1068830 + 663 WP_128408802 conjugal transfer protein TrbF virB8
ELG91_RS29450 (ELG91_29455) 1068848..1069660 + 813 WP_130784877 P-type conjugative transfer protein TrbG virB9
ELG91_RS29455 (ELG91_29460) 1069664..1070104 + 441 WP_128408804 conjugal transfer protein TrbH -
ELG91_RS29460 (ELG91_29465) 1070116..1071414 + 1299 WP_130784878 IncP-type conjugal transfer protein TrbI virB10
ELG91_RS29465 (ELG91_29470) 1071723..1072427 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELG91_RS29470 (ELG91_29475) 1072412..1072753 - 342 WP_128408807 transcriptional repressor TraM -
ELG91_RS29475 (ELG91_29480) 1072979..1073221 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELG91_RS29480 (ELG91_29485) 1073335..1073967 + 633 WP_128408809 DUF433 domain-containing protein -
ELG91_RS29485 (ELG91_29490) 1073964..1074338 + 375 WP_128408810 DUF5615 family PIN-like protein -
ELG91_RS29490 (ELG91_29495) 1074695..1075410 + 716 Protein_999 Crp/Fnr family transcriptional regulator -
ELG91_RS29495 (ELG91_29500) 1075555..1076175 - 621 WP_128408811 TraH family protein virB1
ELG91_RS29500 (ELG91_29505) 1076193..1077359 - 1167 WP_128408812 conjugal transfer protein TraB -
ELG91_RS29505 (ELG91_29510) 1077349..1077861 - 513 WP_245458277 conjugative transfer signal peptidase TraF -
ELG91_RS29510 (ELG91_29515) 1077909..1081235 - 3327 WP_130784879 Ti-type conjugative transfer relaxase TraA -
ELG91_RS29515 (ELG91_29520) 1081490..1081783 + 294 WP_128409207 conjugal transfer protein TraC -
ELG91_RS29520 (ELG91_29525) 1081788..1082003 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELG91_RS29525 (ELG91_29530) 1081990..1083924 + 1935 WP_128409206 Ti-type conjugative transfer system protein TraG virb4
ELG91_RS29535 (ELG91_29540) 1084364..1084666 + 303 Protein_1007 thermonuclease family protein -
ELG91_RS29540 (ELG91_29545) 1084736..1085815 + 1080 WP_130784880 IS630 family transposase -
ELG91_RS29545 (ELG91_29550) 1085812..1085961 + 150 Protein_1009 thermonuclease family protein -
ELG91_RS29550 (ELG91_29555) 1086193..1086507 - 315 WP_128408836 hypothetical protein -
ELG91_RS37815 (ELG91_29560) 1086951..1087259 + 309 WP_130784881 WGR domain-containing protein -
ELG91_RS37485 1087428..1087571 + 144 WP_245488070 hypothetical protein -
ELG91_RS36855 1087793..1087954 - 162 WP_018516739 hypothetical protein -
ELG91_RS29565 (ELG91_29570) 1088255..1088566 - 312 WP_127431460 DUF736 domain-containing protein -

Host bacterium

ID   3000 GenBank   NZ_SIKU01000002
Plasmid name   pSM39_Rh01_Rh07 Incompatibility group   -
Plasmid size   1148096 bp Coordinate of oriT [Strand]   1081307..1081347 [-]
Host baterium   Rhizobium leguminosarum strain SM39

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixA, fixB, nifE, nifK, nifD, nifH, fixC, fixX, nifT, nodJ, nodI, nodC, nodA, nodD, nodF, nodE, nodM
Anti-CRISPR   AcrIIA7