Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102518
Name   oriT_pSM163B_Rh04 in_silico
Organism   Rhizobium leguminosarum strain SM163B
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQO01000005 (196381..196421 [-], 41 nt)
oriT length   41 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: 41 nt

>oriT_pSM163B_Rh04
TCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1869 GenBank   WP_130724856
Name   traA_ELI41_RS32420_pSM163B_Rh04 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: 122905.34 Da        Isoelectric Point: 10.1546

>WP_130724856.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDFEREARTIDYTRKRGLLHEEFVIPAGAPTWLHAMIADR
SVSGASEAFWNKVEAFEKRSDAQLAKDVTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEYGFGAKKVAVTSPDGNPMRNDAGKIVYELWAGSADDFNAVRDGWFACQNRHLALAG
LDIRVDGRSFEKQCIELTPTIHLGVATKAIDRKADQADARSSAWSPKLERVELQEDRRAENARRIQRRPE
IVLDLITREKSVFDERDVAKILHRHIDDAALFQNLMMRVLQSPEALRLERDRIDFATGIRTTAKYTTREM
IRLEAEMVNRAILLSGRASHGVGEAVLEVTFARHARLSDEQRTAIERVVGRERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNRGRDRIDARTVFVLDEAGMVSSRQM
ALFVEAVVEAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASRDLARGNVSQA
VDAYRDHGHVRGLDVKAQAIESLIADWDRDYDPSKSSLILAHLRRDVRMLNDMARAKLVERGIVAVGFAF
KTDDGTRMFAAGDQMVFLKNEGSLGVKNGMLAKVIEAAPGRLVVALGEGDHRRLVTIEQRFYNKLDHGYA
TTIHKSQGATVDCVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFGKSGGLIPILSRRNAKETTLDYQ
KSSLYGQALRFAEARGLHLMNVARTIAHDRLHWVVRQKQKLADLGARLAAIGVKLGRAASAKTSPKPTAK
ESKPMVSGISTFPKSIDQSVEDKLAADPGLKKQWEEVSTRFHLVYAQPESAFKAVNVNAMLKDPTIAKTT
LAKIAGEPERFGALRGKTGVFAIRGDKKDRERAIANVPALARNLERYLRQRAEIERKHETEERAVRRQVS
VDIPALSAPAKQTLERVGDAIDRNDLPAGLEYALADTMVKAELDRFAKAVSERFGERTFLGIASKDPSGE
TFKSVTAGMNPAQKAEIQTAWNSMRTIQQLSAHEKTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-572)

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

(863-959)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(697-740)


  Protein structure



No available structure.




T4CP

ID   1467 GenBank   WP_130724837
Name   t4cp2_ELI41_RS32280_pSM163B_Rh04 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 91630.99 Da        Isoelectric Point: 5.6579

>WP_130724837.1 conjugal transfer protein TrbE [Rhizobium leguminosarum]
MVSLRAFRHTAPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESSTDFERNEVSRQINAILSRLG
SGWMIQVEAVRLATVDYASAGKSHFPDPVTLAIDEERRAHFEREQGHFESRHAIIATYRPTERRRSRLSK
YIYSDEDSRKQSYADTVLFIFRNAIREVEQYLANIISIRRMLTRETAERDGTRVARYDELLQFIRFCVTG
DNHPVRVPDIPMYLDWIVTAELQHGLAPKVENRFLGVVAIDGLPSESWPGILNSLDSLPLGYRWSSRFIF
LDAEEARVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAISMVAETEDAIAQASSQLVAYGYYTPVVVL
FDNDAERLNDKTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GNPQAPCPFYPPDSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLACGGDHYEIGADEDTGLSFCPLSELSSDGDRAWASEWIESLVAMQGITITPDHRNAIS
RQIGLMDGAPGRSISDFVSGVQMREIKDALHHYTVDGPMGQLLDAESDGLELGLFQTFEIEQVMNMGERN
LVPVLTYLFRRIEKRLTGAPSLIVIDEAWLMLGHSVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREAGTRDFYERIGFNERQIEIVATAIPKREYYVASPEGRRLFDMALGPLTL
SFVGASSKDDLKHIRALHHEHGPEWPLHWLQKRGIKDAASLLEDA

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(190-400)

  Protein structure



No available structure.



ID   1468 GenBank   WP_130724858
Name   traG_ELI41_RS32435_pSM163B_Rh04 insolico UniProt ID   _
Length   655 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 655 a.a.        Molecular weight: 71129.03 Da        Isoelectric Point: 8.9838

>WP_130724858.1 Ti-type conjugative transfer system protein TraG [Rhizobium leguminosarum]
MTANKIALVSVPIALMMLVTIGMTGFEQWLSEFGKTETARLILGRTGLALPYIASAAAGIIFLFASTGST
NIKLAGWGVVGGSSATIVIAALRETVRLSAIFDHFPAVRSALSYADPATMIGAGAALTSAGFALRVALVG
NAAFARSEPRRIRGRRALHGDAEWMKSAEAEKLFPDTGGIVIGERYRVDKDITAKQSFRADSVETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVLLDPSNEVAPMVIEHRTNAGRDVRILD
PKTPDTGFNALDWIGLHGRTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGRTEE
DDQTLRQVRKNLSEPEPKLRARLQSIYDNSISDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSESTFSTNDISAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALNGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSVQSKGSSHTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
ENRFHSPVSGDKNAIDPKTPMKLRR

  Protein domains


Predicted by InterproScan.

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

(164-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 165790..175256

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI41_RS32245 (ELI41_32255) 161042..162307 - 1266 WP_130724834 plasmid replication protein RepC -
ELI41_RS32250 (ELI41_32260) 162546..163586 - 1041 WP_130724835 plasmid partitioning protein RepB -
ELI41_RS32255 (ELI41_32265) 163571..164788 - 1218 WP_064649788 plasmid partitioning protein RepA -
ELI41_RS32260 (ELI41_32270) 165153..165776 + 624 WP_064649789 acyl-homoserine-lactone synthase TraI -
ELI41_RS32265 (ELI41_32275) 165790..166755 + 966 WP_130724836 P-type conjugative transfer ATPase TrbB virB11
ELI41_RS32270 (ELI41_32280) 166745..167125 + 381 WP_097629539 TrbC/VirB2 family protein virB2
ELI41_RS32275 (ELI41_32285) 167115..167414 + 300 WP_064649791 conjugal transfer protein TrbD virB3
ELI41_RS32280 (ELI41_32290) 167424..169871 + 2448 WP_130724837 conjugal transfer protein TrbE virb4
ELI41_RS32285 (ELI41_32295) 169843..170643 + 801 WP_130724838 P-type conjugative transfer protein TrbJ virB5
ELI41_RS32290 (ELI41_32300) 170670..170837 + 168 WP_197496372 DUF2749 domain-containing protein -
ELI41_RS32295 (ELI41_32305) 170858..172012 + 1155 WP_130724875 P-type conjugative transfer protein TrbL virB6
ELI41_RS32300 (ELI41_32310) 172032..172694 + 663 WP_012760245 conjugal transfer protein TrbF virB8
ELI41_RS32305 (ELI41_32315) 172710..173531 + 822 WP_064649795 P-type conjugative transfer protein TrbG virB9
ELI41_RS32310 (ELI41_32320) 173534..173962 + 429 WP_130724840 conjugal transfer protein TrbH -
ELI41_RS32315 (ELI41_32325) 173976..175256 + 1281 WP_130724841 IncP-type conjugal transfer protein TrbI virB10
ELI41_RS32320 (ELI41_32330) 175281..175991 - 711 WP_097629533 autoinducer binding domain-containing protein -
ELI41_RS32325 (ELI41_32335) 176397..177092 - 696 WP_245485920 response regulator transcription factor -
ELI41_RS32335 (ELI41_32345) 177753..178463 + 711 WP_130724844 response regulator transcription factor -
ELI41_RS32340 (ELI41_32350) 178453..179847 + 1395 WP_130724845 amidohydrolase family protein -

Host bacterium

ID   2962 GenBank   NZ_SIQO01000005
Plasmid name   pSM163B_Rh04 Incompatibility group   -
Plasmid size   202876 bp Coordinate of oriT [Strand]   196381..196421 [-]
Host baterium   Rhizobium leguminosarum strain SM163B

Cargo genes

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