Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107560
Name   oriT_pSinA in_silico
Organism   Sinorhizobium sp. M14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_021209 (88307..88343 [+], 37 nt)
oriT length   37 nt
IRs (inverted repeats)      22..27, 32..37  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 37 nt

>oriT_pSinA
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5073 GenBank   WP_015647745
Name   traA_HS899_RS00435_pSinA insolico UniProt ID   R4IL57
Length   1107 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1107 a.a.        Molecular weight: 123035.13 Da        Isoelectric Point: 9.7753

>WP_015647745.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Sinorhizobium/Ensifer group]
MAVPHFSVSIVARGSGRSAVLSAAYRHCARMDYEREARTIDYTGKQGLLHEEFVIPADAPDWLRTMIADR
SVSGASEAFWNKVEAFEKRVDAQLAKDITIALPIELSSEQNIALMQDFVAEHLTTKGMVADWVYHDAPGN
PHVHLMTTLRPLSEDGFGAKKVTVRGSDGQPMRNDAGKIIYELWAGGAEDFNAFRDGWFAVQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHIGVGATAIERKSEMENRLATAGSRKLERIELQEERRAENVRRIQRNPG
IVLDLITRERSVFDNQDVAKILHRYVDDAALFQSLMARIMQHLDVLRLDCERINFTSGVRTPARYTTREM
IRLEAEMANRSIWLSQRSSHGVRQKIIEAVFERHKRLSDEQKTAIEHVAGQERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGAALAGKAAEGLEKEAGILSRTLSSWELRWAQGRDQLDDKTVMVLDEAGMVSSKQM
ALLVEEATVRGAKLILIGDPEQLQPIEAGAAFRAITDRIGYAELETIYRQREQWMRDASLDLARGNIAKA
VESYSANGRMMGSTLKSQAVENLISDWNREYDPAHSSLILAHLRRDVRMLNTLARAKLVERGLVDDGHAF
KTEDGVRHFAAGDRIVFLKNESSLGVKNGMLAKVVEATPGRIVAEIGEGEHRKAISVEQRFYNNVDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDIGVYYGARSFAKAGGLAELLSRTNSKETTLDYE
KGAFYRAALRFADARGLHLVNVARTLVRDRLDWTVRQKQKLFDLTARLATIRAQLGLKGPNTQVTSKPDM
EAKPMVSGITTFPKSIDHAVEDRLVADPGLKKQWQEVTTRFIQVFAEPETAFKAVNVDAMLKDPARAQTT
LAKIAAEPERFGALKGKTGIFAGANEKAARDTALVNAPALARNLERYVTARVEAERKHEAQERAIRLKVS
IDIPALSPSARQTLERIRDAIDRNDLSAGLEYALADRNVKAELEGFAKAVSERFGERSLLPISAKDANGE
TFHKITAGMTPSQKSEVKSAWNSMRTVQQLAAHERTTLALKQAETARQTQTKGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

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

(863-958)


  Protein structure


Source ID Structure
AlphaFold DB R4IL57


T4CP

ID   5289 GenBank   WP_015647742
Name   traG_HS899_RS00420_pSinA insolico UniProt ID   _
Length   645 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 645 a.a.        Molecular weight: 69657.82 Da        Isoelectric Point: 9.3417

>WP_015647742.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Sinorhizobium/Ensifer group]
MTANRILLAVVPPLVMIAIALMLPGIEQWLASFGKTAEAKLTLGRIGLSLPYIASAAIGLIFLLSAQGSV
NIKTAGWGVAAGSGAVIAIAVVREGMRLSQFAGQAPAARSILSYVDPATMTGAAAALFSGMFALRVAVIG
NAAFSRSEPKRIRGKRALHGEAEWMKLPEAEKLFADGGGIVIGERYRVDRDSTAALSFRADQPETWGTGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVKAHRIKAGRDVIVLD
PKDPDIGFNALDWIGQHGGTKEEDIAAVASWIMSESGRVSGVRDDFFRASGLQLLTAIIADVCLSGHTEK
KNQTLRTVRMNLSEPEPKLRARLQEIYDNSESDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYPNYA
GLVSGSTFSTDDIASGTTDVFVALDLKTLETHGGLARVIIGSFLNAIYNRDGAMPGRALFLLDEVARLGF
MRILETARDAGRKYGITLLMIYQSIGQMRETYGGRDATSKWFESASWISFSAINDPETADYISRRCGTTT
VEIDQVSRSFQARGSSRTRSKQLASRPLIQPHEVLRMRADEQIVFTGGNAPLRCGRAMWFRRADMKSCVG
DNRFHGNRGPLEIKV

  Protein domains


Predicted by InterproScan.

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

(164-635)

  Protein structure



No available structure.



ID   5290 GenBank   WP_015647761
Name   t4cp2_HS899_RS00525_pSinA insolico UniProt ID   _
Length   811 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 811 a.a.        Molecular weight: 91066.53 Da        Isoelectric Point: 5.7391

>WP_015647761.1 MULTISPECIES: conjugal transfer protein TrbE [Sinorhizobium/Ensifer group]
MVALCSLRPSAPSFADLVPYAGLVDNGTILLKDGSLMAGWYFAGPDSESATDFERNDLSRQINTILSRLG
SGWMIQVEAVRIPTTDYPSAERSHFPDAVTRMIDDERRKHFEQERGHFESRHALVLTYRPPERRRSGVTR
YIYSDTESRTATYADTVLDSFRRSTREIEQYLGNVISIERMRTREVPERGGTRIARYDELFQFIRFCITG
ENHPVCLPEIPMYLDWLATAELEHGLTPKVENRFLSAIAIDGLPAESWPGILNSLDLLPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIIL
FDESREKLADKAESVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLIPLNSVWS
GSPLAPCPFYPPDAPPLTQVASGSSPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYKGAQVFA
FDKGNSILPLTLAVDGNHYEIGGEAGEGARLAFCPLSDLSTETDRAWASEWIETLVSLQGVTVNPDHRNA
ISRQIGLMAGAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDSLTLGQFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAERS
GIIDVLKESCPTKICLPNGAARESGTREFYERIGFNPRQIEIVAAAIPKREYYVTSPDGRRLFDMALGPL
TLSFVGASGKADLARIRELLSTYGKDWPTQWLNERGINRYA

  Protein domains


Predicted by InterproScan.

ABC transporter (ABC_tran)

(449-626)

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

(193-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 93482..108825

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS899_RS00440 (ST430451_p045) 91742..92308 + 567 WP_015647746 conjugative transfer signal peptidase TraF -
HS899_RS00445 (ST430451_p044) 92298..93464 + 1167 WP_015647747 conjugal transfer protein TraB -
HS899_RS00450 (ST430451_p043) 93482..94093 + 612 WP_015647748 TraH family protein virB1
HS899_RS00455 (ST430451_p042) 94126..94746 - 621 WP_015647749 RES family NAD+ phosphorylase -
HS899_RS00460 (ST430451_p088) 94747..95502 - 756 WP_015647750 hypothetical protein -
HS899_RS00465 95637..95888 - 252 WP_115422184 type II toxin-antitoxin system VapB family antitoxin -
HS899_RS00470 (ST430451_p089) 96193..96897 + 705 WP_015647751 transcriptional regulator TraR -
HS899_RS00475 (ST430451_p090) 96912..97211 - 300 WP_015647752 transcriptional repressor TraM -
HS899_RS00480 (ST430451_p091) 97677..98483 + 807 WP_343215831 LuxR family transcriptional regulator -
HS899_RS00485 (ST430451_p092) 98601..99263 + 663 WP_015647754 acyl-homoserine-lactone synthase -
HS899_RS00490 (ST430451_p093) 99303..100598 - 1296 WP_015647755 IncP-type conjugal transfer protein TrbI virB10
HS899_RS00495 (ST430451_p094) 100611..101054 - 444 WP_015647756 conjugal transfer protein TrbH -
HS899_RS00500 (ST430451_p095) 101058..101888 - 831 WP_015647757 P-type conjugative transfer protein TrbG virB9
HS899_RS00505 (ST430451_p096) 101904..102566 - 663 WP_015647758 conjugal transfer protein TrbF virB8
HS899_RS00510 (ST430451_p097) 102588..103769 - 1182 WP_015647759 P-type conjugative transfer protein TrbL virB6
HS899_RS00515 103774..103950 - 177 WP_115422182 entry exclusion protein TrbK -
HS899_RS00520 (ST430451_p098) 103944..104747 - 804 WP_015647760 P-type conjugative transfer protein TrbJ virB5
HS899_RS00525 (ST430451_p099) 104740..107175 - 2436 WP_015647761 conjugal transfer protein TrbE virb4
HS899_RS00530 (ST430451_p100) 107186..107485 - 300 WP_015647762 conjugal transfer protein TrbD virB3
HS899_RS00535 (ST430451_p101) 107478..107870 - 393 WP_015647763 TrbC/VirB2 family protein virB2
HS899_RS00540 (ST430451_p102) 107860..108825 - 966 WP_015647764 P-type conjugative transfer ATPase TrbB virB11

Host bacterium

ID   7995 GenBank   NC_021209
Plasmid name   pSinA Incompatibility group   -
Plasmid size   108938 bp Coordinate of oriT [Strand]   88307..88343 [+]
Host baterium   Sinorhizobium sp. M14

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   aioR/aoxR, aioS/aoxS, aioX/aoxX, arsC, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -