Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104881
Name   oriT_pRGM101a in_silico
Organism   Rhizobium gallicum strain M101
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP092345 (225639..225672 [-], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      17..22, 27..32  (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_pRGM101a
CAAGGGCGCAATTATACGTCGCTGACGCGACGCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3453 GenBank   WP_239600232
Name   traA_L2W42_RS22100_pRGM101a insolico UniProt ID   _
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122478.83 Da        Isoelectric Point: 10.0051

>WP_239600232.1 Ti-type conjugative transfer relaxase TraA [Rhizobium gallicum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTCKQGLAHEEFVIPADAPDWLRTIIADR
SVPGASEAFWNKVEAFEKRSDAQLAKDVTIALPVELTYEQNIALVREFVERHIIATGMVADWVYHDAPGN
PHVHLMTTLRPLTDDGFGAKKVALLGPDGNPIRNDSGKIVYELWAGSADDFNALRDGWFACQNRHLALAG
LDISIDGRSFEKQGIKLTPTIHLGVRTKAIERKSEAATKPLPLERIELQEDRRAENARRVQRHPEIVLDL
ITREKSVFDERDVAKVLHRYIDDADLFQSLLARTLQSPETLQLESERIEFATGVRVSAKHTTREVIQLEA
EMANRAIWLSHRSSHGVREAVLEATFSRHSRLSEEQKIAIVHVAGGERIAAVIGRAGVGKTTMMKAAREA
WQAAGYRVVGGALAGKAAEGLEKEAGITSRTLASWELRWSEGRNQLDDKTVFVLDEAGMVSSRQMALFIE
AATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRKQWMRDASLDLARGKVGKAVDAYR
AYGRFKGSELKAQAVENLIADWNGDYDPVKTTLILAHLRRDVRMLNEMARAKLIERGILAEGFVFKTEDG
NRKFAAGDQIVFLKNEGSLGVKNGMLAKVVEALPGRIVAEIGEGEHRRQVRVEQRFYNKVDHGYATTIHK
SQGATVDRVKILASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSDGLIPILSRRNAKETTLDYEKGPFY
RQALRFAEARGLRLVNVARMLVRDRHEWSIRQKQKLADLAARLAAIGGKLSLSTSAKNSPNQKIIKEVKP
MVSGIATFAKSLEQAVEDKVATDPGLEKQWEEVSSRFHLVYAQPETAFKAINVDAMLKDKATAQSTISRI
GTQPESFGALKGKTGILASRADKQGREKALTNAPALARNIERYLRQRAEAERKHEVEERAVRLKVSVNIP
ALSPAAKQALERVRDAIDRNDLPVGLEYALAAKMVKAELEGFARAVSERFGERTFLPLAAKDTSGQAFQT
VTAGMSAGQKAEVQSAWNSMRTVQQFAAHERTTEALKQAETLRQTKAQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(859-955)

AAA domain (AAA_30)

(382-566)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(689-735)


  Protein structure



No available structure.




T4CP

ID   3398 GenBank   WP_239600215
Name   t4cp2_L2W42_RS22020_pRGM101a insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91381.92 Da        Isoelectric Point: 5.7875

>WP_239600215.1 conjugal transfer protein TrbE [Rhizobium gallicum]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRVSTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDAESRKKSYADTVLFAFRNAIREIEQYLANTLSIRRMETRETAERGGERIARYDELLQFVRFCITG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQNGTVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNAADAFLGSLPGNWYSNIREPLINTSNLADLIPLNAVWS
GNPVAPCPFYPPNSPPLMQVASGSTPFRLNVHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYESAQVFA
FDKGCSLLPLTLATGGDHYEIGGDNAEEGRALTFCPLSDLGSDADRAWATEWVEMLVGLQGVAITPDHRN
AISRQVGLMASAAGRSISDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGTFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLNGSPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESSPTKICLPNGAARESGTREFYERIGFNERQIEIVSSAIPKREYYVATPDGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLQTKGVRDAASLLNFE

  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   3399 GenBank   WP_239600240
Name   traG_L2W42_RS22115_pRGM101a insolico UniProt ID   _
Length   637 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 69063.39 Da        Isoelectric Point: 9.2211

>WP_239600240.1 Ti-type conjugative transfer system protein TraG [Rhizobium gallicum]
MNRVLLAITPIMLMVGVAILASGMAPSLAGFGKTEAAKLLLGRAGIALPYVLAAAIGVVFLFASVGAIRI
HFAGWGVVAGSASAIAIAALREATRLAAFAEQLPAGRFIFAYLDPATMVGAAAALMAGCFALRVALLGNA
AFARSEPTRIRGKRAMHGEADWMKLNEAEKLLPEAGGIVIGERYRVDKDSTAALSFRADSPETWGAGGKS
PLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSDEVAPMVCKRREDAGRRIRILDPR
KPQTGFNALDWIGKFGGTKEEDIAAVASWIMSDSGRASGVREDFFRASGLQLLTAIIADVCLSGHTEKEL
QTLRQVRANLSEPEPKLRQRLQDIYDNSVSPFVKENVAAFVNMTPETFSGVYANAIKETHWLSYPNYAVL
VSGSTFLTEDIASGETDVFINIDLKALETHAGLARVIIGSFVNAIYNRDGVMNGRALFLLDEVARLGHMR
ILETARDAGRKYGITLTMIYQSIGQMRETYGGRDATSKWFESASWISFAAINDPETADYISRRCGMTTVE
IDQVSRSFQAKGSSRTRSKQLTARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRQDMRIWVAEN
RFESPST

  Protein domains


Predicted by InterproScan.

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

(161-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 201643..217562

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
L2W42_RS21960 (L2W42_21960) 197759..198744 + 986 Protein_201 plasmid partitioning protein RepB -
L2W42_RS21965 (L2W42_21965) 200091..200531 + 441 WP_239600196 hypothetical protein -
L2W42_RS21970 (L2W42_21970) 200605..201306 + 702 WP_239600198 IS6 family transposase -
L2W42_RS21975 (L2W42_21975) 201375..201629 + 255 Protein_204 nitrilase-related carbon-nitrogen hydrolase -
L2W42_RS21980 (L2W42_21980) 201643..202290 + 648 WP_239600200 TraH family protein virB1
L2W42_RS21985 (L2W42_21985) 203330..204544 - 1215 WP_239600202 plasmid replication protein RepC -
L2W42_RS21990 (L2W42_21990) 204746..205771 - 1026 WP_239600204 plasmid partitioning protein RepB -
L2W42_RS21995 (L2W42_21995) 205768..207030 - 1263 WP_239600278 plasmid partitioning protein RepA -
L2W42_RS22000 (L2W42_22000) 207373..207996 + 624 WP_239600206 acyl-homoserine-lactone synthase TraI -
L2W42_RS22005 (L2W42_22005) 208007..208984 + 978 WP_239600208 P-type conjugative transfer ATPase TrbB virB11
L2W42_RS22010 (L2W42_22010) 208974..209357 + 384 WP_239600211 TrbC/VirB2 family protein virB2
L2W42_RS22015 (L2W42_22015) 209350..209649 + 300 WP_239600213 conjugal transfer protein TrbD virB3
L2W42_RS22020 (L2W42_22020) 209660..212116 + 2457 WP_239600215 conjugal transfer protein TrbE virb4
L2W42_RS22025 (L2W42_22025) 212088..212891 + 804 WP_239600217 P-type conjugative transfer protein TrbJ virB5
L2W42_RS22030 (L2W42_22030) 212888..213088 + 201 WP_239600219 entry exclusion protein TrbK -
L2W42_RS22035 (L2W42_22035) 213082..214263 + 1182 WP_239600220 P-type conjugative transfer protein TrbL virB6
L2W42_RS22040 (L2W42_22040) 214284..214946 + 663 WP_239600221 conjugal transfer protein TrbF virB8
L2W42_RS22045 (L2W42_22045) 214963..215772 + 810 WP_239600222 P-type conjugative transfer protein TrbG virB9
L2W42_RS22050 (L2W42_22050) 215776..216213 + 438 WP_239600224 conjugal transfer protein TrbH -
L2W42_RS22055 (L2W42_22055) 216225..217562 + 1338 WP_239600226 IncP-type conjugal transfer protein TrbI virB10
L2W42_RS22060 (L2W42_22060) 217859..218563 + 705 WP_239600280 autoinducer binding domain-containing protein -
L2W42_RS22065 (L2W42_22065) 218567..218890 - 324 WP_239600227 transcriptional repressor TraM -
L2W42_RS22070 (L2W42_22070) 219107..219319 + 213 WP_239600229 helix-turn-helix transcriptional regulator -
L2W42_RS22075 (L2W42_22075) 219444..220072 + 629 Protein_224 DUF433 domain-containing protein -
L2W42_RS36075 220069..220356 + 288 Protein_225 DUF5615 family PIN-like protein -
L2W42_RS22085 (L2W42_22085) 220368..220520 - 153 Protein_226 conjugal transfer protein TraH -
L2W42_RS22090 (L2W42_22090) 220537..221700 - 1164 WP_239600230 conjugal transfer protein TraB -
L2W42_RS22095 (L2W42_22095) 221690..222193 - 504 WP_239600231 conjugative transfer signal peptidase TraF -

Host bacterium

ID   5319 GenBank   NZ_CP092345
Plasmid name   pRGM101a Incompatibility group   -
Plasmid size   513852 bp Coordinate of oriT [Strand]   225639..225672 [-]
Host baterium   Rhizobium gallicum strain M101

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   linJ, dxnH, LinG
Symbiosis gene   fixS, fixQ, fixO, fixN, nodM, nodD, mLTONO_5203, nifX, nifN, nifK, nifD, nifH, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifZ, nifT, nodH, nodJ, nodI, nodU, nodS, nodC, nodB, nodA
Anti-CRISPR   AcrIF3, AcrIIC1