Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113721
Name   oriT_pHAMBI1141b in_silico
Organism   Neorhizobium galegae bv. officinalis bv. officinalis str. HAMBI 1141
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_HG938357 (155328..155361 [+], 34 nt)
oriT length   34 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_pHAMBI1141b
TCCAAGGGCGCAATTATACGTCGCTGATACGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8786 GenBank   WP_040126092
Name   traA_RG1141_RS30710_pHAMBI1141b insolico UniProt ID   A0A068TK78
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 122820.24 Da        Isoelectric Point: 9.9897

>WP_040126092.1 Ti-type conjugative transfer relaxase TraA [Neorhizobium galegae]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMDFEREARTIDYTQKQGLLHEEIVIPADAPEWLRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVASHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSTEDFIAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSEASAPKLERIELLEQRRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTRAM
IRLEAEMANRAIWLAGRTSHGVREAMLRATFARHVRLSDEQRTAIEHVAAATRIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIGSRTLSSWELRWNQGRNKLDHKTVFVLDEAGMVSSRQM
ALLVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYTELETIYRQRQQWMRDASLDLARGNIRRA
VDAYTAHGRMIGLRLKDDAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVAEGSPF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMFAKVIEAAPGRLVAEIGEGEHRRLVTIEQRFYNSLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIQILSRRNAQETTLDYE
KASFYRQALRFAEARGLHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGKAIGLARGSNKQTAPNTI
KEAKPMVSGITTFPKSLDQAVEDKLGADPALKKQWEDVSTRFHLVYAQPEAAFKAINVDSMLKDQSVAQS
TLARVAGEPESFGALKGKTGLLASRADRQDREKAIANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTSG
KTFETVTAGMTAGQKAEVQSAWNSMRTVQQLAAYERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-570)

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

(864-960)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(689-740)


  Protein structure


Source ID Structure
AlphaFold DB A0A068TK78


T4CP

ID   10182 GenBank   WP_040126044
Name   traG_RG1141_RS30695_pHAMBI1141b insolico UniProt ID   _
Length   656 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 656 a.a.        Molecular weight: 70706.87 Da        Isoelectric Point: 9.5002

>WP_040126044.1 Ti-type conjugative transfer system protein TraG [Neorhizobium galegae]
MTINRIALVVVPTALMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYIAGAAIGVLLLFANAGSI
NIKQAGWGVVAGSSGTILVAAVRETARLSSFMKTVPADKTVLAFLDTATSIGATAALLCACFALRVALIG
NAAFARAEPKRVQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDNVGARAFRADSAETWGAGG
KSPLLCFDGTFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
SRKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
MEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGRKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEAARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQARGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHTIGDAPKPARSNPARSAMEQS

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   10183 GenBank   WP_040126061
Name   t4cp2_RG1141_RS30795_pHAMBI1141b insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91474.32 Da        Isoelectric Point: 5.9999

>WP_040126061.1 conjugal transfer protein TrbE [Neorhizobium galegae]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWRQKVRPFLDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVLL
FDSDREALQEKAEAIRRVIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHALIFGPTGSGKSTLLALIAAQFRRYEHAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDIAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRILKSEHGHEWPIRWLETRGVHDAASLLK

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 160498..174308

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RG1141_RS30715 (RG1141_PB01540) 158762..159325 + 564 WP_051900784 conjugative transfer signal peptidase TraF -
RG1141_RS30720 (RG1141_PB01550) 159315..160481 + 1167 WP_040126047 conjugal transfer protein TraB -
RG1141_RS30725 (RG1141_PB01560) 160498..161118 + 621 WP_040126048 TraH family protein virB1
RG1141_RS30730 (RG1141_PB01570) 161192..161566 - 375 WP_040126049 DUF4087 domain-containing protein -
RG1141_RS30735 (RG1141_PB01580) 161979..162353 - 375 WP_040126050 DUF5615 family PIN-like protein -
RG1141_RS30740 (RG1141_PB01590) 162350..162982 - 633 WP_040126051 DUF433 domain-containing protein -
RG1141_RS30745 163101..163349 - 249 WP_040126052 helix-turn-helix domain-containing protein -
RG1141_RS30750 (RG1141_PB01600) 163608..163898 + 291 WP_040126053 transcriptional repressor TraM -
RG1141_RS30755 (RG1141_PB01610) 163902..164606 - 705 WP_040126094 autoinducer binding domain-containing protein -
RG1141_RS30760 (RG1141_PB01620) 164791..166089 - 1299 WP_040126054 IncP-type conjugal transfer protein TrbI virB10
RG1141_RS30765 (RG1141_PB01630) 166101..166541 - 441 WP_040126055 conjugal transfer protein TrbH -
RG1141_RS30770 (RG1141_PB01640) 166545..167360 - 816 WP_040126056 P-type conjugative transfer protein TrbG virB9
RG1141_RS30775 (RG1141_PB01650) 167376..168038 - 663 WP_040126057 conjugal transfer protein TrbF virB8
RG1141_RS30780 (RG1141_PB01660) 168059..169246 - 1188 WP_040126058 P-type conjugative transfer protein TrbL virB6
RG1141_RS30785 (RG1141_PB01670) 169251..169427 - 177 WP_040126059 entry exclusion protein TrbK -
RG1141_RS30790 (RG1141_PB01680) 169421..170227 - 807 WP_040126060 P-type conjugative transfer protein TrbJ virB5
RG1141_RS30795 (RG1141_PB01690) 170205..172655 - 2451 WP_040126061 conjugal transfer protein TrbE virb4
RG1141_RS30800 (RG1141_PB01700) 172666..172965 - 300 WP_040126062 conjugal transfer protein TrbD virB3
RG1141_RS30805 (RG1141_PB01710) 172958..173341 - 384 WP_040126063 TrbC/VirB2 family protein virB2
RG1141_RS30810 (RG1141_PB01720) 173331..174308 - 978 WP_040126064 P-type conjugative transfer ATPase TrbB virB11
RG1141_RS30815 (RG1141_PB01730) 174319..174942 - 624 WP_040126065 acyl-homoserine-lactone synthase -

Host bacterium

ID   14156 GenBank   NZ_HG938357
Plasmid name   pHAMBI1141b Incompatibility group   -
Plasmid size   175279 bp Coordinate of oriT [Strand]   155328..155361 [+]
Host baterium   Neorhizobium galegae bv. officinalis bv. officinalis str. HAMBI 1141

Cargo genes

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