Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106853
Name   oriT_pRM41A in_silico
Organism   Sinorhizobium meliloti Rm41
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_018682 (225190..225244 [-], 55 nt)
oriT length   55 nt
IRs (inverted repeats)      25..30, 35..40  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 55 nt

>oriT_pRM41A
CCCCGCCGGGGCGCAAAAGCAGAGCGTCGCAACAGCGACGTATAATTGCGCCCTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4521 GenBank   WP_041169435
Name   traA_BN406_RS18705_pRM41A 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: 123045.14 Da        Isoelectric Point: 10.0902

>WP_041169435.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMQYEREARTIDYTRKQGLLHEEFVIPADAPEWLRSMVADR
SVSSASEAFWNKVEDFEKRSDAQLAKDVTIALPIELTADQNIALVRDFVERHITSKGIVADWVYHDAPGN
PHVHLMTTLRPLTDDGFGAKKVALLGPDGKPIRNDAGKIVYELWAGSLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIEVEPTIHIGVGATAIDRKAEQAKTQSSAGSPKLERIELQEARRSENARRIQRRPE
IVLDLITREKSVFDERDVAKILHRYIDDAALFQSLMIRVLQSPEALRLERERISFATGTRLSAKYTTRKL
IRLEAEMAKRAIWLAGRFSHGVREAVLEATFARHSRLSEEQKTAIEHVAGSERIAAVIGRAGAGKTTMMK
AAREGWEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSSWELRWNEGRNQLDAKTVFVLDEAGMVSSRQM
AHLVETVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGKVRKA
VATYTAHGRMIGLRLKDEAVDTLIADWSRDYDPAKTTLILAHLRRDVRMLNDMARAELVERGILGEGFAF
RTEDGHRNFAVGDQIVFLKNEGSLGVKNGMLGKVVEAAHNRIVAEIGEGEHRRQVAIEQRSYNNVDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHRDDLRVYYGSRSFAFAGGLTKILSRKNAKETTLDYE
KAPFYRQALRFAETRGLHIVNVARTIARDRLEWTVRQKQKLADLAHRLLAIGTKLGFGASTKPTHSQSSK
ETRPMVAGIATFPKTVEQAVADKIEADPGLKKQWEDVSSRFNLVYAQPEAAFKTVNVDAMLKDETVARST
LAKVAGQPESFGPLKGKSGLLASRVDKQDRERAERNIPALAQSLGDYLRQRSQAEQRYQAEEVVARRKLS
INIPALSPNARQTLERVRDAIDRNDLPSALEFALADKMVKAELEGFAKAVADRFGERTFLTLAAKDTNGE
TFKTITAGIGPGQKAEVQSAWSLMRAVQKLSAHERTVEAVKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(863-959)

AAA domain (AAA_30)

(387-570)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(684-741)


  Protein structure



No available structure.




T4CP

ID   4584 GenBank   WP_014989434
Name   traG_BN406_RS18690_pRM41A insolico UniProt ID   _
Length   660 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 660 a.a.        Molecular weight: 71017.95 Da        Isoelectric Point: 8.8337

>WP_014989434.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MTANKITLAVAPVVLMVLAVIGLTGIEQWMSTLGKTDAARLILGRVGIALPYVTAAAIGVIYLFASAGST
SVRVAGWGALAGSATTMLVAMAREATRLATFAGQVPDNTSITSYLDHATMVGATAAFMAGCFALRVALIG
NAAFARAEPKRIRGKRALHGEADWMKMHDAAKLFADTGGIVIGERYRVDKDSTAARSFRADDPETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMIHEHRKGAARFIRILD
PKEPETGFNALDWIGQFGGTKEEDIASVASWIMSDSGGMRGVRDDFFRASALQLLTALLADVCLSGHTGP
ENQTLRQVRANLAEPEPKLRERLQSIYDNSNSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYSNYA
ALVSGSTFSTDALAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGEVEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIAQVSRSFQAKGSSRTRSKQLAARPLIQAHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHPSGTTSEARVIQPARSATSKADPGE

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   4585 GenBank   WP_014989453
Name   t4cp2_BN406_RS18790_pRM41A insolico UniProt ID   _
Length   817 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 817 a.a.        Molecular weight: 91661.63 Da        Isoelectric Point: 6.3231

>WP_014989453.1 conjugal transfer protein TrbE [Sinorhizobium meliloti]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINSILSRLG
SGWMIQVEAVRIPTFDYPSEDRCHFPDTVTRAIDAERRAHFARERGHFESKHALILTYRPIESKKTALSR
YIYSDEESRKRTYADTVLFIFKNAVREIEQYFANTLSIRRMETREAVERGGVRVARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPITYRWSSRFIF
LDAEEARQKLERTRKKWRQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVIIL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPSAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYNQAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDVQEAGPALAFCPLAELATDADRAWATEWIEMLVALQGVTVTPDHRN
AISRQVGLMANAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLTLGAFQTFEIEVLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLILLDEAWLMLGHPVFRRKIQEWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSIATPKREYYIATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPIHWLQTRGVHDAATLLKA

  Protein domains


Predicted by InterproScan.

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: 230357..245098

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BN406_RS18710 (BN406_06824) 228621..229187 + 567 WP_014989437 conjugative transfer signal peptidase TraF -
BN406_RS18715 (BN406_06825) 229177..230340 + 1164 WP_014989438 conjugal transfer protein TraB -
BN406_RS18720 (BN406_06826) 230357..230965 + 609 WP_014989439 TraH family protein virB1
BN406_RS18725 (BN406_06827) 231087..231713 - 627 WP_014989440 DUF433 domain-containing protein -
BN406_RS18730 (BN406_06828) 231985..232701 + 717 WP_014989441 DUF6088 family protein -
BN406_RS18735 (BN406_06829) 232682..233791 + 1110 WP_041169408 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
BN406_RS18740 (BN406_06830) 233821..234039 - 219 WP_014989443 helix-turn-helix transcriptional regulator -
BN406_RS18745 (BN406_06831) 234244..234561 + 318 WP_014989444 transcriptional repressor TraM -
BN406_RS18750 (BN406_06832) 234565..235269 - 705 WP_014989445 autoinducer binding domain-containing protein -
BN406_RS18755 (BN406_06833) 235585..236883 - 1299 WP_014989446 IncP-type conjugal transfer protein TrbI virB10
BN406_RS18760 (BN406_06834) 236896..237333 - 438 WP_014989447 conjugal transfer protein TrbH -
BN406_RS18765 (BN406_06835) 237337..238149 - 813 WP_014989448 P-type conjugative transfer protein TrbG virB9
BN406_RS18770 (BN406_06836) 238167..238829 - 663 WP_014989449 conjugal transfer protein TrbF virB8
BN406_RS18775 (BN406_06837) 238836..240020 - 1185 WP_014989450 P-type conjugative transfer protein TrbL virB6
BN406_RS18780 (BN406_06838) 240014..240214 - 201 WP_014989451 entry exclusion protein TrbK -
BN406_RS18785 (BN406_06839) 240211..240957 - 747 WP_234826536 P-type conjugative transfer protein TrbJ virB5
BN406_RS18790 (BN406_06840) 240986..243439 - 2454 WP_014989453 conjugal transfer protein TrbE virb4
BN406_RS18795 (BN406_06841) 243450..243749 - 300 WP_014989454 conjugal transfer protein TrbD virB3
BN406_RS18800 (BN406_06842) 243742..244131 - 390 WP_014989455 TrbC/VirB2 family protein virB2
BN406_RS18805 (BN406_06843) 244121..245098 - 978 WP_014989456 P-type conjugative transfer ATPase TrbB virB11
BN406_RS18810 (BN406_06844) 245109..245732 - 624 WP_014989457 acyl-homoserine-lactone synthase -

Host bacterium

ID   7290 GenBank   NC_018682
Plasmid name   pRM41A Incompatibility group   -
Plasmid size   246023 bp Coordinate of oriT [Strand]   225190..225244 [-]
Host baterium   Sinorhizobium meliloti Rm41

Cargo genes

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