Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101008
Name   oriT_pSfr64a experimental
Organism   Sinorhizobium fredii GR64
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP137019 (170979..171022 [+], 44 nt)
oriT length   44 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  AAGGGCGCAATTA
Note   

  oriT sequence  


Download         Length: 44 nt

>oriT_pSfr64a
GGATCCGAAGGGCGCAATTATACGTCGCTGGCGCGACGCCCTGC

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Laura Cervantes et al. (2019) Plasmid pSfr64a and the symbiotic plasmid pSfr64b of Sinorhizobium fredii GR64 control each other's conjugative transfer through quorum-sensing elements. Plasmid. 106:102443. [PMID:31689451]


Relaxase

ID   1076 GenBank   WP_013984768
Name   TraA_pSfr64a experimental UniProt ID   _
Length   1103 a.a. PDB ID   
Note   

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122349.35 Da        Isoelectric Point: 9.3572

>WP_013984768.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Sinorhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPEWLRSMIADR
SVSGASEAFWNMVEDFEKRSDAQLAKDVTIALPLELTPEQNIALVRDFVEQHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKIAVTGPDGNPIRNDAGKIVYELWAGSIDDFNAFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIDLEPTIHLGVGTKAIERKSDAASEPVELERLDLQEARRSENVRRIDRNPELVLAL
IMREKSVFDERDVAKILHRYVDDAALFQSLMVRILLCPETFRIEREGIDLASGIRVPAKYTTREMIRLEA
EMANRAVWLSQRSSHGVRDVVLAATFERHERLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMRAAREA
WEAAGYHVVGGALAGKAAEGLEKEAGIISRTLSSWELRWNEGRNQLDSKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGKAVDAYR
ANGRVIGSDLKADAVDNLIAAWDRDYDPAKTSLILAHLRRDVRMLNQMARIKLIERGVLDQGSMFRTVDG
ERNFAVGDQIVFLKNEGSLGVKNGMLAKVVEAGPGRITALIGDGENARQVLVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKNGGLIPILSRRNAKETTLDYEKSAFY
REALRFAEARGLHLVNVARTLVRDRLEWLVGQKQKLANLGARLAAVAGKLGIVRGAAQSPTQNNTKEAKP
MVSGITTFAKSVDQAIEDKVAADPGLKKQWEEVSTRFHLVYAQPESAFKVVDVDAMLKDETFAKSTIAKI
GSEPEHFGALKGKTGILASRADREEREKAQTNAPALARNLERYLRQRTEAERKFEVEERAVRRKVSIDIP
ALSPNAKQTLERVRDAIDRNDLPAGLEFALADKMVKAELEGFAKAVSERFGERTFLSLAAKDPNGQTFNS
VTSGMTAGQKAEVQAAWSSMRTVQQLAAHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-567)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

MobA/MobL family (MobA_MobL)

(17-243)

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

(859-955)


  Protein structure



No available structure.



  Reference


[1] Laura Cervantes et al. (2019) Plasmid pSfr64a and the symbiotic plasmid pSfr64b of Sinorhizobium fredii GR64 control each other's conjugative transfer through quorum-sensing elements. Plasmid. 106:102443. [PMID:31689451]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 176143..189536

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SFGR64A_RS33015 (SFGR64A_33010) 174406..174972 + 567 WP_013984769 conjugative transfer signal peptidase TraF -
SFGR64A_RS33020 (SFGR64A_33015) 174962..176125 + 1164 WP_013984770 conjugal transfer protein TraB -
SFGR64A_RS33025 (SFGR64A_33020) 176143..176754 + 612 WP_013984771 TraH family protein virB1
SFGR64A_RS33030 (SFGR64A_33025) 176885..177301 + 417 WP_013984772 DUF6088 family protein -
SFGR64A_RS33035 (SFGR64A_33030) 177291..178202 + 912 WP_234705213 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
SFGR64A_RS33040 (SFGR64A_33035) 178268..178486 - 219 WP_015341952 helix-turn-helix transcriptional regulator -
SFGR64A_RS33045 (SFGR64A_33040) 178672..178992 + 321 WP_013984775 transcriptional repressor TraM -
SFGR64A_RS33050 (SFGR64A_33045) 178989..179753 - 765 WP_234705210 autoinducer binding domain-containing protein -
SFGR64A_RS33055 (SFGR64A_33050) 180026..181321 - 1296 WP_013984777 IncP-type conjugal transfer protein TrbI virB10
SFGR64A_RS33060 (SFGR64A_33055) 181339..181779 - 441 WP_013984778 conjugal transfer protein TrbH -
SFGR64A_RS33065 (SFGR64A_33060) 181783..182595 - 813 WP_013984779 P-type conjugative transfer protein TrbG virB9
SFGR64A_RS33070 (SFGR64A_33065) 182613..183275 - 663 WP_013984780 conjugal transfer protein TrbF virB8
SFGR64A_RS33075 (SFGR64A_33070) 183300..184478 - 1179 WP_013984781 P-type conjugative transfer protein TrbL virB6
SFGR64A_RS33080 (SFGR64A_33075) 184483..184659 - 177 WP_013984782 entry exclusion protein TrbK -
SFGR64A_RS33085 (SFGR64A_33080) 184653..185456 - 804 WP_028003103 P-type conjugative transfer protein TrbJ virB5
SFGR64A_RS33090 (SFGR64A_33085) 185431..187884 - 2454 WP_013984784 conjugal transfer protein TrbE virb4
SFGR64A_RS33095 (SFGR64A_33090) 187894..188193 - 300 WP_013984785 conjugal transfer protein TrbD virB3
SFGR64A_RS33100 (SFGR64A_33095) 188186..188569 - 384 WP_013984786 TrbC/VirB2 family protein virB2
SFGR64A_RS33105 (SFGR64A_33100) 188559..189536 - 978 WP_015341957 P-type conjugative transfer ATPase TrbB virB11
SFGR64A_RS33110 (SFGR64A_33105) 189547..190173 - 627 WP_013984788 acyl-homoserine-lactone synthase TraI -
SFGR64A_RS33115 (SFGR64A_33110) 190562..191776 + 1215 WP_013984789 plasmid partitioning protein RepA -
SFGR64A_RS33120 (SFGR64A_33115) 191773..192798 + 1026 WP_013984790 plasmid partitioning protein RepB -
SFGR64A_RS33125 (SFGR64A_33120) 192954..194165 + 1212 WP_013984791 plasmid replication protein RepC -

Host bacterium

ID   1469 GenBank   NZ_CP137019
Plasmid name   pSfr64a Incompatibility group   -
Plasmid size   194165 bp Coordinate of oriT [Strand]   170979..171022 [+]
Host baterium   Sinorhizobium fredii GR64

Cargo genes

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