Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100629
Name   oriT_pRetIE4771a in_silico
Organism   Rhizobium etli bv. mimosae str. IE4771
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NZ_CP006987 (221232..221262 [+], 31 nt)
oriT length   31 nt
IRs (inverted repeats)      16..21, 26..31  (CGTCGC..GCGACG)
Location of nic site      5..6
Conserved sequence flanking the
  nic site    		  AGGG|CGCA
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 31 nt

>oriT_pRetIE4771a
AAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   701 GenBank   WP_040140156
Name   TraA_pRetIE4771a insolico UniProt ID   A0A060IDC2
Length   1103 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122223.38 Da        Isoelectric Point: 9.6579

>WP_040140156.1 Ti-type conjugative transfer relaxase TraA [Rhizobium etli]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMDYDREARTIDYTRKQGLLHEEFVIPTDAPEWLRSMIADR
SVAGVSEAFWNRVEDFEKRSDAQLAKDVTIALPIELTAEQNIALVRDFVEQHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKIAVTGPDGNPIRNDAGKIVYELWAGSIDDFNAFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELEPTIHLGVGTKAIERKSDGASEPVELERLDLQEARRSENVRRIDRNPELVLAL
IMREKSVFDERDVAKILHRYVDDAALFQSLMVRILLCPETFRIERERIDLASGIRVPAKYTTREMIRLEA
EMANRAVWLSRRSSHGVRDAVLAATFARHERLSDEQRTAIEHVAGPERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGAALAGKAAEGLEKEAGIISRTLASWELRWNQGRDLLGSKTVFVLDESGMVSSRQMALFVE
AVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGSALDAYR
ANGKIIGSDLKADAVDNLITAWDRDYDPVKTSLILAHLRRDVRMLNQMARIKLIERGVLDQGTMFKTADG
ERNFAVGDQIVFLKNEGSLGVKNGMLAKVVEVGPGRITARIGDGENARQVVVEQRFYDNLDHGYATTIHK
SQGATVDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKNGGLIPILSRRNAKETTLDYEKSDFY
RQALHFAEARGLHLVNVARTLVRDRLEWVVSQKQKLANLGARLAAVAGKLGLVRGAAQSPSQNNIKEAKP
MVSGITTFAKSVDQAIEDKVAADPGLKKQWEEVSTRFHLVYAQPESAFKAVNVDVLLKDETVAKSTIAKI
GSEPEHFGALKGKTGILSSRADKQEREKAQTIAPALARNLERYLRQRAEAERKFEVEERAVRLKVSIDIP
ALSPNAKQTLERVRDAIDRNDLPTGLGYALADKMVKAELEGFAKAVSERFGERTFLSLAAKDPNGQTFNT
VTSGMTAGQKAEVQAAWNSMRTVQQLAAHERTTEALKQAETLRQAKSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

AAA domain (AAA_30)

(382-567)

MobA/MobL family (MobA_MobL)

(17-243)

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

(859-955)


  Protein structure


Source ID Structure
AlphaFold DB A0A060IDC2


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 226387..240104

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IE4771_RS22535 (IE4771_PA00206) 224651..225217 + 567 WP_051649906 conjugative transfer signal peptidase TraF -
IE4771_RS22540 (IE4771_PA00207) 225207..226370 + 1164 WP_040140159 conjugal transfer protein TraB -
IE4771_RS22545 (IE4771_PA00208) 226387..227001 + 615 WP_040140160 TraH family protein virB1
IE4771_RS22550 (IE4771_PA00209) 227019..227396 - 378 WP_040140162 DUF5615 family PIN-like protein -
IE4771_RS22555 (IE4771_PA00210) 227393..228025 - 633 WP_040140164 DUF433 domain-containing protein -
IE4771_RS22560 (IE4771_PA00211) 228127..228348 - 222 WP_040140166 helix-turn-helix transcriptional regulator -
IE4771_RS22565 (IE4771_PA00212) 228578..228892 + 315 WP_040140167 transcriptional repressor TraM -
IE4771_RS22570 (IE4771_PA00213) 228896..229600 - 705 WP_040140168 autoinducer binding domain-containing protein -
IE4771_RS22575 (IE4771_PA00214) 229680..230420 - 741 WP_010048466 LuxR family transcriptional regulator -
IE4771_RS22580 (IE4771_PA00215) 230583..231887 - 1305 WP_040140169 IncP-type conjugal transfer protein TrbI virB10
IE4771_RS22585 (IE4771_PA00216) 231900..232337 - 438 WP_040140170 conjugal transfer protein TrbH -
IE4771_RS22590 (IE4771_PA00217) 232341..233153 - 813 WP_040140171 P-type conjugative transfer protein TrbG virB9
IE4771_RS22595 (IE4771_PA00218) 233171..233833 - 663 WP_040140173 conjugal transfer protein TrbF virB8
IE4771_RS22600 (IE4771_PA00219) 233854..235035 - 1182 WP_040140175 P-type conjugative transfer protein TrbL virB6
IE4771_RS22605 (IE4771_PA00220) 235029..235229 - 201 WP_010058419 entry exclusion protein TrbK -
IE4771_RS22610 (IE4771_PA00221) 235226..236023 - 798 WP_040140177 P-type conjugative transfer protein TrbJ virB5
IE4771_RS22615 (IE4771_PA00222) 236001..238451 - 2451 WP_040140179 conjugal transfer protein TrbE virb4
IE4771_RS22620 (IE4771_PA00223) 238462..238761 - 300 WP_040140181 conjugal transfer protein TrbD virB3
IE4771_RS22625 (IE4771_PA00224) 238754..239137 - 384 WP_040140183 TrbC/VirB2 family protein virB2
IE4771_RS22630 (IE4771_PA00225) 239127..240104 - 978 WP_040140184 P-type conjugative transfer ATPase TrbB virB11
IE4771_RS22635 (IE4771_PA00226) 240115..240738 - 624 WP_040140186 acyl-homoserine-lactone synthase -
IE4771_RS22640 (IE4771_PA00227) 241115..242338 + 1224 WP_040140230 plasmid partitioning protein RepA -
IE4771_RS22645 (IE4771_PA00228) 242335..243372 + 1038 WP_040140188 plasmid partitioning protein RepB -
IE4771_RS22650 (IE4771_PA00229) 243557..244771 + 1215 WP_040140190 plasmid replication protein RepC -

Host bacterium

ID   1089 GenBank   NZ_CP006987
Plasmid name   pRetIE4771a Incompatibility group   _
Plasmid size   244771 bp Coordinate of oriT [Strand]   221232..221262 [+]
Host baterium   Rhizobium etli bv. mimosae str. IE4771

Cargo genes

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