Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100177
Name   oriT_R721 experimental
Organism   Escherichia coli
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_002525 (29007..29059 [-], 53 nt)
oriT length   53 nt
IRs (inverted repeats)      5..21, 25..42  (CGATTGTAACATGACCG..CGGTCTTGTGTACAATCG)
Location of nic site      50..51
Conserved sequence flanking the
  nic site    		  TATCGTG|C
Note   _

  oriT sequence  


Download         Length: 53 nt

>oriT_R721
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Varsaki A et al. (2009) Analysis of ColE1 MbeC unveils an extended ribbon-helix-helix family of nicking accessory proteins. J Bacteriol. 191(5):1446-55. [PMID:19114496]
[2] Kim SR et al. (1992) Nucleotide sequence of the R721 shufflon. J Bacteriol. 174(21):7053-8. [PMID:1400257]


Relaxase

ID   170 GenBank   NP_065331
Name   NikB_R721 insolico UniProt ID   Q9F553
Length   1272 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 1272 a.a.        Molecular weight: 145804.44 Da        Isoelectric Point: 5.1637

>NP_065331.1 relaxase (plasmid) [Escherichia coli]
MIVRYGGGNDGIVDYLINGRKAERQYTRDELDHRVVLDGDLQTTDKIIDSIENKSQERYLHITLSFHESH
VSNEVLKAVVDDYKKLLMNAYHPDEYSFYAEAHLPKIRHIQDNSTGELVERKPHIHIVIPKVNLITEKFL
NPVGDVTKGHTIEQLDAIQEFINNKYNLDSPKDYPRKDADYGKIISRVKGDLYKEHHSELKGELLSRIEN
EKIENYSVFKDIVAEYGELRIRNAGKTNEYLAVKLPGDKKYTNLKSPLFRQNYIETRTLTLEKPTHKEIE
KRLNAWLNKTSHEIKHIFNQAEKTRELYKTLSPSQQIDFLQERIKEYDSREKLNERNSQQTSGRAGGYKS
CPKKFARIRQSEATVGLSRMPQRGMVYGINGFTRPDSVSVLSDISQRDLAKQLPQREHPGQDVRRDYDRQ
FTESGIKSLERSSFLCETMFQTLNEAAEKNEITTMAEIRRNIDPVRFLSSAAERFNIIPAQHKIRTAKDG
SPRFSVGNRNMNASDFLTKHINLAWKDAKSFLLEVYSQQLENTPYTRYPTYRRLTHHEARERLNSLNLSE
KTLRNTIRFERGKLYNDLREMRRELKLIPREQRDIAVGVIVYKKLTTLERLSELDTEGRHIIRQYHADWH
KDKDEMKALERLKSYLNFDEINAISADEPELSLQKAVDSQRRLEEAKKINTKLKDLVMDKQDSRIVYRDQ
ESEKPVFTDKGNFVVAGKNPSKEEIGIMLEYSREKFGGVLKLTGSEDFKKMCAEVAAEQDMKIILRPEQY
QQMMLELKAELQGNKFEQVETQENSQESESRIEKGDALKEQATEQEQATEQAQATEQEQATEQAQATEQA
QATEQAQATEQAQATEQAQATEQAQDTEQAQATEQAQATEQAQATEQAQIAEQATSSYDPGVITRANILD
SQMLSKGTNGEFGYLKSLDSDENEIWEVLGHVPGDSDDIFSVASFDNENDAKEFCKIVNELGIDRTQALI
QEQLSSQQEQAAVQETYQESPEEILASISANEHMISGLENFLVKDRSQFSSCNGDIVVEAEITRGEGGLY
HLAVAGKHGLERGDAVARVDVTEQQFAAITGKTPSEVLTGDQTSARVPVITGIHFSTRAIENVNKLEQQK
DYVYFSTHEGLNAEIKDFSSLKDAIEWGRVECELHDLNKRDTVIYRVESEHISQGIDAVMKNAERVERHE
IEKAQGRDCTPEDGKILEAIDRFEDKFRGEGLKFEREKAESDLLNHGFTREMAEDALGKQFVQAREDHQE
SQQQRDDSQDMH

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(692-774)


  Protein structure


Source ID Structure
AlphaFold DB Q9F553


Auxiliary protein

ID   245 GenBank   NP_065330
Name   NikA_R721 insolico UniProt ID   Q9F554
Length   113 a.a. PDB ID   _
Note   relaxosome component

  Auxiliary protein sequence


Download         Length: 113 a.a.        Molecular weight: 13147.21 Da        Isoelectric Point: 10.4689

>NP_065330.1 relaxosome component (plasmid) [Escherichia coli]
MKKKTNKNVHVTFRLTEEEYAPFDRAIKELNISKSEFFRLLTIGKINTYASDKRNIPEYKRCLSQLSWAG
NNINQIAHRLNSDHLKGIISESLYKKVLNGLIGIRDRLQEIAK

  Protein domains


Predicted by InterproScan.

Bacterial mobilisation protein (MobC) (MobC)

(63-85)


  Protein structure


Source ID Structure
AlphaFold DB Q9F554

  Reference


[1] Varsaki A et al. (2009) Analysis of ColE1 MbeC unveils an extended ribbon-helix-helix family of nicking accessory proteins. J Bacteriol. 191(5):1446-55. [PMID:19114496]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46638..70260

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXE98_RS00265 (R721_54) 42127..43251 - 1125 WP_000486716 site-specific integrase -
HXE98_RS00495 43664..43885 - 222 Protein_54 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HXE98_RS00275 43861..44190 + 330 WP_001141249 hypothetical protein -
HXE98_RS00280 44733..45986 - 1254 WP_010895887 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HXE98_RS00285 (R721_56) 45999..46634 - 636 WP_000934978 A24 family peptidase -
HXE98_RS00290 (R721_57) 46638..47066 - 429 WP_001326801 lytic transglycosylase domain-containing protein virB1
HXE98_RS00295 (R721_58) 47186..47743 - 558 WP_000095048 type 4 pilus major pilin -
HXE98_RS00300 (R721_59) 47788..48897 - 1110 WP_000974903 type II secretion system F family protein -
HXE98_RS00305 (R721_60) 48888..50441 - 1554 WP_000466228 ATPase, T2SS/T4P/T4SS family virB11
HXE98_RS00310 (R721_61) 50466..50960 - 495 WP_000912555 type IV pilus biogenesis protein PilP -
HXE98_RS00315 (R721_62) 50944..52266 - 1323 WP_010895889 type 4b pilus protein PilO2 -
HXE98_RS00320 (R721_63) 52305..53948 - 1644 WP_001035589 PilN family type IVB pilus formation outer membrane protein -
HXE98_RS00325 (R721_64) 53941..54459 - 519 WP_010895890 sigma 54-interacting transcriptional regulator virb4
HXE98_RS00330 (R721_65) 54506..56464 - 1959 WP_010895891 type IV secretory system conjugative DNA transfer family protein -
HXE98_RS00335 (R721_66) 56480..57535 - 1056 WP_001059977 P-type DNA transfer ATPase VirB11 virB11
HXE98_RS00340 (R721_67) 57714..58853 - 1140 WP_000790641 TrbI/VirB10 family protein virB10
HXE98_RS00345 (R721_68) 58843..59574 - 732 WP_044083601 TrbG/VirB9 family P-type conjugative transfer protein virB9
HXE98_RS00350 (R721_69) 59610..60344 - 735 WP_000432283 type IV secretion system protein virB8
HXE98_RS00355 (R721_71) 60510..62867 - 2358 WP_010895892 VirB4 family type IV secretion system protein virb4
HXE98_RS00360 (R721_72) 62873..63193 - 321 WP_010895893 VirB3 family type IV secretion system protein virB3
HXE98_RS00365 (R721_73) 63264..63554 - 291 WP_000865478 TrbC/VirB2 family protein virB2
HXE98_RS00370 (R721_74) 63554..64138 - 585 WP_001177114 lytic transglycosylase domain-containing protein virB1
HXE98_RS00375 (R721_75) 64159..64557 - 399 WP_001153669 hypothetical protein -
HXE98_RS00380 (R721_76) 64676..65113 - 438 WP_000539665 type IV pilus biogenesis protein PilM -
HXE98_RS00385 (R721_77) 65119..66354 - 1236 WP_000733391 toxin co-regulated pilus biosynthesis Q family protein -
HXE98_RS00390 (R721_78) 66357..66644 - 288 WP_029785630 TrbM/KikA/MpfK family conjugal transfer protein -
HXE98_RS00395 (R721_79) 66816..67451 - 636 WP_000835769 hypothetical protein -
HXE98_RS00400 (R721_80) 67499..68308 + 810 WP_001005153 DUF5710 domain-containing protein -
HXE98_RS00405 (R721_81) 68361..68615 - 255 WP_000609210 EexN family lipoprotein -
HXE98_RS00410 (R721_82) 68618..69259 - 642 WP_001434037 type IV secretion system protein -
HXE98_RS00415 (R721_83) 69265..70260 - 996 WP_000276068 type IV secretion system protein virB6
HXE98_RS00425 (R721_85) 70481..70870 - 390 WP_010895894 hypothetical protein -
HXE98_RS00430 (R721_86) 71033..71626 - 594 WP_001243169 hypothetical protein -
HXE98_RS00435 (R721_87) 71777..72439 - 663 WP_001243159 hypothetical protein -
HXE98_RS00440 72450..72620 - 171 WP_000550721 hypothetical protein -
HXE98_RS00445 (R721_88) 72624..73067 - 444 WP_000498521 NfeD family protein -
HXE98_RS00450 (R721_89) 73129..74082 - 954 WP_072097371 SPFH domain-containing protein -
HXE98_RS00455 (R721_90) 74109..74285 - 177 WP_000753050 hypothetical protein -
HXE98_RS00460 (R721_91) 74278..74493 - 216 WP_001127357 DUF1187 family protein -
HXE98_RS00465 (R721_92) 74486..74992 - 507 WP_001326595 CaiF/GrlA family transcriptional regulator -

Host bacterium

ID   170 GenBank   NC_002525
Plasmid name   R721 Incompatibility group   IncI2
Plasmid size   75582 bp Coordinate of oriT [Strand]   29007..29059 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   dfrA1, ant(3'')-Ia
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -