Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100321
Name   oriT1_pO26-Vir in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_012487 (68493..68584 [+], 92 nt)
oriT length   92 nt
IRs (inverted repeats)      IR1: 7..15, 17..25  (GTCGGGGCT..AGCCCTGAC)
  IR2: 32..49, 52..69  (GTAATCGTATAGCCGTGC..GCGCGGTTATACGATTAC)
Location of nic site      77..78
Conserved sequence flanking the
  nic site    		  CATCCTG|T
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 92 nt

>oriT1_pO26-Vir
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAGCCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTTTCAGGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   392 GenBank   YP_002756615
Name   Relaxase_pO26-Vir insolico UniProt ID   C1J8G4
Length   906 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 906 a.a.        Molecular weight: 105063.76 Da        Isoelectric Point: 7.9400

>YP_002756615.1 relaxase (plasmid) [Escherichia coli]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEMKAEIPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAADLAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELEIKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIVQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPLWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPEMARNGELESCLDVHRTLATAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGRNLGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
GLIQCRSLIEEMIADGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAAADIFERVKPECRYNPELAASDEVEPGFRRDPEIRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQLMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNVDRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLDLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure


Source ID Structure
AlphaFold DB C1J8G4


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 105548..144829

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HKK63_RS00535 (p026VIR_p115) 101592..102029 + 438 WP_000539951 type IV pilus biogenesis protein PilM -
HKK63_RS00540 (p026VIR_p116) 102061..103680 + 1620 WP_001035565 PilN family type IVB pilus formation outer membrane protein -
HKK63_RS00545 (p026VIR_p117) 103701..104996 + 1296 WP_000129883 type 4b pilus protein PilO2 -
HKK63_RS00550 (p026VIR_p118) 104986..105444 + 459 WP_000095886 type IV pilus biogenesis protein PilP -
HKK63_RS00555 (p026VIR_p119) 105548..107056 + 1509 WP_000880806 ATPase, T2SS/T4P/T4SS family virB11
HKK63_RS00560 (p026VIR_p120) 107058..108152 + 1095 WP_000697154 type II secretion system F family protein -
HKK63_RS00565 (p026VIR_p121) 108214..108750 + 537 WP_000111521 type 4 pilus major pilin -
HKK63_RS00570 (p026VIR_p122) 108795..109280 + 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
HKK63_RS00575 (p026VIR_p123) 109386..109922 + 537 WP_023649457 prepilin peptidase -
HKK63_RS00580 (p026VIR_p124) 109940..111301 + 1362 WP_001168171 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HKK63_RS00915 111415..111609 + 195 Protein_112 integrase -
HKK63_RS00585 (p026VIR_p126) 111774..112595 + 822 WP_000845373 hypothetical protein traE
HKK63_RS00590 (p026VIR_p127) 112697..113899 + 1203 WP_000979993 conjugal transfer protein TraF -
HKK63_RS00595 (p026VIR_p128) 114003..114461 + 459 WP_001170111 DotD/TraH family lipoprotein -
HKK63_RS00600 (p026VIR_p129) 114458..115294 + 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
HKK63_RS00605 (p026VIR_p130) 115278..116426 + 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
HKK63_RS00890 116423..116713 + 291 WP_000817801 IcmT/TraK family protein traK
HKK63_RS00610 (p026VIR_p132) 116777..120838 + 4062 WP_001441856 LPD7 domain-containing protein -
HKK63_RS00615 (p026VIR_p133) 120855..121205 + 351 WP_001056367 hypothetical protein traL
HKK63_RS00620 (p026VIR_p134) 121217..121912 + 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
HKK63_RS00625 (p026VIR_p135) 121923..122897 + 975 WP_000547385 DotH/IcmK family type IV secretion protein traN
HKK63_RS00630 (p026VIR_p136) 122901..124238 + 1338 WP_001272018 conjugal transfer protein TraO traO
HKK63_RS00635 (p026VIR_p137) 124235..124948 + 714 WP_000787003 conjugal transfer protein TraP traP
HKK63_RS00640 (p026VIR_p138) 124945..125475 + 531 WP_000987021 conjugal transfer protein TraQ traQ
HKK63_RS00645 (p026VIR_p139) 125522..125920 + 399 WP_000088813 DUF6750 family protein traR
HKK63_RS00655 (p026VIR_p141) 126143..126961 + 819 WP_012680981 hypothetical protein traT
HKK63_RS00660 (p026VIR_p142) 126954..127154 - 201 WP_179894028 hypothetical protein -
HKK63_RS00665 (p026VIR_p143) 127256..130300 + 3045 WP_001024766 conjugal transfer protein traU
HKK63_RS00925 130300..130596 + 297 WP_012680982 hypothetical protein traV
HKK63_RS00930 130696..130920 + 225 WP_284488195 hypothetical protein traV
HKK63_RS00675 (p026VIR_p145) 130878..132083 + 1206 WP_168989887 conjugal transfer protein TraW traW
HKK63_RS00680 (p026VIR_p146) 132080..132649 + 570 WP_000650752 conjugal transfer protein TraX -
HKK63_RS00685 (p026VIR_p147) 132724..134889 + 2166 WP_168989888 DotA/TraY family protein traY
HKK63_RS00690 (p026VIR_p148) 134977..135630 + 654 WP_001402874 plasmid IncI1-type surface exclusion protein ExcA -
HKK63_RS00695 (p026VIR_p149) 135904..137490 + 1587 WP_012680985 TnsA endonuclease N-terminal domain-containing protein -
HKK63_RS00700 (p026VIR_p150) 137628..137780 - 153 WP_001302699 Hok/Gef family protein -
HKK63_RS00705 (p026VIR_p151) 138110..138352 + 243 WP_001363144 hypothetical protein -
HKK63_RS00710 (p026VIR_p153) 138652..139020 + 369 WP_001363143 hypothetical protein -
HKK63_RS00715 (p026VIR_p154) 139024..139239 + 216 WP_000266543 hypothetical protein -
HKK63_RS00720 (p026VIR_p155) 139437..140060 - 624 WP_001155250 helix-turn-helix domain-containing protein -
HKK63_RS00725 (p026VIR_p156) 140220..140687 + 468 WP_000598962 thermonuclease family protein -
HKK63_RS00730 (p026VIR_p157) 140837..141013 + 177 WP_001054907 hypothetical protein -
HKK63_RS00935 141076..141171 - 96 WP_001363141 DinQ-like type I toxin DqlB -
HKK63_RS00940 141760..141855 - 96 WP_001363141 DinQ-like type I toxin DqlB -
HKK63_RS00740 (p026VIR_p162) 142392..143708 + 1317 WP_044192348 IncI1-type conjugal transfer protein TrbA trbA
HKK63_RS00745 (p026VIR_p163) 143705..144829 + 1125 WP_000152384 DsbC family protein trbB
HKK63_RS00750 (p026VIR_p164) 144810..147110 + 2301 WP_000077653 F-type conjugative transfer protein TrbC -

Host bacterium

ID   783 GenBank   NC_012487
Plasmid name   pO26-Vir Incompatibility group   IncB/O/K/Z
Plasmid size   168100 bp Coordinate of oriT [Strand]   68493..68584 [+]; 150410..150495 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   -
Virulence gene   virulence region: toxB gene, the serine protease gene (espP), the catalase-peroxidase gene (katP), and the hemolysin (hly) gene cluster
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -