Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100613
Name   oriT_p92-9000 in_silico
Organism   Shigella dysenteriae
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_032099 (24104..24189 [-], 86 nt)
oriT length   86 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: 86 nt

>oriT_p92-9000
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAGCCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   685 GenBank   YP_009328414
Name   Putativerelaxaseofp92-9000 insolico UniProt ID   A0A142CND5
Length   906 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 906 a.a.        Molecular weight: 104908.50 Da        Isoelectric Point: 8.2690

>YP_009328414.1 hypothetical protein (plasmid) [Shigella dysenteriae 1]
MNAIIPKKRRDGKSSFEDLIAYTSVRDDVPEDELRPDTEVKGEVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCLSLESAAEEMQKAADLAHFSKDDTDPVFHYILSWPAHESPRSEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINCLPWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGIALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVEAPGRYDPEAINVDIRPEKVAETE
SLKQYASRHFAERLPAMARNGELKSCLAVHRTLAEAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVVPGERFRGHSIGSQPVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
GLIQCRSLIEEMIADGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAAADIFERVKPECRYNPELAASDEVEPGFRRDPEIRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNVDRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLNLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CND5


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29770..68452

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPG17_RS00170 (BTU53_p045) 27489..29789 - 2301 WP_000077653 F-type conjugative transfer protein TrbC -
HPG17_RS00175 (BTU53_p046) 29770..30894 - 1125 WP_000152384 DsbC family protein trbB
HPG17_RS00180 (BTU53_p047) 30891..32216 - 1326 WP_171265269 IncI1-type conjugal transfer protein TrbA trbA
HPG17_RS00680 32753..32848 + 96 WP_001363141 DinQ-like type I toxin DqlB -
HPG17_RS00685 33437..33532 + 96 WP_001363141 DinQ-like type I toxin DqlB -
HPG17_RS00190 (BTU53_p052) 33595..33771 - 177 WP_001054907 hypothetical protein -
HPG17_RS00195 (BTU53_p053) 33922..34389 - 468 WP_000598962 thermonuclease family protein -
HPG17_RS00200 (BTU53_p054) 34549..35172 + 624 WP_001155250 helix-turn-helix domain-containing protein -
HPG17_RS00205 (BTU53_p055) 35370..35585 - 216 WP_000266543 hypothetical protein -
HPG17_RS00210 (BTU53_p056) 35589..35957 - 369 WP_001363143 hypothetical protein -
HPG17_RS00215 (BTU53_p058) 36257..36499 - 243 WP_001363144 hypothetical protein -
HPG17_RS00220 (BTU53_p060) 36829..36981 + 153 WP_001302699 Hok/Gef family protein -
HPG17_RS00225 (BTU53_p063) 37608..38255 - 648 WP_015056434 plasmid IncI1-type surface exclusion protein ExcA -
HPG17_RS00230 (BTU53_p064) 38343..40502 - 2160 WP_000691811 DotA/TraY family protein traY
HPG17_RS00235 (BTU53_p065) 40577..41146 - 570 WP_000650752 conjugal transfer protein TraX -
HPG17_RS00240 (BTU53_p066) 41143..42348 - 1206 WP_001189548 conjugal transfer protein TraW traW
HPG17_RS00245 (BTU53_p067) 42306..42926 - 621 WP_048967127 hypothetical protein traV
HPG17_RS00250 (BTU53_p068) 42926..45970 - 3045 WP_001024766 conjugal transfer protein traU
HPG17_RS00255 (BTU53_p070) 46265..47083 - 819 WP_000753550 hypothetical protein traT
HPG17_RS00675 46998..47282 - 285 WP_001353683 hypothetical protein -
HPG17_RS00265 (BTU53_p072) 47306..47704 - 399 WP_000088813 DUF6750 family protein traR
HPG17_RS00270 (BTU53_p073) 47751..48281 - 531 WP_000987021 conjugal transfer protein TraQ traQ
HPG17_RS00275 (BTU53_p074) 48278..48991 - 714 WP_000787003 conjugal transfer protein TraP traP
HPG17_RS00280 (BTU53_p075) 48988..50325 - 1338 WP_072105525 conjugal transfer protein TraO traO
HPG17_RS00285 (BTU53_p076) 50329..51303 - 975 WP_000547385 DotH/IcmK family type IV secretion protein traN
HPG17_RS00290 (BTU53_p077) 51314..52009 - 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
HPG17_RS00295 (BTU53_p078) 52021..52371 - 351 WP_001056367 hypothetical protein traL
HPG17_RS00300 (BTU53_p079) 52388..56449 - 4062 WP_000842453 LPD7 domain-containing protein -
HPG17_RS00655 56513..56803 - 291 WP_000817801 IcmT/TraK family protein traK
HPG17_RS00305 (BTU53_p081) 56800..57948 - 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
HPG17_RS00310 (BTU53_p082) 57932..58768 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
HPG17_RS00315 (BTU53_p083) 58765..59223 - 459 WP_001170111 DotD/TraH family lipoprotein -
HPG17_RS00320 (BTU53_p085) 59327..60529 - 1203 WP_000979993 conjugal transfer protein TraF -
HPG17_RS00325 (BTU53_p086) 60631..61452 - 822 WP_000845373 hypothetical protein traE
HPG17_RS00670 61617..61811 - 195 Protein_69 integrase -
HPG17_RS00330 (BTU53_p088) 61925..63286 - 1362 WP_001168171 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPG17_RS00335 (BTU53_p089) 63304..63840 - 537 WP_023649457 prepilin peptidase -
HPG17_RS00340 (BTU53_p090) 63946..64431 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
HPG17_RS00345 (BTU53_p091) 64476..65012 - 537 WP_000111534 type 4 pilus major pilin -
HPG17_RS00350 (BTU53_p092) 65074..65463 - 390 Protein_74 type II secretion system F family protein -
HPG17_RS00355 65522..66216 + 695 WP_087786203 IS1-like element IS1N family transposase -
HPG17_RS00360 (BTU53_p095) 66232..66942 - 711 Protein_76 type II secretion system F family protein -
HPG17_RS00365 (BTU53_p096) 66944..68452 - 1509 WP_032425678 ATPase, T2SS/T4P/T4SS family virB11
HPG17_RS00370 (BTU53_p097) 68556..69014 - 459 WP_000095885 type IV pilus biogenesis protein PilP -
HPG17_RS00375 (BTU53_p098) 69004..70299 - 1296 WP_000129883 type 4b pilus protein PilO2 -
HPG17_RS00380 (BTU53_p099) 70320..71939 - 1620 WP_001035565 PilN family type IVB pilus formation outer membrane protein -
HPG17_RS00385 (BTU53_p100) 71971..72408 - 438 WP_000539952 type IV pilus biogenesis protein PilM -

Host bacterium

ID   1073 GenBank   NC_032099
Plasmid name   p92-9000 Incompatibility group   IncB/O/K/Z
Plasmid size   121262 bp Coordinate of oriT [Strand]   24104..24189 [-]
Host baterium   Shigella dysenteriae

Cargo genes

Drug resistance gene   tet(B), catA1, ant(3'')-Ia, qacE, sul1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -