Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103106
Name   oriT_p69-3818 in_silico
Organism   Shigella dysenteriae
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT754167 (104620..104705 [+], 86 nt)
oriT length   86 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_p69-3818
CGGGGTGTCGGGGCTAAGCCCTGACCAGGTGGTAATCGTATAGCCGTGCGTGCGCGGTTATACGATTACACATCCTGTCCCGTTTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2328 GenBank   WP_000991407
Name   Relaxase_HPG12_RS00525_p69-3818 insolico UniProt ID   A0A142CND5
Length   906 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


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

>WP_000991407.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
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


Auxiliary protein

ID   989 GenBank   WP_001291057
Name   WP_001291057_p69-3818 insolico UniProt ID   A0A142CND4
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12596.69 Da        Isoelectric Point: 10.7335

>WP_001291057.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSEKKTRSGSEKRQKNVLIAVRFSPEEAEIVKEKAEKNGLTVSTLIRKTVLGKQINARIDEDFLKELMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITELANTLRRNLMGR

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF6290) (DUF6290)

(19-66)


  Protein structure


Source ID Structure
AlphaFold DB A0A142CND4


T4CP

ID   2055 GenBank   WP_052985224
Name   trbC_HPG12_RS00515_p69-3818 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 82779.16 Da        Isoelectric Point: 6.8170

>WP_052985224.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Shigella]
MSQHHVNPDLIHRTAWGNPLWNALHNLNIIGLCLAGSIITALIWPLALPVCLLFTLVTSVIFTLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETSPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFVTQQSMLLARDLGYRLE
GTDAQTLEVKKYKGSFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYISVEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTAKPSRKRRKNRTEPYRIIDTFQRQLATAQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
VCYITLNRPEEEHSGPEDIPSVKVIRLAP

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(439-528)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 59796..97703

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPG12_RS00310 55840..56277 + 438 WP_000539952 type IV pilus biogenesis protein PilM -
HPG12_RS00315 56309..57928 + 1620 WP_001035565 PilN family type IVB pilus formation outer membrane protein -
HPG12_RS00320 57949..59244 + 1296 WP_000129883 type 4b pilus protein PilO2 -
HPG12_RS00325 59234..59692 + 459 WP_000095885 type IV pilus biogenesis protein PilP -
HPG12_RS00330 59796..61304 + 1509 WP_032425678 ATPase, T2SS/T4P/T4SS family virB11
HPG12_RS00335 61306..62400 + 1095 WP_000697158 type II secretion system F family protein -
HPG12_RS00340 62462..62998 + 537 WP_000111534 type 4 pilus major pilin -
HPG12_RS00345 63043..63528 + 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
HPG12_RS00350 63634..64170 + 537 WP_023649457 prepilin peptidase -
HPG12_RS00355 64188..65549 + 1362 WP_001168171 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPG12_RS00665 65663..65857 + 195 Protein_72 integrase -
HPG12_RS00360 66022..66843 + 822 WP_000845373 hypothetical protein traE
HPG12_RS00365 66945..68147 + 1203 WP_000979993 conjugal transfer protein TraF -
HPG12_RS00370 68251..68709 + 459 WP_001170111 DotD/TraH family lipoprotein -
HPG12_RS00375 68706..69542 + 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
HPG12_RS00380 69526..70674 + 1149 WP_000775210 plasmid transfer ATPase TraJ virB11
HPG12_RS00640 70671..70961 + 291 WP_000817801 IcmT/TraK family protein traK
HPG12_RS00385 71025..75086 + 4062 WP_000842453 LPD7 domain-containing protein -
HPG12_RS00390 75103..75453 + 351 WP_001056367 hypothetical protein traL
HPG12_RS00395 75465..76160 + 696 WP_001287545 DotI/IcmL family type IV secretion protein traM
HPG12_RS00400 76171..77145 + 975 WP_000547385 DotH/IcmK family type IV secretion protein traN
HPG12_RS00405 77149..78486 + 1338 WP_072105525 conjugal transfer protein TraO traO
HPG12_RS00410 78483..79196 + 714 WP_000787003 conjugal transfer protein TraP traP
HPG12_RS00415 79193..79723 + 531 WP_000987021 conjugal transfer protein TraQ traQ
HPG12_RS00420 79770..80168 + 399 WP_000088813 DUF6750 family protein traR
HPG12_RS00675 80192..80476 + 285 WP_001353683 hypothetical protein -
HPG12_RS00430 80391..81209 + 819 WP_000753550 hypothetical protein traT
HPG12_RS00435 81504..84548 + 3045 WP_001024766 conjugal transfer protein traU
HPG12_RS00440 84548..85168 + 621 WP_048967127 hypothetical protein traV
HPG12_RS00445 85126..86331 + 1206 WP_001189548 conjugal transfer protein TraW traW
HPG12_RS00450 86432..86896 + 465 WP_000946265 conjugal transfer protein TraX -
HPG12_RS00455 86971..89130 + 2160 WP_000691811 DotA/TraY family protein traY
HPG12_RS00460 89218..89865 + 648 WP_015056434 plasmid IncI1-type surface exclusion protein ExcA -
HPG12_RS00465 90492..90644 - 153 WP_001302699 Hok/Gef family protein -
HPG12_RS00470 90974..91216 + 243 WP_001363144 hypothetical protein -
HPG12_RS00475 91516..91884 + 369 WP_001363143 hypothetical protein -
HPG12_RS00480 91888..92103 + 216 WP_000266543 hypothetical protein -
HPG12_RS00485 92301..92924 - 624 WP_001155250 helix-turn-helix domain-containing protein -
HPG12_RS00490 93084..93551 + 468 WP_000598962 thermonuclease family protein -
HPG12_RS00495 93702..93878 + 177 WP_001054907 hypothetical protein -
HPG12_RS00680 93941..94036 - 96 WP_001363141 DinQ-like type I toxin DqlB -
HPG12_RS00685 94625..94720 - 96 WP_001363141 DinQ-like type I toxin DqlB -
HPG12_RS00505 95257..96582 + 1326 WP_171265269 IncI1-type conjugal transfer protein TrbA trbA
HPG12_RS00510 96579..97703 + 1125 WP_000152384 DsbC family protein trbB
HPG12_RS00515 97684..99873 + 2190 WP_052985224 F-type conjugative transfer protein TrbC -
HPG12_RS00520 99949..101177 + 1229 WP_171265270 IS3-like element IS2 family transposase -

Host bacterium

ID   3549 GenBank   NZ_KT754167
Plasmid name   p69-3818 Incompatibility group   IncB/O/K/Z
Plasmid size   119227 bp Coordinate of oriT [Strand]   104620..104705 [+]
Host baterium   Shigella dysenteriae

Cargo genes

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