Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103179
Name   oriT_pSH15sh104 in_silico
Organism   Shigella sonnei strain SH15sh105
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY471629 (43619..43691 [-], 73 nt)
oriT length   73 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 73 nt

>oriT_pSH15sh104
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2380 GenBank   WP_000991387
Name   Relaxase_HPJ83_RS00315_pSH15sh104 insolico UniProt ID   A0A7I0L2J7
Length   903 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 903 a.a.        Molecular weight: 104567.95 Da        Isoelectric Point: 7.5259

>WP_000991387.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRYFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGRNLGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
TTVQCESLIEDMIAGGNFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEL
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAVQGDRAALSQLRGWDYRDRRKDKRRTTNADRCVILCEPGGTPLYEDTGVLEARLQKDGS
VRFRDRRNGELVCVDYGDRVVFYHHQDRNELVDKLNLIAPVLFDREPGMGFEPEGSYQQFNDVFAEMVAW
HNAAGITGNGHFVISRPDVDLHRQRSEQYYHEYIRQQKSISGGHGASYAPVQDNEWTPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure


Source ID Structure
AlphaFold DB A0A7I0L2J7


Auxiliary protein

ID   1004 GenBank   WP_001291058
Name   WP_001291058_pSH15sh104 insolico UniProt ID   A0A7I0L241
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12730.52 Da        Isoelectric Point: 9.9656

>WP_001291058.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSEKKTRTGSENRKRIVKFTARFTEDEAEIVREKAESSGQTVSTFIRSSSLDKVVNCRTDDRMIDEIMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITEYVNALRRDLMGR

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A7I0L241


T4CP

ID   2128 GenBank   WP_171265815
Name   trbC_HPJ83_RS00330_pSH15sh104 insolico UniProt ID   _
Length   767 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 767 a.a.        Molecular weight: 87022.16 Da        Isoelectric Point: 7.4857

>WP_171265815.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHITLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFVTQQSMLLARDLGYRLE
GTDAQTLEVKKYKGSFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYISVEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTAKPSRKRRKNRTEPYRIIDTFQRRLATAQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
VCYITLNRPEEEHSGPEDIPSVKAILNTLLPLEMLLPVPDLTASPPHKKNVAQTPSGGKQESRKKRF

  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: 50345..95700

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPJ83_RS00320 46835..47266 + 432 WP_001335086 cell envelope integrity TolA C-terminal domain-containing protein -
HPJ83_RS00325 47364..47594 - 231 WP_071591569 hypothetical protein -
HPJ83_RS00330 48061..50364 - 2304 WP_171265815 F-type conjugative transfer protein TrbC -
HPJ83_RS00335 50345..51469 - 1125 WP_000152387 DsbC family protein trbB
HPJ83_RS00340 51466..52773 - 1308 WP_021577249 IncI1-type conjugal transfer protein TrbA trbA
HPJ83_RS00645 53570..53665 + 96 WP_001363141 DinQ-like type I toxin DqlB -
HPJ83_RS00350 53728..53904 - 177 WP_001054907 hypothetical protein -
HPJ83_RS00355 54054..54521 - 468 WP_000598962 thermonuclease family protein -
HPJ83_RS00360 54680..55303 + 624 WP_001155247 helix-turn-helix domain-containing protein -
HPJ83_RS00365 55501..55716 - 216 WP_000266543 hypothetical protein -
HPJ83_RS00370 55720..56088 - 369 WP_001345852 hypothetical protein -
HPJ83_RS00375 56100..56291 - 192 WP_000751583 hypothetical protein -
HPJ83_RS00380 56379..56621 - 243 WP_000650923 hypothetical protein -
HPJ83_RS00385 56951..57103 + 153 WP_001335079 Hok/Gef family protein -
HPJ83_RS00390 57241..58827 - 1587 WP_000004564 TnsA endonuclease N-terminal domain-containing protein -
HPJ83_RS00395 59101..59748 - 648 WP_015056434 plasmid IncI1-type surface exclusion protein ExcA -
HPJ83_RS00400 59836..61995 - 2160 WP_000691811 DotA/TraY family protein traY
HPJ83_RS00405 62070..62639 - 570 WP_000650752 conjugal transfer protein TraX -
HPJ83_RS00410 62636..63841 - 1206 WP_001189548 conjugal transfer protein TraW traW
HPJ83_RS00415 63799..64419 - 621 WP_171265816 conjugal transfer protein TraV traV
HPJ83_RS00420 64419..67463 - 3045 WP_001024766 conjugal transfer protein traU
HPJ83_RS00425 67758..68576 - 819 WP_000753550 hypothetical protein traT
HPJ83_RS00640 68491..68742 - 252 WP_001277573 hypothetical protein -
HPJ83_RS00435 68799..69197 - 399 WP_000088813 DUF6750 family protein traR
HPJ83_RS00440 69244..69774 - 531 WP_000987023 conjugal transfer protein TraQ traQ
HPJ83_RS00445 69771..70484 - 714 WP_000787003 conjugal transfer protein TraP traP
HPJ83_RS00450 70481..71818 - 1338 WP_013307873 conjugal transfer protein TraO traO
HPJ83_RS00455 71822..72796 - 975 WP_000547383 DotH/IcmK family type IV secretion protein traN
HPJ83_RS00460 72807..73502 - 696 WP_001681668 DotI/IcmL family type IV secretion protein traM
HPJ83_RS00465 73514..73864 - 351 WP_001056367 hypothetical protein traL
HPJ83_RS00470 73881..77942 - 4062 WP_013307874 LPD7 domain-containing protein -
HPJ83_RS00475 78296..78877 - 582 WP_025750394 hypothetical protein -
HPJ83_RS00480 78885..79340 - 456 Protein_94 IS5 family transposase -
HPJ83_RS00485 79375..80250 - 876 WP_001617865 extended-spectrum class A beta-lactamase CTX-M-14 -
HPJ83_RS00495 80500..81762 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HPJ83_RS00500 82174..82464 - 291 WP_000817801 IcmT/TraK family protein traK
HPJ83_RS00505 82461..83609 - 1149 WP_013307876 plasmid transfer ATPase TraJ virB11
HPJ83_RS00510 83593..84429 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
HPJ83_RS00515 84426..84884 - 459 WP_025750398 DotD/TraH family lipoprotein -
HPJ83_RS00520 84988..86190 - 1203 WP_013307879 conjugal transfer protein TraF -
HPJ83_RS00525 86292..87113 - 822 WP_001681675 hypothetical protein traE
HPJ83_RS00530 87326..88450 - 1125 WP_013307880 site-specific integrase -
HPJ83_RS00535 88505..88864 + 360 WP_013307881 hypothetical protein -
HPJ83_RS00540 88869..89258 - 390 Protein_105 phage tail protein -
HPJ83_RS00545 89529..89684 - 156 WP_001358489 hypothetical protein -
HPJ83_RS00550 90073..91308 - 1236 WP_085008799 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPJ83_RS00555 91326..91952 - 627 WP_013307883 prepilin peptidase -
HPJ83_RS00560 91968..92453 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
HPJ83_RS00565 92498..93034 - 537 WP_000111521 type 4 pilus major pilin -
HPJ83_RS00570 93096..94190 - 1095 WP_032253914 type II secretion system F family protein -
HPJ83_RS00575 94192..95700 - 1509 WP_000880806 ATPase, T2SS/T4P/T4SS family virB11
HPJ83_RS00580 95804..96262 - 459 WP_000095886 type IV pilus biogenesis protein PilP -
HPJ83_RS00585 96252..97547 - 1296 WP_000129883 type 4b pilus protein PilO2 -
HPJ83_RS00590 97568..99187 - 1620 WP_001035562 PilN family type IVB pilus formation outer membrane protein -
HPJ83_RS00595 99219..99632 - 414 WP_124983997 type IV pilus biogenesis protein PilM -

Host bacterium

ID   3622 GenBank   NZ_KY471629
Plasmid name   pSH15sh104 Incompatibility group   IncB/O/K/Z
Plasmid size   104285 bp Coordinate of oriT [Strand]   43619..43691 [-]
Host baterium   Shigella sonnei strain SH15sh105

Cargo genes

Drug resistance gene   mph(A), aac(3)-IId, blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -