Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113597
Name   oriT_pSH278-2 in_silico
Organism   Shigella sonnei strain SH278-2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MG299143 (49179..49251 [-], 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_pSH278-2
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8706 GenBank   WP_000991387
Name   Relaxase_HPI88_RS00355_pSH278-2 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   5090 GenBank   WP_001291058
Name   WP_001291058_pSH278-2 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   10081 GenBank   WP_000077664
Name   trbC_HPI88_RS00370_pSH278-2 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: 87040.19 Da        Isoelectric Point: 7.4857

>WP_000077664.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
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: 55905..101260

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPI88_RS00360 52395..52826 + 432 WP_001335086 cell envelope integrity TolA C-terminal domain-containing protein -
HPI88_RS00690 52924..53073 - 150 WP_001536674 hypothetical protein -
HPI88_RS00370 53621..55924 - 2304 WP_000077664 F-type conjugative transfer protein TrbC -
HPI88_RS00375 55905..57029 - 1125 WP_000152387 DsbC family protein trbB
HPI88_RS00380 57026..58333 - 1308 WP_021577249 IncI1-type conjugal transfer protein TrbA trbA
HPI88_RS00695 59130..59225 + 96 WP_001363141 DinQ-like type I toxin DqlB -
HPI88_RS00390 59288..59464 - 177 WP_001054907 hypothetical protein -
HPI88_RS00395 59614..60081 - 468 WP_000598962 thermonuclease family protein -
HPI88_RS00400 60240..60863 + 624 WP_001155247 helix-turn-helix domain-containing protein -
HPI88_RS00405 61061..61276 - 216 WP_000266543 hypothetical protein -
HPI88_RS00410 61280..61648 - 369 WP_001345852 hypothetical protein -
HPI88_RS00415 61660..61851 - 192 WP_000751583 hypothetical protein -
HPI88_RS00420 61939..62181 - 243 WP_000650923 hypothetical protein -
HPI88_RS00425 62511..62663 + 153 WP_001335079 Hok/Gef family protein -
HPI88_RS00430 62801..64387 - 1587 WP_000004564 TnsA endonuclease N-terminal domain-containing protein -
HPI88_RS00435 64661..65308 - 648 WP_015056434 plasmid IncI1-type surface exclusion protein ExcA -
HPI88_RS00440 65396..67555 - 2160 WP_000691811 DotA/TraY family protein traY
HPI88_RS00445 67630..68199 - 570 WP_000650752 conjugal transfer protein TraX -
HPI88_RS00450 68196..69401 - 1206 WP_001189548 conjugal transfer protein TraW traW
HPI88_RS00455 69359..69979 - 621 WP_000286854 hypothetical protein traV
HPI88_RS00460 69979..73023 - 3045 WP_001024766 conjugal transfer protein traU
HPI88_RS00465 73089..73325 + 237 WP_005082508 hypothetical protein -
HPI88_RS00470 73318..74136 - 819 WP_000753550 hypothetical protein traT
HPI88_RS00700 74051..74335 - 285 WP_001353683 hypothetical protein -
HPI88_RS00480 74359..74757 - 399 WP_000088813 DUF6750 family protein traR
HPI88_RS00485 74804..75334 - 531 WP_000987023 conjugal transfer protein TraQ traQ
HPI88_RS00490 75331..76044 - 714 WP_000787003 conjugal transfer protein TraP traP
HPI88_RS00495 76041..77378 - 1338 WP_013307873 conjugal transfer protein TraO traO
HPI88_RS00500 77382..78356 - 975 WP_000547383 DotH/IcmK family type IV secretion protein traN
HPI88_RS00505 78367..79062 - 696 WP_001681668 DotI/IcmL family type IV secretion protein traM
HPI88_RS00510 79074..79424 - 351 WP_001056367 hypothetical protein traL
HPI88_RS00515 79441..83502 - 4062 WP_013307874 LPD7 domain-containing protein -
HPI88_RS00520 83856..84437 - 582 WP_025750394 hypothetical protein -
HPI88_RS00525 84445..84900 - 456 Protein_102 IS5 family transposase -
HPI88_RS00530 84935..85810 - 876 WP_001617865 extended-spectrum class A beta-lactamase CTX-M-14 -
HPI88_RS00540 86060..87322 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HPI88_RS00545 87734..88024 - 291 WP_000817801 IcmT/TraK family protein traK
HPI88_RS00550 88021..89169 - 1149 WP_013307876 plasmid transfer ATPase TraJ virB11
HPI88_RS00555 89153..89989 - 837 WP_000745049 type IV secretory system conjugative DNA transfer family protein traI
HPI88_RS00560 89986..90444 - 459 WP_025750398 DotD/TraH family lipoprotein -
HPI88_RS00565 90548..91750 - 1203 WP_013307879 conjugal transfer protein TraF -
HPI88_RS00570 91852..92673 - 822 WP_001681675 hypothetical protein traE
HPI88_RS00575 92886..94010 - 1125 WP_013307880 site-specific integrase -
HPI88_RS00580 94060..94368 + 309 WP_102166912 pilus assembly protein -
HPI88_RS00585 94663..95001 + 339 WP_072106734 prepilin, shufflon protein A -
HPI88_RS00590 95006..95395 - 390 Protein_114 phage tail protein -
HPI88_RS00595 95481..95636 + 156 WP_001358489 hypothetical protein -
HPI88_RS00600 95633..96868 - 1236 WP_032151497 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPI88_RS00605 96886..97512 - 627 WP_013307883 prepilin peptidase -
HPI88_RS00610 97528..98013 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
HPI88_RS00615 98058..98594 - 537 WP_000111521 type 4 pilus major pilin -
HPI88_RS00620 98656..99750 - 1095 WP_032253914 type II secretion system F family protein -
HPI88_RS00625 99752..101260 - 1509 WP_000880806 GspE/PulE family protein virB11
HPI88_RS00630 101364..101822 - 459 WP_000095886 type IV pilus biogenesis protein PilP -
HPI88_RS00635 101812..103107 - 1296 WP_000129883 type 4b pilus protein PilO2 -
HPI88_RS00640 103128..104747 - 1620 WP_001035562 PilN family type IVB pilus formation outer membrane protein -
HPI88_RS00645 104779..105192 - 414 WP_124983997 type IV pilus biogenesis protein PilM -

Host bacterium

ID   14032 GenBank   NZ_MG299143
Plasmid name   pSH278-2 Incompatibility group   IncB/O/K/Z
Plasmid size   109845 bp Coordinate of oriT [Strand]   49179..49251 [-]
Host baterium   Shigella sonnei strain SH278-2

Cargo genes

Drug resistance gene   mph(A), sul1, qacE, aadA5, aac(3)-IId, blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -