Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114665
Name   oriT_pSH12sh288-1 in_silico
Organism   Shigella sonnei strain SH12sh288
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ230387 (64056..64128 [-], 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_pSH12sh288-1
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9405 GenBank   WP_000991384
Name   Relaxase_RA126_RS00380_pSH12sh288-1 insolico UniProt ID   A0A8H8Z9E5
Length   903 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 903 a.a.        Molecular weight: 104595.99 Da        Isoelectric Point: 7.6377

>WP_000991384.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGRNLGTQAVSDYEWYRIRMGTGPQGAIKRELFSDKESLWGY
TTVQCESLIEDMIAGGNFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAGADIFERVKPECRYNPELAASDEVELGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQLRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAVQGDRAALSQLRGWDYRDRRKDKRRTTNADRCVILCEPGGTPLYEDTGVLEARLQKDGS
VRFRDRRNGELVCVDYGDRVVFYHHQDRNELVDKLNLIAPVLFDREPRMGFEPEGSYQQFNDVFAEMVAW
HNAAGITGSGHFVISRPDVDLHRQRSEQYYHEYIRQQKSISGGHGASYAPVQDNEWTPPSPGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-315)


  Protein structure



No available structure.




Auxiliary protein

ID   5516 GenBank   WP_001291058
Name   WP_001291058_pSH12sh288-1 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   10922 GenBank   WP_000077663
Name   trbC_RA126_RS00410_pSH12sh288-1 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: 87012.13 Da        Isoelectric Point: 7.3008

>WP_000077663.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSQHHVNPDLIHRTAWGNPLWNALHNLNITGLCLAGSIITALIWPLALPVCLLFTLVTSVIFMLQRWRCP
LRMPMTLSLDDPSQDRKVRRSLFSFWPTLFQYEADETFPARGIFYVGYRRINDIGRELWLSMDDLTRHVM
FFATTGGGKTETTFAWLLNPLCWGRGFTFVDGKAQNDTTRTIWYLSRRFGREDDIEVINFMNGGKSRSEI
IQSGEKSRPQSNTWNPFAFSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDMSLVRTPSAWTEEPRKQHAYLSGQFSE
TFTTFAETFGDVFAADAGDIDIRDSIHSDRILIVMIPALDTSAHTTSALGRMFVTQQSMLLARDLGYRLE
GTDAQTLEVKKYKGSFPYICILDEVGAYYTDRIAVEATQVRSLEFSLIMTAQDQERIEGQTSATNTATLM
QNAGTKFAGRIVSDDKTARTVKNAAGEEARARMGSLQRHDGVMGESWVDGNQITIQMESKIDVQDLIRLN
AGEFFTVFQGDVVPSASVYIPDSEKSCDSDPVVINRYISVEAPRLERLRRLVPRTVQRRLPTPEHVSSII
GVLTAKPSRKRRKNRTEPYRIIDTFQRQLATAQTSLDLLPQYDTDIESRANELWKKAVHTINNTTREERR
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: 73973..104346

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RA126_RS00400 69145..69948 - 804 WP_001082319 aminoglycoside O-phosphotransferase APH(3'')-Ib -
RA126_RS00405 (pSH12sh288-1_00075) 70009..70824 - 816 WP_001043260 sulfonamide-resistant dihydropteroate synthase Sul2 -
RA126_RS00410 (pSH12sh288-1_00078) 71689..73992 - 2304 WP_000077663 F-type conjugative transfer protein TrbC -
RA126_RS00415 (pSH12sh288-1_00079) 73973..75097 - 1125 WP_000152378 DsbC family protein trbB
RA126_RS00420 (pSH12sh288-1_00080) 75094..76401 - 1308 WP_001513486 IncI1-type conjugal transfer protein TrbA trbA
RA126_RS00425 (pSH12sh288-1_00081) 77033..77815 - 783 WP_001300609 IS21-like element IS100kyp family helper ATPase IstB -
RA126_RS00430 (pSH12sh288-1_00082) 77812..78834 - 1023 WP_000255944 IS21-like element IS100 family transposase -
RA126_RS00435 78921..79013 + 93 WP_025766395 DinQ-like type I toxin DqlB -
RA126_RS00440 79602..79697 + 96 WP_001363141 DinQ-like type I toxin DqlB -
RA126_RS00445 (pSH12sh288-1_00084) 79760..79936 - 177 WP_001054907 hypothetical protein -
RA126_RS00450 (pSH12sh288-1_00085) 80088..80555 - 468 WP_000598962 thermonuclease family protein -
RA126_RS00455 (pSH12sh288-1_00086) 80714..81337 + 624 WP_001155251 helix-turn-helix domain-containing protein -
RA126_RS00460 (pSH12sh288-1_00088) 81535..81750 - 216 WP_000266543 hypothetical protein -
RA126_RS00465 (pSH12sh288-1_00089) 81754..82122 - 369 WP_001390887 hypothetical protein -
RA126_RS00470 (pSH12sh288-1_00090) 82421..82663 - 243 WP_001363144 hypothetical protein -
RA126_RS00475 82993..83145 + 153 WP_001302699 Hok/Gef family protein -
RA126_RS00480 (pSH12sh288-1_00092) 83283..83957 - 675 WP_305847066 TnsA endonuclease N-terminal domain-containing protein -
RA126_RS00485 (pSH12sh288-1_00093) 83906..84868 - 963 WP_241381294 sigma factor-like helix-turn-helix DNA-binding protein -
RA126_RS00490 (pSH12sh288-1_00094) 85142..85792 - 651 WP_001044247 plasmid IncI1-type surface exclusion protein ExcA -
RA126_RS00495 (pSH12sh288-1_00095) 85881..88046 - 2166 WP_000691812 DotA/TraY family protein traY
RA126_RS00500 (pSH12sh288-1_00096) 88121..88690 - 570 WP_000650752 conjugal transfer protein TraX -
RA126_RS00505 (pSH12sh288-1_00097) 88687..89892 - 1206 WP_001189547 conjugal transfer protein TraW traW
RA126_RS00510 (pSH12sh288-1_00098) 89850..90470 - 621 WP_000286854 hypothetical protein traV
RA126_RS00515 (pSH12sh288-1_00099) 90470..93514 - 3045 WP_001024769 conjugal transfer protein traU
RA126_RS00520 (pSH12sh288-1_00100) 93809..94627 - 819 WP_000753550 hypothetical protein traT
RA126_RS00525 (pSH12sh288-1_00102) 94850..95248 - 399 WP_000088813 DUF6750 family protein traR
RA126_RS00530 (pSH12sh288-1_00103) 95295..95825 - 531 WP_000987021 conjugal transfer protein TraQ traQ
RA126_RS00535 (pSH12sh288-1_00104) 95822..96535 - 714 WP_000787002 conjugal transfer protein TraP traP
RA126_RS00540 (pSH12sh288-1_00105) 96532..97869 - 1338 WP_001272020 conjugal transfer protein TraO traO
RA126_RS00545 97873..98847 - 975 WP_000547386 DotH/IcmK family type IV secretion protein traN
RA126_RS00550 99028..99552 - 525 Protein_109 DotI/IcmL/TraM family protein -
RA126_RS00555 (pSH12sh288-1_00107) 99564..99914 - 351 WP_001056367 hypothetical protein traL
RA126_RS00560 (pSH12sh288-1_00108) 99931..103992 - 4062 WP_000842456 LPD7 domain-containing protein -
RA126_RS00565 (pSH12sh288-1_00109) 104056..104346 - 291 WP_000817801 IcmT/TraK family protein traK

Host bacterium

ID   15100 GenBank   NZ_OQ230387
Plasmid name   pSH12sh288-1 Incompatibility group   IncB/O/K/Z
Plasmid size   104958 bp Coordinate of oriT [Strand]   64056..64128 [-]
Host baterium   Shigella sonnei strain SH12sh288

Cargo genes

Drug resistance gene   dfrA12, aac(3)-IId, blaTEM-1B, tet(A), aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -