Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111004
Name   oriT_S18BD05612|p83 in_silico
Organism   Shigella sonnei strain S18BD05612
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099767 (39705..39790 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_S18BD05612|p83
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7241 GenBank   WP_000948354
Name   traI_NHV92_RS00430_S18BD05612|p83 insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   4038 GenBank   WP_001354030
Name   WP_001354030_S18BD05612|p83 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   4039 GenBank   WP_000089263
Name   WP_000089263_S18BD05612|p83 insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   8246 GenBank   WP_000069777
Name   traC_NHV92_RS00330_S18BD05612|p83 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   8247 GenBank   WP_001617742
Name   traD_NHV92_RS00425_S18BD05612|p83 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83547.19 Da        Isoelectric Point: 5.1644

>WP_001617742.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39137..67226

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV92_RS00215 35109..35543 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
NHV92_RS00220 35540..36259 + 720 WP_001276217 plasmid SOS inhibition protein A -
NHV92_RS00225 36481..36630 + 150 Protein_44 plasmid maintenance protein Mok -
NHV92_RS00230 36572..36697 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NHV92_RS00235 37016..37312 - 297 Protein_46 hypothetical protein -
NHV92_RS00240 37612..37908 + 297 WP_001272251 hypothetical protein -
NHV92_RS00245 38019..38840 + 822 WP_001234445 DUF932 domain-containing protein -
NHV92_RS00250 39137..39739 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
NHV92_RS00255 40062..40445 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
NHV92_RS00260 40639..41310 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
NHV92_RS00265 41447..41674 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
NHV92_RS00270 41707..42066 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
NHV92_RS00275 42081..42392 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
NHV92_RS00280 42414..42980 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
NHV92_RS00285 42967..43695 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
NHV92_RS00290 43695..45146 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
NHV92_RS00295 45136..45702 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
NHV92_RS00300 45689..46009 + 321 WP_001057307 conjugal transfer protein TrbD -
NHV92_RS00305 46006..46521 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
NHV92_RS00310 46656..46877 + 222 WP_001278683 conjugal transfer protein TraR -
NHV92_RS00315 46870..47346 + 477 WP_000549587 hypothetical protein -
NHV92_RS00320 47426..47644 + 219 WP_000556745 hypothetical protein -
NHV92_RS00325 47672..48019 + 348 WP_000836682 hypothetical protein -
NHV92_RS00330 48145..50775 + 2631 WP_000069777 type IV secretion system protein TraC virb4
NHV92_RS00335 50772..51158 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
NHV92_RS00340 51155..51787 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
NHV92_RS00345 51784..52776 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NHV92_RS00350 52806..53111 + 306 WP_000224416 hypothetical protein -
NHV92_RS00355 53120..53758 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
NHV92_RS00360 53755..55605 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NHV92_RS00365 55632..55889 + 258 WP_000864353 conjugal transfer protein TrbE -
NHV92_RS00370 55882..56625 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
NHV92_RS00375 56639..56983 + 345 WP_000556796 conjugal transfer protein TrbA -
NHV92_RS00380 57102..57386 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
NHV92_RS00385 57373..57918 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NHV92_RS00390 57848..58195 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
NHV92_RS00395 58176..58568 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
NHV92_RS00400 58555..59928 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
NHV92_RS00405 59925..62747 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
NHV92_RS00410 62763..63248 + 486 WP_000605870 hypothetical protein -
NHV92_RS00415 63297..64028 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
NHV92_RS00420 64231..64968 + 738 WP_000199905 hypothetical protein -
NHV92_RS00425 65019..67226 + 2208 WP_001617742 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   11439 GenBank   NZ_CP099767
Plasmid name   S18BD05612|p83 Incompatibility group   IncFII
Plasmid size   77572 bp Coordinate of oriT [Strand]   39705..39790 [-]
Host baterium   Shigella sonnei strain S18BD05612

Cargo genes

Drug resistance gene   qnrS1, blaCTX-M-15
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -