Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113606
Name   oriT_S18BD03178|p67 in_silico
Organism   Shigella sonnei strain S18BD03178
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099770 (40020..40105 [-], 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_S18BD03178|p67
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8715 GenBank   WP_000948354
Name   traI_NHV89_RS00445_S18BD03178|p67 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   5100 GenBank   WP_001354030
Name   WP_001354030_S18BD03178|p67 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   5101 GenBank   WP_000089263
Name   WP_000089263_S18BD03178|p67 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   10091 GenBank   WP_000069777
Name   traC_NHV89_RS00345_S18BD03178|p67 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   10092 GenBank   WP_000009332
Name   traD_NHV89_RS00440_S18BD03178|p67 insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83193.81 Da        Isoelectric Point: 5.1644

>WP_000009332.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 39452..67532

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV89_RS00230 35424..35858 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
NHV89_RS00235 35855..36574 + 720 WP_001276217 plasmid SOS inhibition protein A -
NHV89_RS00240 36796..36945 + 150 Protein_48 plasmid maintenance protein Mok -
NHV89_RS00245 36887..37012 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NHV89_RS00250 37331..37627 - 297 Protein_50 hypothetical protein -
NHV89_RS00255 37927..38223 + 297 WP_001272251 hypothetical protein -
NHV89_RS00260 38334..39155 + 822 WP_001234445 DUF932 domain-containing protein -
NHV89_RS00265 39452..40054 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
NHV89_RS00270 40377..40760 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
NHV89_RS00275 40954..41625 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
NHV89_RS00280 41762..41989 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
NHV89_RS00285 42022..42381 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
NHV89_RS00290 42396..42707 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
NHV89_RS00295 42729..43295 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
NHV89_RS00300 43282..44010 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
NHV89_RS00305 44010..45437 + 1428 WP_021524689 F-type conjugal transfer pilus assembly protein TraB traB
NHV89_RS00310 45427..46017 + 591 WP_032308032 conjugal transfer pilus-stabilizing protein TraP -
NHV89_RS00315 46004..46324 + 321 WP_001057307 conjugal transfer protein TrbD -
NHV89_RS00320 46321..46836 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
NHV89_RS00325 46971..47192 + 222 WP_001278683 conjugal transfer protein TraR -
NHV89_RS00330 47185..47661 + 477 WP_000549587 hypothetical protein -
NHV89_RS00335 47741..47959 + 219 WP_000556745 hypothetical protein -
NHV89_RS00340 47987..48334 + 348 WP_000836682 hypothetical protein -
NHV89_RS00345 48460..51090 + 2631 WP_000069777 type IV secretion system protein TraC virb4
NHV89_RS00350 51087..51473 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
NHV89_RS00355 51470..52102 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
NHV89_RS00360 52099..53091 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NHV89_RS00365 53121..53426 + 306 WP_000224416 hypothetical protein -
NHV89_RS00370 53435..54073 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
NHV89_RS00375 54070..55920 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NHV89_RS00380 55947..56204 + 258 WP_000864353 conjugal transfer protein TrbE -
NHV89_RS00385 56197..56940 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
NHV89_RS00390 56954..57298 + 345 WP_000556796 conjugal transfer protein TrbA -
NHV89_RS00395 57417..57701 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
NHV89_RS00400 57688..58233 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NHV89_RS00405 58163..58510 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
NHV89_RS00410 58491..58883 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
NHV89_RS00415 58870..60243 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
NHV89_RS00420 60240..63062 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
NHV89_RS00425 63078..63563 + 486 WP_000605870 hypothetical protein -
NHV89_RS00430 63612..64343 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
NHV89_RS00435 64546..65283 + 738 WP_000199905 hypothetical protein -
NHV89_RS00440 65334..67532 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14041 GenBank   NZ_CP099770
Plasmid name   S18BD03178|p67 Incompatibility group   IncFII
Plasmid size   77878 bp Coordinate of oriT [Strand]   40020..40105 [-]
Host baterium   Shigella sonnei strain S18BD03178

Cargo genes

Drug resistance gene   mph(A), erm(B), blaCTX-M-27
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -