Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111002
Name   oriT_S17BD04134|p34 in_silico
Organism   Shigella sonnei strain S17BD04134
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099776 (28033..28118 [-], 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_S17BD04134|p34
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7239 GenBank   WP_000948354
Name   traI_NHV86_RS00370_S17BD04134|p34 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   4035 GenBank   WP_001354030
Name   WP_001354030_S17BD04134|p34 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   4036 GenBank   WP_000089263
Name   WP_000089263_S17BD04134|p34 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   8243 GenBank   WP_000069777
Name   traC_NHV86_RS00270_S17BD04134|p34 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   8244 GenBank   WP_000009332
Name   traD_NHV86_RS00365_S17BD04134|p34 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: 27465..55545

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV86_RS00155 23437..23871 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
NHV86_RS00160 23868..24587 + 720 WP_001276217 plasmid SOS inhibition protein A -
NHV86_RS00165 24809..24958 + 150 Protein_32 plasmid maintenance protein Mok -
NHV86_RS00170 24900..25025 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
NHV86_RS00175 25344..25640 - 297 Protein_34 hypothetical protein -
NHV86_RS00180 25940..26236 + 297 WP_001272251 hypothetical protein -
NHV86_RS00185 26347..27168 + 822 WP_001234445 DUF932 domain-containing protein -
NHV86_RS00190 27465..28067 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
NHV86_RS00195 28390..28773 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
NHV86_RS00200 28967..29638 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
NHV86_RS00205 29775..30002 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
NHV86_RS00210 30035..30394 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
NHV86_RS00215 30409..30720 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
NHV86_RS00220 30742..31308 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
NHV86_RS00225 31295..32023 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
NHV86_RS00230 32023..33474 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
NHV86_RS00235 33464..34030 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
NHV86_RS00240 34017..34337 + 321 WP_001057307 conjugal transfer protein TrbD -
NHV86_RS00245 34334..34849 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
NHV86_RS00250 34984..35205 + 222 WP_001278683 conjugal transfer protein TraR -
NHV86_RS00255 35198..35674 + 477 WP_000549587 hypothetical protein -
NHV86_RS00260 35754..35972 + 219 WP_000556745 hypothetical protein -
NHV86_RS00265 36000..36347 + 348 WP_000836682 hypothetical protein -
NHV86_RS00270 36473..39103 + 2631 WP_000069777 type IV secretion system protein TraC virb4
NHV86_RS00275 39100..39486 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
NHV86_RS00280 39483..40115 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
NHV86_RS00285 40112..41104 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
NHV86_RS00290 41134..41439 + 306 WP_000224416 hypothetical protein -
NHV86_RS00295 41448..42086 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
NHV86_RS00300 42083..43933 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NHV86_RS00305 43960..44217 + 258 WP_000864353 conjugal transfer protein TrbE -
NHV86_RS00310 44210..44953 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
NHV86_RS00315 44967..45311 + 345 WP_000556796 conjugal transfer protein TrbA -
NHV86_RS00320 45430..45714 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
NHV86_RS00325 45701..46246 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NHV86_RS00330 46176..46523 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
NHV86_RS00335 46504..46896 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
NHV86_RS00340 46883..48256 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
NHV86_RS00345 48253..51075 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
NHV86_RS00350 51091..51576 + 486 WP_000605870 hypothetical protein -
NHV86_RS00355 51625..52356 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
NHV86_RS00360 52559..53296 + 738 WP_000199905 hypothetical protein -
NHV86_RS00365 53347..55545 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   11437 GenBank   NZ_CP099776
Plasmid name   S17BD04134|p34 Incompatibility group   IncFII
Plasmid size   65891 bp Coordinate of oriT [Strand]   28033..28118 [-]
Host baterium   Shigella sonnei strain S17BD04134

Cargo genes

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