Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102673
Name   oriT_WH333|unnamed1 in_silico
Organism   Escherichia coli strain WH333
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_PSNS01000016 (54960..55045 [+], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..13, 21..26  (TGATTT..AAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_WH333|unnamed1
AATTACATGATTTAAAACACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1975 GenBank   WP_000986963
Name   traI_C4M75_RS22130_WH333|unnamed1 insolico UniProt ID   A0A2X5DJ87
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192006.86 Da        Isoelectric Point: 5.8722

>WP_000986963.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   799 GenBank   WP_001352842
Name   WP_001352842_WH333|unnamed1 insolico UniProt ID   A0A6Y3H4U0
Length   71 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 71 a.a.        Molecular weight: 8117.19 Da        Isoelectric Point: 9.9216

>WP_001352842.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MSRGRTRAAPGNKVLLILDETTNQKLLAARDRSGRTKTNEVFIRLKDHLNRFPDFYNASLVKEEAESIDD
I

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A6Y3H4U0

ID   800 GenBank   WP_001063020
Name   WP_001063020_WH333|unnamed1 insolico UniProt ID   A0A6Y3HD60
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14442.54 Da        Isoelectric Point: 5.3125

>WP_001063020.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]
MAKIQVYVNDHVSEKINAIAVQRRAEGAKEKDVSYSSIASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGKPKFEYANMVEDIREKVSVEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A6Y3HD60


T4CP

ID   1612 GenBank   WP_000009324
Name   traD_C4M75_RS22145_WH333|unnamed1 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81528.14 Da        Isoelectric Point: 5.1126

>WP_000009324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGEDVEPGDDF

  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.



ID   1613 GenBank   WP_001064245
Name   traC_C4M75_RS22235_WH333|unnamed1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29391..55613

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C4M75_RS22135 (C4M75_22135) 28757..28984 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
C4M75_RS22140 (C4M75_22140) 28984..29382 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
C4M75_RS22145 (C4M75_22145) 29391..31544 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
C4M75_RS22150 (C4M75_22150) 31797..32528 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
C4M75_RS22155 (C4M75_22155) 32560..33057 - 498 WP_000605857 entry exclusion protein -
C4M75_RS22160 (C4M75_22160) 33073..35895 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
C4M75_RS22165 (C4M75_22165) 35892..37265 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
C4M75_RS22170 (C4M75_22170) 37265..37645 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
C4M75_RS22175 (C4M75_22175) 37632..37973 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
C4M75_RS22180 (C4M75_22180) 37903..38448 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C4M75_RS22185 (C4M75_22185) 38435..38719 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
C4M75_RS22190 (C4M75_22190) 38800..39114 + 315 WP_001324103 hypothetical protein -
C4M75_RS22195 (C4M75_22195) 39116..39463 - 348 WP_001287910 conjugal transfer protein TrbA -
C4M75_RS22200 (C4M75_22200) 39479..40222 - 744 WP_001030377 type-F conjugative transfer system pilin assembly protein TraF traF
C4M75_RS22205 (C4M75_22205) 40215..40472 - 258 WP_000864318 conjugal transfer protein TrbE -
C4M75_RS22210 (C4M75_22210) 40499..42307 - 1809 WP_000821838 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C4M75_RS22215 (C4M75_22215) 42304..42942 - 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
C4M75_RS22220 (C4M75_22220) 42951..43943 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
C4M75_RS22225 (C4M75_22225) 43940..44572 - 633 WP_001203717 type-F conjugative transfer system protein TraW traW
C4M75_RS22230 (C4M75_22230) 44569..44955 - 387 WP_000099691 type-F conjugative transfer system protein TrbI -
C4M75_RS22235 (C4M75_22235) 44952..47579 - 2628 WP_001064245 type IV secretion system protein TraC virb4
C4M75_RS22240 (C4M75_22240) 47739..47960 - 222 WP_001278689 conjugal transfer protein TraR -
C4M75_RS22245 (C4M75_22245) 48095..48610 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
C4M75_RS22250 (C4M75_22250) 48607..48858 - 252 WP_001038342 conjugal transfer protein TrbG -
C4M75_RS22255 (C4M75_22255) 48870..49067 - 198 WP_024179215 conjugal transfer protein TrbD -
C4M75_RS22260 (C4M75_22260) 49054..49644 - 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
C4M75_RS22265 (C4M75_22265) 49634..51061 - 1428 WP_000146676 F-type conjugal transfer pilus assembly protein TraB traB
C4M75_RS22270 (C4M75_22270) 51061..51789 - 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
C4M75_RS22275 (C4M75_22275) 51776..52342 - 567 WP_000399790 type IV conjugative transfer system protein TraE traE
C4M75_RS22280 (C4M75_22280) 52364..52675 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
C4M75_RS22285 (C4M75_22285) 52690..53055 - 366 WP_000340282 type IV conjugative transfer system pilin TraA -
C4M75_RS22290 (C4M75_22290) 53098..53313 - 216 WP_001352842 conjugal transfer relaxosome protein TraY -
C4M75_RS22295 (C4M75_22295) 53449..54096 - 648 WP_000332520 conjugal transfer transcriptional regulator TraJ -
C4M75_RS22300 (C4M75_22300) 54288..54671 - 384 WP_001063020 conjugal transfer relaxosome DNA-binding protein TraM -
C4M75_RS22305 (C4M75_22305) 55011..55613 + 603 WP_077248356 transglycosylase SLT domain-containing protein virB1
C4M75_RS22310 (C4M75_22310) 55908..56729 - 822 WP_001234475 DUF932 domain-containing protein -
C4M75_RS22315 (C4M75_22315) 56848..57135 - 288 WP_000107546 hypothetical protein -
C4M75_RS22320 (C4M75_22320) 57160..57366 - 207 WP_000547965 hypothetical protein -
C4M75_RS26095 57436..57540 + 105 Protein_63 hypothetical protein -

Host bacterium

ID   3117 GenBank   NZ_PSNS01000016
Plasmid name   WH333|unnamed1 Incompatibility group   IncFIC
Plasmid size   57540 bp Coordinate of oriT [Strand]   54960..55045 [+]
Host baterium   Escherichia coli strain WH333

Cargo genes

Drug resistance gene   blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -