Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103134
Name   oriT_pCERC9 in_silico
Organism   Escherichia coli strain 14.3-R4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY007017 (82706..83058 [-], 353 nt)
oriT length   353 nt
IRs (inverted repeats)      256..263, 272..279  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 353 nt

>oriT_pCERC9
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2351 GenBank   WP_172687685
Name   traI_HTK42_RS00275_pCERC9 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192028.75 Da        Isoelectric Point: 5.8531

>WP_172687685.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAWLHTPAQQAIHLALPVVESKNLAFSMVDLLTEVKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGERMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTRSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPGSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPITAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREITGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(575-627)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   994 GenBank   WP_001369361
Name   WP_001369361_pCERC9 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   995 GenBank   WP_001151524
Name   WP_001151524_pCERC9 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   2080 GenBank   WP_001514238
Name   traD_HTK42_RS00280_pCERC9 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: 81446.01 Da        Isoelectric Point: 5.1693

>WP_001514238.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFKPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.



ID   2081 GenBank   WP_001064252
Name   traC_HTK42_RS00350_pCERC9 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: 99164.84 Da        Isoelectric Point: 5.8486

>WP_001064252.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRESGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 59642..83629

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTK42_RS00280 59642..61795 - 2154 WP_001514238 type IV conjugative transfer system coupling protein TraD virb4
HTK42_RS00285 62048..62779 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HTK42_RS00290 62793..63302 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
HTK42_RS00295 63368..65761 - 2394 Protein_59 conjugal transfer mating-pair stabilization protein TraG -
HTK42_RS00705 65834..66115 - 282 Protein_60 P-type conjugative transfer protein TrbJ -
HTK42_RS00300 66045..66590 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTK42_RS00305 66577..66861 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HTK42_RS00310 66980..67327 - 348 WP_001287677 conjugal transfer protein TrbA -
HTK42_RS00315 67343..68086 - 744 WP_001514239 type-F conjugative transfer system pilin assembly protein TraF traF
HTK42_RS00320 68079..68336 - 258 WP_000864325 conjugal transfer protein TrbE -
HTK42_RS00325 68363..70171 - 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTK42_RS00330 70168..70806 - 639 WP_000777693 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTK42_RS00335 70815..71807 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HTK42_RS00340 71804..72436 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTK42_RS00345 72433..72819 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
HTK42_RS00350 72816..75443 - 2628 WP_001064252 type IV secretion system protein TraC virb4
HTK42_RS00355 75603..75824 - 222 WP_001278689 conjugal transfer protein TraR -
HTK42_RS00360 75959..76474 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HTK42_RS00365 76471..76722 - 252 WP_001038342 conjugal transfer protein TrbG -
HTK42_RS00370 76734..76931 - 198 WP_001324648 conjugal transfer protein TrbD -
HTK42_RS00375 76918..77508 - 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
HTK42_RS00380 77498..78925 - 1428 WP_172687686 F-type conjugal transfer pilus assembly protein TraB traB
HTK42_RS00385 78925..79653 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTK42_RS00390 79640..80206 - 567 WP_000399785 type IV conjugative transfer system protein TraE traE
HTK42_RS00395 80228..80539 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTK42_RS00400 80554..80919 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HTK42_RS00405 80952..81347 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HTK42_RS00410 81446..82135 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HTK42_RS00415 82322..82705 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HTK42_RS00420 83120..83629 + 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
HTK42_RS00425 83925..84746 - 822 WP_001234468 DUF932 domain-containing protein -
HTK42_RS00430 84865..85152 - 288 WP_000107520 hypothetical protein -
HTK42_RS00710 85177..85317 - 141 WP_001445060 hypothetical protein -
HTK42_RS00440 85453..85750 + 298 Protein_89 hypothetical protein -
HTK42_RS00445 86051..86173 - 123 WP_223195199 Hok/Gef family protein -
HTK42_RS00750 86118..86270 - 153 Protein_91 DUF5431 family protein -
HTK42_RS00450 86421..87207 - 787 Protein_92 plasmid SOS inhibition protein A -
HTK42_RS00455 87204..87638 - 435 WP_000845922 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   3577 GenBank   NZ_KY007017
Plasmid name   pCERC9 Incompatibility group   IncFII
Plasmid size   135661 bp Coordinate of oriT [Strand]   82706..83058 [-]
Host baterium   Escherichia coli strain 14.3-R4

Cargo genes

Drug resistance gene   tet(A), sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN, iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -