Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103083
Name   oriT_pCERC5 in_silico
Organism   Escherichia coli strain 11.3-R3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU664810 (89403..89755 [-], 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_pCERC5
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2306 GenBank   WP_001514237
Name   traI_HTH27_RS00295_pCERC5 insolico UniProt ID   A0A0F6X1E3
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191942.70 Da        Isoelectric Point: 5.7462

>WP_001514237.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Gammaproteobacteria]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAWLHTPAQQAIHLALPVVESKNLAFSMVDLLTEVKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPGSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPITAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREITGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

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   967 GenBank   WP_001369361
Name   WP_001369361_pCERC5 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   968 GenBank   WP_001151524
Name   WP_001151524_pCERC5 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   2027 GenBank   WP_061092446
Name   traD_HTH27_RS00300_pCERC5 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: 81462.05 Da        Isoelectric Point: 5.1693

>WP_061092446.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFKPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVLAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
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   2028 GenBank   WP_001064252
Name   traC_HTH27_RS00380_pCERC5 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: 64598..90326

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH27_RS00300 64598..66751 - 2154 WP_061092446 type IV conjugative transfer system coupling protein TraD virb4
HTH27_RS00305 67004..67735 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HTH27_RS00310 67749..68258 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
HTH27_RS00315 68255..71080 - 2826 Protein_63 conjugal transfer mating-pair stabilization protein TraG -
HTH27_RS00320 71077..72450 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HTH27_RS00325 72450..72812 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HTH27_RS00330 72742..73287 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTH27_RS00335 73274..73558 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HTH27_RS00340 73677..74024 - 348 WP_061092447 conjugal transfer protein TrbA -
HTH27_RS00345 74040..74783 - 744 WP_001514239 type-F conjugative transfer system pilin assembly protein TraF traF
HTH27_RS00350 74776..75033 - 258 WP_000864325 conjugal transfer protein TrbE -
HTH27_RS00355 75060..76868 - 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTH27_RS00360 76865..77503 - 639 WP_000777693 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTH27_RS00365 77512..78504 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HTH27_RS00370 78501..79133 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTH27_RS00375 79130..79516 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
HTH27_RS00380 79513..82140 - 2628 WP_001064252 type IV secretion system protein TraC virb4
HTH27_RS00385 82300..82521 - 222 WP_001278689 conjugal transfer protein TraR -
HTH27_RS00390 82656..83171 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HTH27_RS00395 83168..83419 - 252 WP_001038342 conjugal transfer protein TrbG -
HTH27_RS00400 83431..83628 - 198 WP_001324648 conjugal transfer protein TrbD -
HTH27_RS00405 83615..84205 - 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
HTH27_RS00410 84195..85622 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HTH27_RS00415 85622..86350 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTH27_RS00420 86337..86903 - 567 WP_000399785 type IV conjugative transfer system protein TraE traE
HTH27_RS00425 86925..87236 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTH27_RS00430 87251..87616 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HTH27_RS00435 87649..88044 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HTH27_RS00440 88143..88832 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HTH27_RS00445 89019..89402 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HTH27_RS00450 89817..90326 + 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
HTH27_RS00455 90622..91443 - 822 WP_001234468 DUF932 domain-containing protein -
HTH27_RS00460 91562..91849 - 288 WP_000107520 hypothetical protein -
HTH27_RS00740 91874..92014 - 141 WP_001445060 hypothetical protein -
HTH27_RS00470 92150..92447 + 298 Protein_94 hypothetical protein -
HTH27_RS00475 92748..92870 - 123 WP_223195199 Hok/Gef family protein -
HTH27_RS00770 92815..92967 - 153 Protein_96 DUF5431 family protein -
HTH27_RS00480 93118..93904 - 787 Protein_97 plasmid SOS inhibition protein A -
HTH27_RS00485 93901..94335 - 435 WP_000845922 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   3526 GenBank   NZ_KU664810
Plasmid name   pCERC5 Incompatibility group   IncFII
Plasmid size   142359 bp Coordinate of oriT [Strand]   89403..89755 [-]
Host baterium   Escherichia coli strain 11.3-R3

Cargo genes

Drug resistance gene   tet(A), blaTEM-1C, sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN, iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -