Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103082
Name   oriT_pCERC4 in_silico
Organism   Escherichia coli
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU578032 (90856..91208 [-], 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_pCERC4
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2305 GenBank   WP_001514237
Name   traI_HTH25_RS00325_pCERC4 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   965 GenBank   WP_001369361
Name   WP_001369361_pCERC4 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   966 GenBank   WP_001151524
Name   WP_001151524_pCERC4 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   2025 GenBank   WP_001369365
Name   traD_HTH25_RS00330_pCERC4 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: 81446.95 Da        Isoelectric Point: 5.0524

>WP_001369365.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
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   2026 GenBank   WP_001064252
Name   traC_HTH25_RS00415_pCERC4 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: 64790..91779

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH25_RS00330 64790..66943 - 2154 WP_001369365 type IV conjugative transfer system coupling protein TraD virb4
HTH25_RS00335 67196..67927 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HTH25_RS00830 67941..68195 - 255 Protein_67 conjugal transfer protein TraS -
HTH25_RS00340 68262..69424 + 1163 WP_087121889 IS3-like element IS3 family transposase -
HTH25_RS00345 69454..69711 - 258 Protein_69 conjugal transfer protein TraS -
HTH25_RS00350 69708..72533 - 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
HTH25_RS00355 72530..73903 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HTH25_RS00360 73903..74265 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HTH25_RS00365 74195..74740 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTH25_RS00370 74727..75011 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HTH25_RS00375 75130..75477 - 348 WP_001287677 conjugal transfer protein TrbA -
HTH25_RS00380 75493..76236 - 744 WP_001514239 type-F conjugative transfer system pilin assembly protein TraF traF
HTH25_RS00385 76229..76486 - 258 WP_000864325 conjugal transfer protein TrbE -
HTH25_RS00390 76513..78321 - 1809 WP_000821846 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTH25_RS00395 78318..78956 - 639 WP_000777693 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTH25_RS00400 78965..79957 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HTH25_RS00405 79954..80586 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTH25_RS00410 80583..80969 - 387 WP_000214082 type-F conjugative transfer system protein TrbI -
HTH25_RS00415 80966..83593 - 2628 WP_001064252 type IV secretion system protein TraC virb4
HTH25_RS00420 83753..83974 - 222 WP_001278689 conjugal transfer protein TraR -
HTH25_RS00425 84109..84624 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HTH25_RS00430 84621..84872 - 252 WP_001038342 conjugal transfer protein TrbG -
HTH25_RS00435 84884..85081 - 198 WP_001324648 conjugal transfer protein TrbD -
HTH25_RS00440 85068..85658 - 591 WP_000002796 conjugal transfer pilus-stabilizing protein TraP -
HTH25_RS00445 85648..87075 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HTH25_RS00450 87075..87803 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTH25_RS00455 87790..88356 - 567 WP_000399785 type IV conjugative transfer system protein TraE traE
HTH25_RS00460 88378..88689 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTH25_RS00465 88704..89069 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HTH25_RS00470 89102..89497 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HTH25_RS00475 89596..90285 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HTH25_RS00480 90472..90855 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HTH25_RS00485 91270..91779 + 510 WP_000759163 transglycosylase SLT domain-containing protein virB1
HTH25_RS00490 92075..92896 - 822 WP_001234468 DUF932 domain-containing protein -
HTH25_RS00495 93015..93302 - 288 WP_000107520 hypothetical protein -
HTH25_RS00500 93327..93446 - 120 WP_001127499 hypothetical protein -
HTH25_RS00505 93603..93900 + 298 Protein_101 hypothetical protein -
HTH25_RS00510 94201..94323 - 123 WP_223195199 Hok/Gef family protein -
HTH25_RS00800 94268..94420 - 153 Protein_103 DUF5431 family protein -
HTH25_RS00515 94571..95357 - 787 Protein_104 plasmid SOS inhibition protein A -
HTH25_RS00520 95354..95788 - 435 WP_000845922 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   3525 GenBank   NZ_KU578032
Plasmid name   pCERC4 Incompatibility group   IncFII
Plasmid size   143812 bp Coordinate of oriT [Strand]   90856..91208 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   dfrA5, qacE, sul1, sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN, iutA, iucC, iucB, iucA
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -