Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102959
Name   oriT_pHeBE7 in_silico
Organism   Escherichia coli strain HeB7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT002541 (42314..42437 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pHeBE7
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2217 GenBank   WP_015059123
Name   traI_HTF34_RS00405_pHeBE7 insolico UniProt ID   I1WZQ7
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191914.74 Da        Isoelectric Point: 6.1060

>WP_015059123.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKISGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

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

(575-627)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




Auxiliary protein

ID   910 GenBank   WP_000124981
Name   WP_000124981_pHeBE7 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9

ID   911 GenBank   WP_001254386
Name   WP_001254386_pHeBE7 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   1904 GenBank   WP_000069764
Name   traC_HTF34_RS00320_pHeBE7 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: 99302.93 Da        Isoelectric Point: 5.8486

>WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.



ID   1905 GenBank   WP_015059124
Name   traD_HTF34_RS00400_pHeBE7 insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84273.98 Da        Isoelectric Point: 5.0524

>WP_015059124.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 41742..68591

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTF34_RS00205 37709..38143 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTF34_RS00210 38140..38902 + 763 Protein_40 plasmid SOS inhibition protein A -
HTF34_RS00490 39081..39230 + 150 Protein_41 plasmid maintenance protein Mok -
HTF34_RS00215 39172..39297 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTF34_RS00495 39517..39747 + 231 WP_001426396 hypothetical protein -
HTF34_RS00500 39745..39918 - 174 Protein_44 hypothetical protein -
HTF34_RS00505 39988..40194 + 207 WP_000547968 hypothetical protein -
HTF34_RS00225 40219..40506 + 288 WP_000107544 hypothetical protein -
HTF34_RS00230 40624..41445 + 822 WP_001234469 DUF932 domain-containing protein -
HTF34_RS00235 41742..42389 - 648 WP_031943493 transglycosylase SLT domain-containing protein virB1
HTF34_RS00240 42666..43049 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTF34_RS00245 43240..43926 + 687 WP_000332484 PAS domain-containing protein -
HTF34_RS00250 44020..44247 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTF34_RS00255 44281..44640 + 360 WP_000340272 type IV conjugative transfer system pilin TraA -
HTF34_RS00260 44655..44966 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTF34_RS00265 44988..45554 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HTF34_RS00270 45541..46269 + 729 WP_001230813 type-F conjugative transfer system secretin TraK traK
HTF34_RS00275 46269..47696 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HTF34_RS00280 47686..48276 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
HTF34_RS00285 48263..48583 + 321 WP_001057287 conjugal transfer protein TrbD virb4
HTF34_RS00290 48576..48827 + 252 WP_001038342 conjugal transfer protein TrbG -
HTF34_RS00295 48824..49339 + 516 WP_015059130 type IV conjugative transfer system lipoprotein TraV traV
HTF34_RS00300 49474..49695 + 222 WP_001278695 conjugal transfer protein TraR -
HTF34_RS00305 49688..50164 + 477 WP_015059129 hypothetical protein -
HTF34_RS00310 50244..50458 + 215 Protein_63 hypothetical protein -
HTF34_RS00315 50486..50848 + 363 WP_000836675 hypothetical protein -
HTF34_RS00320 50974..53604 + 2631 WP_000069764 type IV secretion system protein TraC virb4
HTF34_RS00325 53601..53987 + 387 WP_000214092 type-F conjugative transfer system protein TrbI -
HTF34_RS00330 53984..54616 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTF34_RS00335 54613..55605 + 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HTF34_RS00340 55614..56252 + 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTF34_RS00345 56249..58057 + 1809 WP_000821821 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTF34_RS00350 58084..58341 + 258 WP_000864352 conjugal transfer protein TrbE -
HTF34_RS00355 58334..59077 + 744 WP_159122582 type-F conjugative transfer system pilin assembly protein TraF traF
HTF34_RS00360 59093..59440 + 348 WP_001287891 conjugal transfer protein TrbA -
HTF34_RS00365 59559..59843 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HTF34_RS00370 59830..60375 + 546 WP_000059821 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTF34_RS00375 60305..60667 + 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HTF34_RS00380 60667..62040 + 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HTF34_RS00385 62037..64862 + 2826 WP_001007045 conjugal transfer mating-pair stabilization protein TraG traG
HTF34_RS00390 64859..65368 + 510 WP_031943494 conjugal transfer entry exclusion protein TraS -
HTF34_RS00395 65382..66113 + 732 WP_094658456 conjugal transfer complement resistance protein TraT -
HTF34_RS00400 66366..68591 + 2226 WP_015059124 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3402 GenBank   NZ_KT002541
Plasmid name   pHeBE7 Incompatibility group   IncFII
Plasmid size   86015 bp Coordinate of oriT [Strand]   42314..42437 [+]
Host baterium   Escherichia coli strain HeB7

Cargo genes

Drug resistance gene   blaTEM-1B, rmtB, blaCTX-M-98
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11