Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103045
Name   oriT_pHNEC55 in_silico
Organism   Escherichia coli strain HNEC55
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT879914 (35834..35957 [+], 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_pHNEC55
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2276 GenBank   WP_015059021
Name   traI_HTH24_RS00425_pHNEC55 insolico UniProt ID   A0A0X8XR69
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192132.90 Da        Isoelectric Point: 6.0788

>WP_015059021.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Gammaproteobacteria]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAENRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   934 GenBank   WP_000124981
Name   WP_000124981_pHNEC55 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   935 GenBank   WP_001254386
Name   WP_001254386_pHNEC55 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   1978 GenBank   WP_015059012
Name   traC_HTH24_RS00315_pHNEC55 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: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   1979 GenBank   WP_059274178
Name   traD_HTH24_RS00420_pHNEC55 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83906.57 Da        Isoelectric Point: 5.0504

>WP_059274178.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 35262..63441

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH24_RS00210 31234..31668 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTH24_RS00215 31665..32427 + 763 Protein_43 plasmid SOS inhibition protein A -
HTH24_RS00550 32606..32755 + 150 Protein_44 plasmid maintenance protein Mok -
HTH24_RS00220 32697..32822 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTH24_RS00525 33141..33437 - 297 Protein_46 hypothetical protein -
HTH24_RS00235 33737..34033 + 297 WP_001272251 hypothetical protein -
HTH24_RS00240 34144..34965 + 822 WP_001234445 DUF932 domain-containing protein -
HTH24_RS00245 35262..35909 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HTH24_RS00250 36186..36569 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTH24_RS00255 36760..37446 + 687 WP_015059009 PAS domain-containing protein -
HTH24_RS00260 37540..37767 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTH24_RS00265 37801..38166 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HTH24_RS00270 38181..38492 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTH24_RS00275 38514..39080 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HTH24_RS00280 39067..39795 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTH24_RS00285 39795..41222 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HTH24_RS00290 41212..41802 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HTH24_RS00295 41789..41986 + 198 WP_001324648 conjugal transfer protein TrbD -
HTH24_RS00300 41998..42249 + 252 WP_001038341 conjugal transfer protein TrbG -
HTH24_RS00305 42246..42761 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HTH24_RS00310 42896..43117 + 222 WP_001278692 conjugal transfer protein TraR -
HTH24_RS00315 43277..45904 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HTH24_RS00320 45901..46287 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HTH24_RS00325 46284..46916 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HTH24_RS00330 46913..47905 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTH24_RS00335 47932..48240 + 309 WP_000412447 hypothetical protein -
HTH24_RS00340 48303..48824 + 522 WP_015059014 hypothetical protein -
HTH24_RS00345 48851..49489 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTH24_RS00350 49486..49857 + 372 WP_000056336 hypothetical protein -
HTH24_RS00355 49883..50305 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HTH24_RS00360 50302..52152 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTH24_RS00365 52179..52436 + 258 WP_053913405 conjugal transfer protein TrbE -
HTH24_RS00370 52429..53172 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
HTH24_RS00375 53333..53569 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
HTH24_RS00380 53556..54101 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTH24_RS00385 54091..54405 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HTH24_RS00390 54359..54751 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HTH24_RS00395 54738..56111 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HTH24_RS00400 56108..58924 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HTH24_RS00405 58957..59478 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HTH24_RS00410 59503..60234 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HTH24_RS00415 60437..61174 + 738 WP_015059020 hypothetical protein -
HTH24_RS00420 61225..63441 + 2217 WP_059274178 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3488 GenBank   NZ_KT879914
Plasmid name   pHNEC55 Incompatibility group   IncFII
Plasmid size   81498 bp Coordinate of oriT [Strand]   35834..35957 [+]
Host baterium   Escherichia coli strain HNEC55

Cargo genes

Drug resistance gene   blaNDM-1, fosA3, blaTEM-1B, rmtB, aph(3')-VI
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -