Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104591
Name   oriT_STEFF_2|unnamed2 in_silico
Organism   Klebsiella pneumoniae strain STEFF_2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055212 (65492..65615 [+], 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_STEFF_2|unnamed2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3303 GenBank   WP_061093447
Name   traI_HUZ38_RS27750_STEFF_2|unnamed2 insolico UniProt ID   A0A2Z4I1F4
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192119.90 Da        Isoelectric Point: 6.0788

>WP_061093447.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
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.

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)

AAA domain (AAA_30)

(969-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   1479 GenBank   WP_000124981
Name   WP_000124981_STEFF_2|unnamed2 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   1480 GenBank   WP_001254386
Name   WP_001254386_STEFF_2|unnamed2 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   3242 GenBank   WP_015059012
Name   traC_HUZ38_RS27640_STEFF_2|unnamed2 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   3243 GenBank   WP_239612347
Name   traD_HUZ38_RS27745_STEFF_2|unnamed2 insolico UniProt ID   _
Length   744 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 744 a.a.        Molecular weight: 84603.29 Da        Isoelectric Point: 5.0504

>WP_239612347.1 type IV conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPSGISESGEVV
DMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 64920..93117

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ38_RS27535 (HUZ38_27440) 60892..61326 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HUZ38_RS27540 (HUZ38_27445) 61323..62042 + 720 WP_001276217 plasmid SOS inhibition protein A -
HUZ38_RS27545 62264..62413 + 150 Protein_77 plasmid maintenance protein Mok -
HUZ38_RS27550 (HUZ38_27450) 62355..62480 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ38_RS27555 (HUZ38_27455) 62799..63095 - 297 Protein_79 hypothetical protein -
HUZ38_RS27560 (HUZ38_27460) 63395..63691 + 297 WP_001272251 hypothetical protein -
HUZ38_RS27565 (HUZ38_27465) 63802..64623 + 822 WP_001234445 DUF932 domain-containing protein -
HUZ38_RS27570 (HUZ38_27470) 64920..65567 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HUZ38_RS27575 (HUZ38_27475) 65844..66227 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ38_RS27580 (HUZ38_27480) 66418..67104 + 687 WP_015059009 PAS domain-containing protein -
HUZ38_RS27585 (HUZ38_27485) 67198..67425 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HUZ38_RS27590 (HUZ38_27490) 67459..67824 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HUZ38_RS27595 (HUZ38_27495) 67839..68150 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ38_RS27600 (HUZ38_27500) 68172..68738 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HUZ38_RS27605 (HUZ38_27505) 68725..69453 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ38_RS27610 (HUZ38_27510) 69453..70880 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HUZ38_RS27615 (HUZ38_27515) 70870..71460 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HUZ38_RS27620 (HUZ38_27520) 71447..71644 + 198 WP_001324648 conjugal transfer protein TrbD -
HUZ38_RS27625 (HUZ38_27525) 71656..71907 + 252 WP_001038341 conjugal transfer protein TrbG -
HUZ38_RS27630 (HUZ38_27530) 71904..72419 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HUZ38_RS27635 (HUZ38_27535) 72554..72775 + 222 WP_001278692 conjugal transfer protein TraR -
HUZ38_RS27640 (HUZ38_27540) 72935..75562 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HUZ38_RS27645 (HUZ38_27545) 75559..75945 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HUZ38_RS27650 (HUZ38_27550) 75942..76574 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HUZ38_RS27655 (HUZ38_27555) 76571..77563 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HUZ38_RS27660 (HUZ38_27560) 77590..77898 + 309 WP_000412447 hypothetical protein -
HUZ38_RS27665 (HUZ38_27565) 77961..78482 + 522 WP_015059014 hypothetical protein -
HUZ38_RS27670 (HUZ38_27570) 78509..79147 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ38_RS27675 (HUZ38_27575) 79144..79515 + 372 WP_000056336 hypothetical protein -
HUZ38_RS27680 (HUZ38_27580) 79541..79963 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HUZ38_RS27685 (HUZ38_27585) 79960..81810 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ38_RS27690 (HUZ38_27590) 81837..82094 + 258 WP_053913405 conjugal transfer protein TrbE -
HUZ38_RS27695 (HUZ38_27595) 82081..82830 + 750 WP_072354014 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ38_RS27700 (HUZ38_27600) 82991..83227 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
HUZ38_RS27705 (HUZ38_27605) 83214..83759 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ38_RS27710 (HUZ38_27610) 83749..84063 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HUZ38_RS27715 (HUZ38_27615) 84017..84409 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HUZ38_RS27720 (HUZ38_27620) 84396..85769 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HUZ38_RS27725 (HUZ38_27625) 85766..88582 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ38_RS27730 (HUZ38_27630) 88615..89136 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HUZ38_RS27735 (HUZ38_27635) 89161..89892 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HUZ38_RS27740 (HUZ38_27640) 90095..90832 + 738 WP_015059020 hypothetical protein -
HUZ38_RS27745 (HUZ38_27645) 90883..93117 + 2235 WP_239612347 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5030 GenBank   NZ_CP055212
Plasmid name   STEFF_2|unnamed2 Incompatibility group   IncFII
Plasmid size   102776 bp Coordinate of oriT [Strand]   65492..65615 [+]
Host baterium   Klebsiella pneumoniae strain STEFF_2

Cargo genes

Drug resistance gene   floR, sul2, aph(3')-IIa, blaTEM-1B, rmtB, blaCTX-M-55
Virulence gene   -
Metal resistance gene   arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -