Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102828
Name   oriT_pNY9_3 in_silico
Organism   Klebsiella pneumoniae strain NY9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP015388 (50246..50331 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pNY9_3
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2096 GenBank   WP_000948354
Name   traI_A6P56_RS30895_pNY9_3 insolico UniProt ID   A0AA36L3I8
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   843 GenBank   WP_001354030
Name   WP_001354030_pNY9_3 insolico UniProt ID   A0A734M5H3
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14508.47 Da        Isoelectric Point: 4.7116

>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A734M5H3

ID   844 GenBank   WP_227518118
Name   WP_227518118_pNY9_3 insolico UniProt ID   _
Length   39 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 39 a.a.        Molecular weight: 4551.15 Da        Isoelectric Point: 4.4883

>WP_227518118.1 TraY domain-containing protein [Klebsiella pneumoniae]
MFAPSLVRLRDHLNRFPDFYNLDAIKEGAEETDSIIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(7-24)


  Protein structure



No available structure.




T4CP

ID   1756 GenBank   WP_000069777
Name   traC_A6P56_RS30795_pNY9_3 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: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   1757 GenBank   WP_000009332
Name   traD_A6P56_RS30890_pNY9_3 insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 83193.81 Da        Isoelectric Point: 5.1644

>WP_000009332.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 49678..80024

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
A6P56_RS30655 45056..45481 + 426 WP_000422741 transposase -
A6P56_RS30660 (A6P56_29070) 45478..45828 + 351 WP_000624722 IS66 family insertion sequence element accessory protein TnpB -
A6P56_RS30665 (A6P56_29075) 45859..47472 + 1614 WP_000080200 IS66-like element ISEc23 family transposase -
A6P56_RS34445 47557..47853 - 297 Protein_56 hypothetical protein -
A6P56_RS30685 (A6P56_29080) 48153..48449 + 297 WP_001272251 hypothetical protein -
A6P56_RS30690 (A6P56_29085) 48560..49381 + 822 WP_001234445 DUF932 domain-containing protein -
A6P56_RS30695 (A6P56_29090) 49678..50268 - 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
A6P56_RS30700 (A6P56_29095) 50603..50986 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
A6P56_RS30705 (A6P56_29100) 51180..51851 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
A6P56_RS35030 51988..52073 + 86 Protein_62 conjugal transfer protein TraY -
A6P56_RS35035 52056..52280 - 225 WP_335617514 hypothetical protein -
A6P56_RS30720 (A6P56_29105) 52262..53242 - 981 WP_000019473 IS5-like element ISKpn26 family transposase -
A6P56_RS30725 53296..53415 + 120 WP_227518118 TraY domain-containing protein -
A6P56_RS30730 (A6P56_29110) 53448..53807 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
A6P56_RS30735 (A6P56_29115) 53822..54133 + 312 WP_033550688 type IV conjugative transfer system protein TraL traL
A6P56_RS30740 (A6P56_29120) 54155..54721 + 567 WP_000399791 type IV conjugative transfer system protein TraE traE
A6P56_RS30745 (A6P56_29125) 54708..55436 + 729 WP_001230808 type-F conjugative transfer system secretin TraK traK
A6P56_RS30750 (A6P56_29130) 55436..56887 + 1452 WP_075995132 F-type conjugal transfer pilus assembly protein TraB traB
A6P56_RS30755 (A6P56_29135) 56877..57443 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
A6P56_RS30760 57430..57750 + 321 WP_001057307 conjugal transfer protein TrbD -
A6P56_RS30765 (A6P56_29140) 57747..58262 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
A6P56_RS30770 58397..58618 + 222 WP_001278683 conjugal transfer protein TraR -
A6P56_RS30775 (A6P56_29145) 58611..59087 + 477 WP_000549587 hypothetical protein -
A6P56_RS30780 59167..59367 + 201 WP_075995133 hypothetical protein -
A6P56_RS30785 (A6P56_29150) 59413..60381 - 969 WP_004099053 IS5-like element IS903B family transposase -
A6P56_RS30790 (A6P56_29155) 60479..60826 + 348 WP_000836682 hypothetical protein -
A6P56_RS30795 (A6P56_29160) 60952..63582 + 2631 WP_000069777 type IV secretion system protein TraC virb4
A6P56_RS30800 (A6P56_29165) 63579..63965 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
A6P56_RS30805 (A6P56_29170) 63962..64594 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
A6P56_RS30810 (A6P56_29175) 64591..65583 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
A6P56_RS30815 (A6P56_29180) 65613..65918 + 306 WP_000224416 hypothetical protein -
A6P56_RS30820 (A6P56_29185) 65927..66565 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
A6P56_RS30825 (A6P56_29190) 66562..68412 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
A6P56_RS30830 (A6P56_29195) 68439..68696 + 258 WP_000864353 conjugal transfer protein TrbE -
A6P56_RS30835 (A6P56_29200) 68683..69432 + 750 WP_001336806 type-F conjugative transfer system pilin assembly protein TraF traF
A6P56_RS30840 69446..69790 + 345 WP_000556796 conjugal transfer protein TrbA -
A6P56_RS30845 (A6P56_29205) 69909..70193 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
A6P56_RS30850 (A6P56_29210) 70180..70725 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
A6P56_RS30855 70655..71002 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
A6P56_RS30860 (A6P56_29215) 70983..71375 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
A6P56_RS30865 (A6P56_29220) 71353..72735 + 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
A6P56_RS30870 (A6P56_29225) 72732..75554 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
A6P56_RS30875 75570..76055 + 486 WP_000605870 hypothetical protein -
A6P56_RS30880 (A6P56_29230) 76104..76835 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
A6P56_RS30885 (A6P56_29235) 77038..77775 + 738 WP_000199905 hypothetical protein -
A6P56_RS30890 (A6P56_29240) 77826..80024 + 2199 WP_000009332 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3271 GenBank   NZ_CP015388
Plasmid name   pNY9_3 Incompatibility group   IncFII
Plasmid size   89067 bp Coordinate of oriT [Strand]   50246..50331 [-]
Host baterium   Klebsiella pneumoniae strain NY9

Cargo genes

Drug resistance gene   tet(A), aac(6')-Ib-cr, blaOXA-1, blaCTX-M-15, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -