Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102427
Name   oriT_pIncFII in_silico
Organism   Klebsiella pneumoniae strain BA9984
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JACWHM010000024 (26734..26819 [-], 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_pIncFII
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1815 GenBank   WP_000948354
Name   traI_IDM42_RS25380_pIncFII 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   677 GenBank   WP_001354030
Name   WP_001354030_pIncFII 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   678 GenBank   WP_000089263
Name   WP_000089263_pIncFII insolico UniProt ID   A0A3U3XJL9
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8541.74 Da        Isoelectric Point: 8.6796

>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-60)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U3XJL9


T4CP

ID   1402 GenBank   WP_000069777
Name   traC_IDM42_RS25280_pIncFII 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   1403 GenBank   WP_046072940
Name   traD_IDM42_RS25375_pIncFII insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85667.46 Da        Isoelectric Point: 5.1644

>WP_046072940.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP
GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 26166..54309

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IDM42_RS25170 (IDM42_25160) 22138..22572 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
IDM42_RS25175 (IDM42_25165) 22569..23288 + 720 WP_001276217 plasmid SOS inhibition protein A -
IDM42_RS28535 23510..23659 + 150 Protein_28 plasmid maintenance protein Mok -
IDM42_RS25180 (IDM42_25170) 23601..23726 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
IDM42_RS25185 (IDM42_25175) 24045..24341 - 297 Protein_30 hypothetical protein -
IDM42_RS25190 (IDM42_25180) 24641..24937 + 297 WP_001272251 hypothetical protein -
IDM42_RS25195 (IDM42_25185) 25048..25869 + 822 WP_001234445 DUF932 domain-containing protein -
IDM42_RS25200 (IDM42_25190) 26166..26756 - 591 WP_000252683 transglycosylase SLT domain-containing protein virB1
IDM42_RS25205 (IDM42_25195) 27091..27474 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
IDM42_RS25210 (IDM42_25200) 27668..28339 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
IDM42_RS25215 (IDM42_25205) 28476..28703 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
IDM42_RS25220 (IDM42_25210) 28736..29095 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
IDM42_RS25225 (IDM42_25215) 29110..29421 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
IDM42_RS25230 (IDM42_25220) 29443..30009 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
IDM42_RS25235 (IDM42_25225) 29996..30724 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
IDM42_RS25240 (IDM42_25230) 30724..32175 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
IDM42_RS25245 (IDM42_25235) 32165..32731 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
IDM42_RS25250 (IDM42_25240) 32718..33038 + 321 WP_001057307 conjugal transfer protein TrbD -
IDM42_RS25255 (IDM42_25245) 33035..33550 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
IDM42_RS25260 (IDM42_25250) 33685..33906 + 222 WP_001278683 conjugal transfer protein TraR -
IDM42_RS25265 (IDM42_25255) 33899..34375 + 477 WP_000549587 hypothetical protein -
IDM42_RS25270 (IDM42_25260) 34455..34673 + 219 WP_000556745 hypothetical protein -
IDM42_RS25275 (IDM42_25265) 34701..35048 + 348 WP_000836682 hypothetical protein -
IDM42_RS25280 (IDM42_25270) 35174..37804 + 2631 WP_000069777 type IV secretion system protein TraC virb4
IDM42_RS25285 (IDM42_25275) 37801..38187 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
IDM42_RS25290 (IDM42_25280) 38184..38816 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
IDM42_RS25295 (IDM42_25285) 38813..39805 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
IDM42_RS25300 (IDM42_25290) 39835..40140 + 306 WP_000224416 hypothetical protein -
IDM42_RS25305 (IDM42_25295) 40149..40787 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
IDM42_RS25310 (IDM42_25300) 40784..42634 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
IDM42_RS25315 (IDM42_25305) 42661..42918 + 258 WP_000864353 conjugal transfer protein TrbE -
IDM42_RS25320 (IDM42_25310) 42905..43654 + 750 WP_001336806 type-F conjugative transfer system pilin assembly protein TraF traF
IDM42_RS25325 (IDM42_25315) 43668..44012 + 345 WP_000556796 conjugal transfer protein TrbA -
IDM42_RS25330 (IDM42_25320) 44131..44415 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
IDM42_RS25335 (IDM42_25325) 44402..44947 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
IDM42_RS25340 (IDM42_25330) 44877..45224 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
IDM42_RS25345 (IDM42_25335) 45205..45597 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
IDM42_RS25350 (IDM42_25340) 45575..46957 + 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
IDM42_RS25355 (IDM42_25345) 46954..49776 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
IDM42_RS25360 (IDM42_25350) 49792..50277 + 486 WP_000605870 hypothetical protein -
IDM42_RS25365 (IDM42_25355) 50326..51057 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
IDM42_RS25370 (IDM42_25360) 51260..51997 + 738 WP_000199905 hypothetical protein -
IDM42_RS25375 (IDM42_25365) 52048..54309 + 2262 WP_046072940 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   2871 GenBank   NZ_JACWHM010000024
Plasmid name   pIncFII Incompatibility group   IncFII
Plasmid size   67982 bp Coordinate of oriT [Strand]   26734..26819 [-]
Host baterium   Klebsiella pneumoniae strain BA9984

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11