Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103092
Name   oriT_pCC1409-1 in_silico
Organism   Klebsiella pneumoniae strain ST147
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT725789 (27247..27332 [-], 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_pCC1409-1
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2315 GenBank   WP_000948354
Name   traI_HTG16_RS00345_pCC1409-1 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   978 GenBank   WP_001354030
Name   WP_001354030_pCC1409-1 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   979 GenBank   WP_000089263
Name   WP_000089263_pCC1409-1 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   2039 GenBank   WP_000069777
Name   traC_HTG16_RS00245_pCC1409-1 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   2040 GenBank   WP_015059147
Name   traD_HTG16_RS00340_pCC1409-1 insolico UniProt ID   _
Length   750 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 750 a.a.        Molecular weight: 85314.08 Da        Isoelectric Point: 5.1644

>WP_015059147.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGIS
ESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  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: 26679..54813

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG16_RS00130 22651..23085 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTG16_RS00135 23082..23801 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTG16_RS00560 24023..24172 + 150 Protein_27 plasmid maintenance protein Mok -
HTG16_RS00140 24114..24239 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTG16_RS00545 24558..24854 - 297 Protein_29 hypothetical protein -
HTG16_RS00155 25154..25450 + 297 WP_001272251 hypothetical protein -
HTG16_RS00160 25561..26382 + 822 WP_001234445 DUF932 domain-containing protein -
HTG16_RS00165 26679..27281 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HTG16_RS00170 27604..27987 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTG16_RS00175 28181..28852 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTG16_RS00180 28989..29216 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTG16_RS00185 29249..29608 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTG16_RS00190 29623..29934 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTG16_RS00195 29956..30522 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTG16_RS00200 30509..31237 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTG16_RS00205 31237..32688 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTG16_RS00210 32678..33244 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTG16_RS00215 33231..33551 + 321 WP_001057307 conjugal transfer protein TrbD -
HTG16_RS00220 33548..34063 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTG16_RS00225 34198..34419 + 222 WP_001278683 conjugal transfer protein TraR -
HTG16_RS00230 34412..34888 + 477 WP_000549587 hypothetical protein -
HTG16_RS00235 34968..35186 + 219 WP_000556745 hypothetical protein -
HTG16_RS00240 35214..35561 + 348 WP_000836682 hypothetical protein -
HTG16_RS00245 35687..38317 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HTG16_RS00250 38314..38700 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTG16_RS00255 38697..39329 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTG16_RS00260 39326..40318 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTG16_RS00265 40348..40653 + 306 WP_000224416 hypothetical protein -
HTG16_RS00270 40662..41300 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTG16_RS00275 41297..43147 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTG16_RS00280 43174..43431 + 258 WP_000864353 conjugal transfer protein TrbE -
HTG16_RS00285 43418..44167 + 750 WP_001336806 type-F conjugative transfer system pilin assembly protein TraF traF
HTG16_RS00290 44181..44525 + 345 WP_000556796 conjugal transfer protein TrbA -
HTG16_RS00295 44644..44928 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTG16_RS00300 44915..45460 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTG16_RS00305 45390..45737 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTG16_RS00310 45718..46110 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTG16_RS00315 46088..47470 + 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
HTG16_RS00320 47467..50289 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTG16_RS00325 50305..50790 + 486 WP_000605870 hypothetical protein -
HTG16_RS00330 50839..51570 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTG16_RS00335 51773..52510 + 738 WP_000199905 hypothetical protein -
HTG16_RS00340 52561..54813 + 2253 WP_015059147 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3535 GenBank   NZ_KT725789
Plasmid name   pCC1409-1 Incompatibility group   IncFII
Plasmid size   89745 bp Coordinate of oriT [Strand]   27247..27332 [-]
Host baterium   Klebsiella pneumoniae strain ST147

Cargo genes

Drug resistance gene   mph(A), blaTEM-1B, rmtB, blaNDM-5, sul1, qacE, aadA2, dfrA12
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11