Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105020
Name   oriT1_pC2660-3-KPC in_silico
Organism   Klebsiella pneumoniae strain C2660
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039810 (42749..42872 [+], 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

>oriT1_pC2660-3-KPC
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3513 GenBank   WP_071177725
Name   traI_FA957_RS29240_pC2660-3-KPC insolico UniProt ID   A0A7G3L5Q3
Length   1711 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1711 a.a.        Molecular weight: 186716.81 Da        Isoelectric Point: 6.1728

>WP_071177725.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAENRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALLQS

  Protein domains


Predicted by InterproScan.

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

(575-626)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)


  Protein structure



No available structure.




Auxiliary protein

ID   1562 GenBank   WP_000124981
Name   WP_000124981_pC2660-3-KPC 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   1563 GenBank   WP_001254386
Name   WP_001254386_pC2660-3-KPC 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   3469 GenBank   WP_015059012
Name   traC_FA957_RS29130_pC2660-3-KPC 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   3470 GenBank   WP_000009363
Name   traD_FA957_RS29235_pC2660-3-KPC insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84259.95 Da        Isoelectric Point: 5.0504

>WP_000009363.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42177..70365

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FA957_RS29030 (FA957_29170) 38149..38583 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
FA957_RS29035 (FA957_29175) 38580..39299 + 720 WP_001276217 plasmid SOS inhibition protein A -
FA957_RS30770 39521..39670 + 150 Protein_50 plasmid maintenance protein Mok -
FA957_RS29040 (FA957_29180) 39612..39737 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
FA957_RS30475 40056..40352 - 297 Protein_52 hypothetical protein -
FA957_RS29050 (FA957_29200) 40652..40948 + 297 WP_001272251 hypothetical protein -
FA957_RS29055 (FA957_29205) 41059..41880 + 822 WP_001234445 DUF932 domain-containing protein -
FA957_RS29060 (FA957_29210) 42177..42824 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
FA957_RS29065 (FA957_29215) 43101..43484 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
FA957_RS29070 (FA957_29220) 43675..44361 + 687 WP_015059009 PAS domain-containing protein -
FA957_RS29075 (FA957_29225) 44455..44682 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
FA957_RS29080 (FA957_29230) 44716..45081 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
FA957_RS29085 (FA957_29235) 45096..45407 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
FA957_RS29090 (FA957_29240) 45429..45995 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
FA957_RS29095 (FA957_29245) 45982..46710 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
FA957_RS29100 (FA957_29250) 46710..48137 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
FA957_RS29105 (FA957_29255) 48127..48717 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
FA957_RS29110 (FA957_29260) 48704..48901 + 198 WP_001324648 conjugal transfer protein TrbD -
FA957_RS29115 (FA957_29265) 48913..49164 + 252 WP_001038341 conjugal transfer protein TrbG -
FA957_RS29120 (FA957_29270) 49161..49676 + 516 WP_062955122 type IV conjugative transfer system lipoprotein TraV traV
FA957_RS29125 (FA957_29275) 49811..50032 + 222 WP_001278692 conjugal transfer protein TraR -
FA957_RS29130 (FA957_29280) 50192..52819 + 2628 WP_015059012 type IV secretion system protein TraC virb4
FA957_RS29135 (FA957_29285) 52816..53202 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
FA957_RS29140 (FA957_29290) 53199..53831 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
FA957_RS29145 (FA957_29295) 53828..54820 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
FA957_RS29150 (FA957_29300) 54847..55155 + 309 WP_000412447 hypothetical protein -
FA957_RS29155 (FA957_29305) 55218..55739 + 522 WP_015059014 hypothetical protein -
FA957_RS29160 (FA957_29310) 55766..56404 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
FA957_RS29165 (FA957_29315) 56401..56772 + 372 WP_000056336 hypothetical protein -
FA957_RS29170 (FA957_29320) 56798..57220 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
FA957_RS29175 (FA957_29325) 57217..59067 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FA957_RS29180 (FA957_29330) 59094..59351 + 258 WP_053913405 conjugal transfer protein TrbE -
FA957_RS29185 (FA957_29335) 59338..60087 + 750 WP_072354014 type-F conjugative transfer system pilin assembly protein TraF traF
FA957_RS29190 (FA957_29340) 60248..60484 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
FA957_RS29195 (FA957_29345) 60471..61016 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
FA957_RS29200 (FA957_29350) 61006..61320 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
FA957_RS29205 (FA957_29355) 61274..61666 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
FA957_RS29210 (FA957_29360) 61653..63026 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
FA957_RS29215 (FA957_29365) 63023..65839 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
FA957_RS29220 (FA957_29370) 65872..66393 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
FA957_RS29225 (FA957_29375) 66418..67149 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
FA957_RS29230 (FA957_29380) 67352..68089 + 738 WP_015059020 hypothetical protein -
FA957_RS29235 (FA957_29385) 68140..70365 + 2226 WP_000009363 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5458 GenBank   NZ_CP039810
Plasmid name   pC2660-3-KPC Incompatibility group   IncR
Plasmid size   153556 bp Coordinate of oriT [Strand]   42749..42872 [+]; 101911..101960 [+]
Host baterium   Klebsiella pneumoniae strain C2660

Cargo genes

Drug resistance gene   blaKPC-2, blaCTX-M-65, blaTEM-1B, rmtB
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9