Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101380
Name   oriT_pKP2000557_2 in_silico
Organism   Klebsiella pneumoniae subsp. pneumoniae strain KP2000557
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAENHY010000004 (38330..38453 [+], 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_pKP2000557_2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1265 GenBank   WP_071177725
Name   traI_JDY82_RS28575_pKP2000557_2 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   449 GenBank   WP_000124981
Name   WP_000124981_pKP2000557_2 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   450 GenBank   WP_001254386
Name   WP_001254386_pKP2000557_2 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   875 GenBank   WP_015059012
Name   traC_JDY82_RS28465_pKP2000557_2 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   876 GenBank   WP_059274178
Name   traD_JDY82_RS28570_pKP2000557_2 insolico UniProt ID   _
Length   738 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 738 a.a.        Molecular weight: 83906.57 Da        Isoelectric Point: 5.0504

>WP_059274178.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE
AWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  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: 37758..65937

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JDY82_RS28365 (JDY82_28365) 33730..34164 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
JDY82_RS28370 (JDY82_28370) 34161..34880 + 720 WP_001276217 plasmid SOS inhibition protein A -
JDY82_RS30735 35102..35251 + 150 Protein_46 plasmid maintenance protein Mok -
JDY82_RS28375 (JDY82_28375) 35193..35318 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
JDY82_RS28380 (JDY82_28380) 35637..35933 - 297 Protein_48 hypothetical protein -
JDY82_RS28385 (JDY82_28385) 36233..36529 + 297 WP_001272251 hypothetical protein -
JDY82_RS28390 (JDY82_28390) 36640..37461 + 822 WP_001234445 DUF932 domain-containing protein -
JDY82_RS28395 (JDY82_28395) 37758..38405 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
JDY82_RS28400 (JDY82_28400) 38682..39065 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
JDY82_RS28405 (JDY82_28405) 39256..39942 + 687 WP_015059009 PAS domain-containing protein -
JDY82_RS28410 (JDY82_28410) 40036..40263 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
JDY82_RS28415 (JDY82_28415) 40297..40662 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
JDY82_RS28420 (JDY82_28420) 40677..40988 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
JDY82_RS28425 (JDY82_28425) 41010..41576 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
JDY82_RS28430 (JDY82_28430) 41563..42291 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
JDY82_RS28435 (JDY82_28435) 42291..43718 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
JDY82_RS28440 (JDY82_28440) 43708..44298 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
JDY82_RS28445 (JDY82_28445) 44285..44482 + 198 WP_001324648 conjugal transfer protein TrbD -
JDY82_RS28450 (JDY82_28450) 44494..44745 + 252 WP_001038341 conjugal transfer protein TrbG -
JDY82_RS28455 (JDY82_28455) 44742..45257 + 516 WP_062955122 type IV conjugative transfer system lipoprotein TraV traV
JDY82_RS28460 (JDY82_28460) 45392..45613 + 222 WP_001278692 conjugal transfer protein TraR -
JDY82_RS28465 (JDY82_28465) 45773..48400 + 2628 WP_015059012 type IV secretion system protein TraC virb4
JDY82_RS28470 (JDY82_28470) 48397..48783 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
JDY82_RS28475 (JDY82_28475) 48780..49412 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
JDY82_RS28480 (JDY82_28480) 49409..50401 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
JDY82_RS28485 (JDY82_28485) 50428..50736 + 309 WP_000412447 hypothetical protein -
JDY82_RS28490 (JDY82_28490) 50799..51320 + 522 WP_015059014 hypothetical protein -
JDY82_RS28495 (JDY82_28495) 51347..51985 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
JDY82_RS28500 (JDY82_28500) 51982..52353 + 372 WP_000056336 hypothetical protein -
JDY82_RS28505 (JDY82_28505) 52379..52801 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
JDY82_RS28510 (JDY82_28510) 52798..54648 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JDY82_RS28515 (JDY82_28515) 54675..54932 + 258 WP_053913405 conjugal transfer protein TrbE -
JDY82_RS28520 (JDY82_28520) 54919..55668 + 750 WP_072354014 type-F conjugative transfer system pilin assembly protein TraF traF
JDY82_RS28525 (JDY82_28525) 55829..56065 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
JDY82_RS28530 (JDY82_28530) 56052..56597 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JDY82_RS28535 (JDY82_28535) 56587..56901 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
JDY82_RS28540 (JDY82_28540) 56855..57247 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
JDY82_RS28545 (JDY82_28545) 57234..58607 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
JDY82_RS28550 (JDY82_28550) 58604..61420 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
JDY82_RS28555 (JDY82_28555) 61453..61974 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
JDY82_RS28560 (JDY82_28560) 61999..62730 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
JDY82_RS28565 (JDY82_28565) 62933..63670 + 738 WP_015059020 hypothetical protein -
JDY82_RS28570 (JDY82_28570) 63721..65937 + 2217 WP_059274178 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1824 GenBank   NZ_JAENHY010000004
Plasmid name   pKP2000557_2 Incompatibility group   IncR
Plasmid size   147185 bp Coordinate of oriT [Strand]   38330..38453 [+]
Host baterium   Klebsiella pneumoniae subsp. pneumoniae strain KP2000557

Cargo genes

Drug resistance gene   blaCTX-M-65, blaTEM-1B, rmtB, blaSHV-187, blaKPC-2
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9