Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119537
Name   oriT_pJF-787 in_silico
Organism   Klebsiella variicola strain H152460787
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX868552 (41682..41738 [-], 57 nt)
oriT length   57 nt
IRs (inverted repeats)      13..20, 23..30  (GCAAAATT..AATTTTGC)
Location of nic site      39..40
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_pJF-787
TAAAGTTAATCAGCAAAATTTCAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12345 GenBank   WP_172688917
Name   traI_HTK15_RS00450_pJF-787 insolico UniProt ID   _
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189104.25 Da        Isoelectric Point: 6.0690

>WP_172688917.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEARSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLKGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLINRDIGSALTTIERVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAM
AAGDLLPGGEPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQDAGEVGEKEVTLPVL
TTANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGDAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENAQSGVVVRLVGEARPWN
PGAITGGRVWADGLPDSTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMERIKETPASPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

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

(573-625)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1152)


  Protein structure



No available structure.




T4CP

ID   14490 GenBank   WP_058654351
Name   traC_HTK15_RS00370_pJF-787 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: 98855.54 Da        Isoelectric Point: 5.7676

>WP_058654351.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNPLDTVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(470-765)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   14491 GenBank   WP_172688916
Name   traD_HTK15_RS00445_pJF-787 insolico UniProt ID   _
Length   722 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 722 a.a.        Molecular weight: 80850.29 Da        Isoelectric Point: 5.1609

>WP_172688916.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVIAPEASAENTGQPQQPQQLTP
APRAADAPSASASAAGAAGTGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDELSPQERQR
REEVNINVHRAPEKDLEPGGYI

  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)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 41134..66683

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTK15_RS00265 36200..36523 + 324 WP_172688910 theronine dehydrogenase -
HTK15_RS00270 36585..36959 + 375 WP_172688911 hypothetical protein -
HTK15_RS00275 37608..37982 + 375 WP_032637252 hypothetical protein -
HTK15_RS00280 38033..38317 + 285 WP_228719144 hypothetical protein -
HTK15_RS00285 38364..38708 + 345 WP_047359689 hypothetical protein -
HTK15_RS00290 38794..39057 + 264 WP_008324174 hypothetical protein -
HTK15_RS00295 39100..39930 + 831 WP_172688912 N-6 DNA methylase -
HTK15_RS00300 40557..41087 + 531 WP_172688913 antirestriction protein -
HTK15_RS00305 41134..41610 - 477 WP_058673456 transglycosylase SLT domain-containing protein virB1
HTK15_RS00310 42041..42436 + 396 WP_040218546 conjugal transfer relaxosome DNA-binding protein TraM -
HTK15_RS00315 42622..43320 + 699 WP_172688914 hypothetical protein -
HTK15_RS00320 43314..43802 + 489 WP_228719134 TraY domain-containing protein -
HTK15_RS00325 43867..44217 + 351 WP_058610053 type IV conjugative transfer system pilin TraA -
HTK15_RS00330 44368..44673 + 306 WP_045911931 type IV conjugative transfer system protein TraL traL
HTK15_RS00335 44688..45254 + 567 WP_172688915 type IV conjugative transfer system protein TraE traE
HTK15_RS00340 45241..45984 + 744 WP_151413346 type-F conjugative transfer system secretin TraK traK
HTK15_RS00345 45971..47365 + 1395 WP_058670648 F-type conjugal transfer pilus assembly protein TraB traB
HTK15_RS00350 47387..47926 + 540 WP_151413344 type IV conjugative transfer system lipoprotein TraV traV
HTK15_RS00355 48046..48270 + 225 WP_045379436 TraR/DksA C4-type zinc finger protein -
HTK15_RS00360 48440..48736 + 297 WP_151413343 hypothetical protein -
HTK15_RS00365 48726..49292 + 567 WP_045379430 conjugal transfer pilus-stabilizing protein TraP -
HTK15_RS00370 49285..51915 + 2631 WP_058654351 type IV secretion system protein TraC virb4
HTK15_RS00375 51912..52259 + 348 WP_163277223 type-F conjugative transfer system protein TrbI -
HTK15_RS00380 52259..52906 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
HTK15_RS00385 52909..53895 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
HTK15_RS00390 53912..54541 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTK15_RS00395 54538..56391 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTK15_RS00400 56423..56611 + 189 WP_008324128 conjugal transfer protein TrbE -
HTK15_RS00405 56642..57391 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
HTK15_RS00410 57408..57656 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
HTK15_RS00415 57646..58200 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTK15_RS00420 58193..58621 + 429 WP_008324122 hypothetical protein -
HTK15_RS00425 58608..59978 + 1371 WP_032672666 conjugal transfer pilus assembly protein TraH traH
HTK15_RS00430 59978..62839 + 2862 WP_126336474 conjugal transfer mating-pair stabilization protein TraG traG
HTK15_RS00440 63419..64144 + 726 WP_060446836 conjugal transfer complement resistance protein TraT -
HTK15_RS00445 64515..66683 + 2169 WP_172688916 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   19967 GenBank   NZ_KX868552
Plasmid name   pJF-787 Incompatibility group   IncFII
Plasmid size   77843 bp Coordinate of oriT [Strand]   41682..41738 [-]
Host baterium   Klebsiella variicola strain H152460787

Cargo genes

Drug resistance gene   blaIMI-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -