Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103120
Name   oriT_F5111 in_silico
Organism   Klebsiella pneumoniae strain 05K0261
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU987453 (10039..10095 [-], 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    		  GGTGTGGAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_F5111
TAAAGTTAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGAGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2339 GenBank   WP_100663238
Name   traI_HTH64_RS00225_F5111 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: 188949.98 Da        Isoelectric Point: 6.1101

>WP_100663238.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRSALKDDVAA
MGYETETVGRHGMWEFKGVPVAPFSSRSRTIGEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADQRVVQGNIPATAPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMTFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGAVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEARSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVQLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDGLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLHVIEKEADRQV
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSILRHVLEGKEAVTPLMDKVPDAQLAGLTDGQQNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLINRDIGSALTTIERVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLLPGGQPATLLETIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQDAGEVGEKEVTLPVL
TPANIRDGELRRMTTWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLGGEGRLMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLAGEARPWN
PGAITGGRVWADGLPDSTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMARIKETPASPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

TrwC relaxase (TrwC)

(10-283)

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

(573-625)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1152)


  Protein structure



No available structure.




T4CP

ID   2067 GenBank   WP_025759816
Name   traC_HTH64_RS00145_F5111 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: 98881.62 Da        Isoelectric Point: 5.7676

>WP_025759816.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacterales]
MSNPLDTVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIL

  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   2068 GenBank   WP_100663239
Name   traD_HTH64_RS00220_F5111 insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 81860.36 Da        Isoelectric Point: 5.0430

>WP_100663239.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRDRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGIDESGEVVDMAAWEAWQAEQDE
LSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9491..35134

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH64_RS00035 4523..4846 + 324 WP_057069613 hypothetical protein -
HTH64_RS00040 4908..5282 + 375 WP_032637367 hypothetical protein -
HTH64_RS00045 5929..6336 + 408 WP_100663247 ammonia monooxygenase -
HTH64_RS00050 6387..6674 + 288 WP_100663246 hypothetical protein -
HTH64_RS00055 6721..7065 + 345 WP_016582953 hypothetical protein -
HTH64_RS00060 7151..7414 + 264 WP_008324174 hypothetical protein -
HTH64_RS00065 7457..8287 + 831 WP_025760338 N-6 DNA methylase -
HTH64_RS00070 8914..9444 + 531 WP_100663245 antirestriction protein -
HTH64_RS00075 9491..9967 - 477 WP_008324168 transglycosylase SLT domain-containing protein -
HTH64_RS00080 10399..10794 + 396 WP_040218546 conjugal transfer relaxosome DNA-binding protein TraM -
HTH64_RS00085 10979..11683 + 705 WP_059514208 hypothetical protein -
HTH64_RS00090 11741..12166 + 426 WP_323829697 TraY domain-containing protein -
HTH64_RS00095 12232..12582 + 351 WP_071667438 type IV conjugative transfer system pilin TraA -
HTH64_RS00100 12732..13037 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
HTH64_RS00105 13052..13618 + 567 WP_025759824 type IV conjugative transfer system protein TraE traE
HTH64_RS00110 13605..14348 + 744 WP_100663244 type-F conjugative transfer system secretin TraK traK
HTH64_RS00115 14335..15729 + 1395 WP_058670648 F-type conjugal transfer pilus assembly protein TraB traB
HTH64_RS00120 15751..16290 + 540 WP_025759821 type IV conjugative transfer system lipoprotein TraV traV
HTH64_RS00125 16410..16634 + 225 WP_058670649 TraR/DksA C4-type zinc finger protein -
HTH64_RS00130 16638..16823 + 186 WP_016674194 hypothetical protein -
HTH64_RS00135 16807..17211 + 405 WP_058670650 hypothetical protein -
HTH64_RS00140 17201..17767 + 567 WP_058670651 conjugal transfer pilus-stabilizing protein TraP -
HTH64_RS00145 17760..20390 + 2631 WP_025759816 type IV secretion system protein TraC virb4
HTH64_RS00150 20387..20734 + 348 WP_011201813 type-F conjugative transfer system protein TrbI -
HTH64_RS00155 20734..21381 + 648 WP_025759814 type-F conjugative transfer system protein TraW traW
HTH64_RS00160 21384..22370 + 987 WP_032637387 conjugal transfer pilus assembly protein TraU traU
HTH64_RS00165 22386..23015 + 630 WP_100663243 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTH64_RS00170 23012..24865 + 1854 WP_100663242 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTH64_RS00175 24897..25085 + 189 WP_100663241 hypothetical protein -
HTH64_RS00180 25122..25865 + 744 WP_071667457 type-F conjugative transfer system pilin assembly protein TraF traF
HTH64_RS00185 25882..26130 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
HTH64_RS00190 26120..26674 + 555 WP_025759806 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTH64_RS00195 26667..27095 + 429 WP_129468605 conjugal transfer protein TrbF -
HTH64_RS00200 27082..28452 + 1371 WP_059514056 conjugal transfer pilus assembly protein TraH traH
HTH64_RS00205 28452..31316 + 2865 WP_059514053 conjugal transfer mating-pair stabilization protein TraG traG
HTH64_RS00210 31333..31764 + 432 WP_059514050 hypothetical protein -
HTH64_RS00215 31839..32570 + 732 WP_059514045 conjugal transfer complement resistance protein TraT -
HTH64_RS00220 32942..35134 + 2193 WP_100663239 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3563 GenBank   NZ_KU987453
Plasmid name   F5111 Incompatibility group   IncFII
Plasmid size   85862 bp Coordinate of oriT [Strand]   10039..10095 [-]
Host baterium   Klebsiella pneumoniae strain 05K0261

Cargo genes

Drug resistance gene   blaTEM-1B, armA, aph(6)-Id, aph(3'')-Ib
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -