Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122133
Name   oriT_IncFII(Yp) in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain 4661:NRCR8
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAGYXN010000026 (15002..15104 [+], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
 28..33, 40..45  (GCAAAA..TTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_IncFII(Yp)
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13950 GenBank   WP_016479978
Name   traI_KHP34_RS23495_IncFII(Yp) insolico UniProt ID   A0A0G3B767
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189285.41 Da        Isoelectric Point: 6.0099

>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWAAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQPHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  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)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   16362 GenBank   WP_008324134
Name   traC_KHP34_RS23410_IncFII(Yp) 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: 98841.51 Da        Isoelectric Point: 5.7676

>WP_008324134.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacterales]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
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   16363 GenBank   WP_149385136
Name   traD_KHP34_RS23490_IncFII(Yp) insolico UniProt ID   _
Length   724 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 724 a.a.        Molecular weight: 81124.61 Da        Isoelectric Point: 5.1609

>WP_149385136.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDELSPQER
QRREEVNINVHRAPEKDLEPGGYI

  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: 14454..39553

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KHP34_RS23300 (KHP34_23295) 9551..9874 + 324 WP_008324183 hypothetical protein -
KHP34_RS23305 (KHP34_23300) 9936..10295 + 360 WP_015493069 hypothetical protein -
KHP34_RS23310 (KHP34_23305) 10922..11296 + 375 WP_008324180 hypothetical protein -
KHP34_RS23315 (KHP34_23310) 11350..11637 + 288 WP_008324178 hypothetical protein -
KHP34_RS23320 (KHP34_23315) 11684..12028 + 345 WP_008324177 hypothetical protein -
KHP34_RS23325 (KHP34_23320) 12114..12377 + 264 WP_008324174 hypothetical protein -
KHP34_RS23330 (KHP34_23325) 12420..13250 + 831 WP_008324171 N-6 DNA methylase -
KHP34_RS23335 (KHP34_23330) 13877..14407 + 531 WP_008324170 antirestriction protein -
KHP34_RS23340 (KHP34_23335) 14454..14930 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
KHP34_RS23345 (KHP34_23340) 15362..15754 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
KHP34_RS23350 (KHP34_23345) 15943..16632 + 690 WP_008324166 hypothetical protein -
KHP34_RS23355 (KHP34_23350) 16719..16943 + 225 WP_008324165 TraY domain-containing protein -
KHP34_RS23360 (KHP34_23355) 17001..17351 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
KHP34_RS23365 (KHP34_23360) 17502..17807 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
KHP34_RS23370 (KHP34_23365) 17822..18388 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
KHP34_RS23375 (KHP34_23370) 18375..19118 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
KHP34_RS23380 (KHP34_23375) 19105..20499 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
KHP34_RS23385 (KHP34_23380) 20521..21060 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
KHP34_RS23390 (KHP34_23385) 21180..21404 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
KHP34_RS23395 (KHP34_23390) 21408..21593 + 186 WP_008324139 hypothetical protein -
KHP34_RS23400 (KHP34_23395) 21577..21978 + 402 WP_016479985 hypothetical protein -
KHP34_RS23405 (KHP34_23400) 21968..22534 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
KHP34_RS23410 (KHP34_23405) 22527..25157 + 2631 WP_008324134 type IV secretion system protein TraC virb4
KHP34_RS23415 (KHP34_23410) 25154..25501 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
KHP34_RS23420 (KHP34_23415) 25501..26148 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
KHP34_RS23425 (KHP34_23420) 26151..27137 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
KHP34_RS23430 (KHP34_23425) 27154..27783 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
KHP34_RS23435 (KHP34_23430) 27780..29633 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KHP34_RS23440 (KHP34_23435) 29665..29853 + 189 WP_008324128 conjugal transfer protein TrbE -
KHP34_RS23445 (KHP34_23440) 29884..30633 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
KHP34_RS23450 (KHP34_23445) 30650..30898 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
KHP34_RS23455 (KHP34_23450) 30888..31442 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KHP34_RS23460 (KHP34_23455) 31435..31863 + 429 WP_008324122 hypothetical protein -
KHP34_RS23465 (KHP34_23460) 31850..33220 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
KHP34_RS23470 (KHP34_23465) 33220..36042 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
KHP34_RS23475 (KHP34_23470) 36064..36495 + 432 WP_008324118 entry exclusion protein -
KHP34_RS23480 (KHP34_23475) 36570..36908 + 339 WP_032072912 tetratricopeptide repeat protein -
KHP34_RS23485 (KHP34_23480) 36916..37245 + 330 WP_223856629 tetratricopeptide repeat protein -
KHP34_RS23490 (KHP34_23485) 37379..39553 + 2175 WP_149385136 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   22560 GenBank   NZ_JAGYXN010000026
Plasmid name   IncFII(Yp) Incompatibility group   IncFII
Plasmid size   54937 bp Coordinate of oriT [Strand]   15002..15104 [+]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain 4661:NRCR8

Cargo genes

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