Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122118
Name   oriT_IncFII(Yp) in_silico
Organism   Enterobacter cloacae subsp. cloacae strain PEER 374
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAUISY010000031 (46760..46862 [-], 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)
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13944 GenBank   WP_023307204
Name   traI_QYE93_RS19900_IncFII(Yp) insolico UniProt ID   A0A1Q1PS85
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189264.44 Da        Isoelectric Point: 6.1121

>WP_023307204.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
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)

AAA domain (AAA_30)

(967-1150)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   16352 GenBank   WP_148868889
Name   traD_QYE93_RS19905_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: 81152.66 Da        Isoelectric Point: 5.1609

>WP_148868889.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
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.



ID   16353 GenBank   WP_008324134
Name   traC_QYE93_RS19980_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 22312..47410

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QYE93_RS19905 (QYE93_19910) 22312..24486 - 2175 WP_148868889 type IV conjugative transfer system coupling protein TraD virb4
QYE93_RS19910 (QYE93_19915) 24620..25294 - 675 WP_310840103 tetratricopeptide repeat protein -
QYE93_RS19915 (QYE93_19920) 25369..25800 - 432 WP_008324118 entry exclusion protein -
QYE93_RS19920 (QYE93_19925) 25822..28644 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
QYE93_RS19925 (QYE93_19930) 28644..30014 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
QYE93_RS19930 (QYE93_19935) 30001..30429 - 429 WP_008324122 hypothetical protein -
QYE93_RS19935 (QYE93_19940) 30422..30976 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QYE93_RS19940 (QYE93_19945) 30966..31214 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
QYE93_RS19945 (QYE93_19950) 31231..31980 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
QYE93_RS19950 (QYE93_19955) 32011..32199 - 189 WP_008324128 conjugal transfer protein TrbE -
QYE93_RS19955 (QYE93_19960) 32231..34084 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QYE93_RS19960 (QYE93_19965) 34081..34710 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
QYE93_RS19965 (QYE93_19970) 34727..35713 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
QYE93_RS19970 (QYE93_19975) 35716..36363 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
QYE93_RS19975 (QYE93_19980) 36363..36710 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
QYE93_RS19980 (QYE93_19985) 36707..39337 - 2631 WP_008324134 type IV secretion system protein TraC virb4
QYE93_RS19985 (QYE93_19990) 39330..39896 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
QYE93_RS19990 (QYE93_19995) 39886..40287 - 402 WP_008324137 hypothetical protein -
QYE93_RS19995 (QYE93_20000) 40271..40456 - 186 WP_008324139 hypothetical protein -
QYE93_RS20000 (QYE93_20005) 40460..40684 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
QYE93_RS20005 (QYE93_20010) 40804..41343 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
QYE93_RS20010 (QYE93_20015) 41365..42759 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
QYE93_RS20015 (QYE93_20020) 42746..43489 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
QYE93_RS20020 (QYE93_20025) 43476..44042 - 567 WP_025759824 type IV conjugative transfer system protein TraE traE
QYE93_RS20025 (QYE93_20030) 44057..44362 - 306 WP_045911931 type IV conjugative transfer system protein TraL traL
QYE93_RS20030 (QYE93_20035) 44513..44863 - 351 WP_057069654 type IV conjugative transfer system pilin TraA -
QYE93_RS20035 (QYE93_20040) 44921..45145 - 225 WP_008324165 TraY domain-containing protein -
QYE93_RS20040 (QYE93_20045) 45232..45921 - 690 WP_008324166 hypothetical protein -
QYE93_RS20045 (QYE93_20050) 46110..46502 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
QYE93_RS20050 (QYE93_20055) 46934..47410 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
QYE93_RS20055 (QYE93_20060) 47457..47987 - 531 WP_008324170 antirestriction protein -
QYE93_RS20060 (QYE93_20065) 48614..49444 - 831 WP_008324171 N-6 DNA methylase -
QYE93_RS20065 (QYE93_20070) 49487..49750 - 264 WP_008324174 hypothetical protein -
QYE93_RS20070 (QYE93_20075) 49836..50180 - 345 WP_008324177 hypothetical protein -
QYE93_RS20075 (QYE93_20080) 50227..50514 - 288 WP_008324178 hypothetical protein -
QYE93_RS20080 (QYE93_20085) 50568..50942 - 375 WP_008324180 hypothetical protein -
QYE93_RS20085 (QYE93_20090) 51569..51928 - 360 WP_008324181 hypothetical protein -
QYE93_RS20090 (QYE93_20095) 51990..52313 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   22545 GenBank   NZ_JAUISY010000031
Plasmid name   IncFII(Yp) Incompatibility group   IncFII
Plasmid size   61807 bp Coordinate of oriT [Strand]   46760..46862 [-]
Host baterium   Enterobacter cloacae subsp. cloacae strain PEER 374

Cargo genes

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