Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120818
Name   oriT_p2_SCLZS62 in_silico
Organism   Raoultella planticola strain SCLZS62
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP082170 (45767..45869 [+], 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_p2_SCLZS62
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13128 GenBank   WP_016479978
Name   traI_K6028_RS26260_p2_SCLZS62 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   15408 GenBank   WP_008324134
Name   traC_K6028_RS26180_p2_SCLZS62 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   15409 GenBank   WP_016479979
Name   traD_K6028_RS26255_p2_SCLZS62 insolico UniProt ID   _
Length   748 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 748 a.a.        Molecular weight: 83951.64 Da        Isoelectric Point: 5.1609

>WP_016479979.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISES
GEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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: 45219..70390

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
K6028_RS26070 (K6028_26070) 40316..40639 + 324 WP_008324183 hypothetical protein -
K6028_RS26075 (K6028_26075) 40701..41060 + 360 WP_015493069 hypothetical protein -
K6028_RS26080 (K6028_26080) 41687..42061 + 375 WP_008324180 hypothetical protein -
K6028_RS26085 (K6028_26085) 42115..42402 + 288 WP_008324178 hypothetical protein -
K6028_RS26090 (K6028_26090) 42449..42793 + 345 WP_008324177 hypothetical protein -
K6028_RS26095 (K6028_26095) 42879..43142 + 264 WP_008324174 hypothetical protein -
K6028_RS26100 (K6028_26100) 43185..44015 + 831 WP_008324171 N-6 DNA methylase -
K6028_RS26105 (K6028_26105) 44642..45172 + 531 WP_008324170 antirestriction protein -
K6028_RS26110 (K6028_26110) 45219..45695 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
K6028_RS26115 (K6028_26115) 46127..46519 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
K6028_RS26120 (K6028_26120) 46708..47397 + 690 WP_008324166 hypothetical protein -
K6028_RS26125 (K6028_26125) 47484..47708 + 225 WP_008324165 TraY domain-containing protein -
K6028_RS26130 (K6028_26130) 47766..48116 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
K6028_RS26135 (K6028_26135) 48267..48572 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
K6028_RS26140 (K6028_26140) 48587..49153 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
K6028_RS26145 (K6028_26145) 49140..49883 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
K6028_RS26150 (K6028_26150) 49870..51264 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
K6028_RS26155 (K6028_26155) 51286..51825 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
K6028_RS26160 (K6028_26160) 51945..52169 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
K6028_RS26165 (K6028_26165) 52173..52358 + 186 WP_008324139 hypothetical protein -
K6028_RS26170 (K6028_26170) 52342..52743 + 402 WP_016479985 hypothetical protein -
K6028_RS26175 (K6028_26175) 52733..53299 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
K6028_RS26180 (K6028_26180) 53292..55922 + 2631 WP_008324134 type IV secretion system protein TraC virb4
K6028_RS26185 (K6028_26185) 55919..56266 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
K6028_RS26190 (K6028_26190) 56266..56913 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
K6028_RS26195 (K6028_26195) 56916..57902 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
K6028_RS26200 (K6028_26200) 57919..58548 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
K6028_RS26205 (K6028_26205) 58545..60398 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
K6028_RS26210 (K6028_26210) 60430..60618 + 189 WP_008324128 conjugal transfer protein TrbE -
K6028_RS26215 (K6028_26215) 60649..61398 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
K6028_RS26220 (K6028_26220) 61415..61663 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
K6028_RS26225 (K6028_26225) 61653..62207 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
K6028_RS26230 (K6028_26230) 62200..62628 + 429 WP_008324122 hypothetical protein -
K6028_RS26235 (K6028_26235) 62615..63985 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
K6028_RS26240 (K6028_26240) 63985..66807 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
K6028_RS26245 (K6028_26245) 66829..67260 + 432 WP_008324118 entry exclusion protein -
K6028_RS33110 67335..67673 + 339 WP_032072912 tetratricopeptide repeat protein -
K6028_RS33115 67681..68010 + 330 WP_223856629 tetratricopeptide repeat protein -
K6028_RS26255 (K6028_26255) 68144..70390 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21247 GenBank   NZ_CP082170
Plasmid name   p2_SCLZS62 Incompatibility group   IncFIB
Plasmid size   110781 bp Coordinate of oriT [Strand]   45767..45869 [+]
Host baterium   Raoultella planticola strain SCLZS62

Cargo genes

Drug resistance gene   sul1, rmtC, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -