Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106382
Name   oriT_pNDM_7209 in_silico
Organism   Serratia marcescens strain 7209
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM008885 (16192..16294 [+], 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_pNDM_7209
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4273 GenBank   WP_101452705
Name   traI_CS371_RS00225_pNDM_7209 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: 189283.40 Da        Isoelectric Point: 6.0099

>WP_101452705.1 conjugative transfer relaxase/helicase TraI [Serratia marcescens]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREAPKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGAGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
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)

AAA domain (AAA_30)

(967-1150)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   4292 GenBank   WP_008324134
Name   traC_CS371_RS00185_pNDM_7209 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   4293 GenBank   WP_144236160
Name   t4cp2_CS371_RS28440_pNDM_7209 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 88755.30 Da        Isoelectric Point: 4.8209

>WP_144236160.1 type IV secretion system DNA-binding domain-containing protein [Serratia marcescens]
MKRAILMSVLAIATTMASVNAFADADAQYRAGADFARQVQGQGESSLKNFNPSASIPNYTASPGEKKYYG
GVTATGDGALKADGTTGWTTNEATKAVTDSFVNNPKEPISPDAPFIKASQDVQSRADTIIGKTGQTQCEA
QNISRSEFTNYTCERDLLVEQACTRTASITGHYEDTSETKQIVIQSQNISFASSEAGYTGTWTAPVTGKV
VAATATYSWNKRLAFSNPNWFMRVTTPFGLISMDNDTGSLALSSGMQLKKGAGMVFSIRTRRNNPTTDSI
WKHSNMRYSFTVTLQIEIPAKKWVPDVVWNESCPFSKSEGTLKKTECIEPGSTKTVVVDGVSYPVTQACW
KYKDTYMTQAADNGTCKTYMNNPACTLASRTCAFTAEDGSGCLHEYATYSCETRTSGQVMICGGDTFCLD
GDCERAQNGKNNDFAPVVSALAALAAAGKDVAAINSVNVRAFISMWLSIAIRGLLAMGENRNRRVWIFAD
ELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIAEFAAG
EIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMALKYQQR
PKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQPQQPQ
QPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGE
VVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

Type-1V conjugative transfer system mating pair stabilisation (F_T4SS_TraN)

(322-455)

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

(459-625)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15644..30351

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CS371_RS00075 (CS371_13255) 10741..11064 + 324 WP_008324183 hypothetical protein -
CS371_RS00080 (CS371_13260) 11126..11485 + 360 WP_015493069 hypothetical protein -
CS371_RS00085 (CS371_13265) 12112..12486 + 375 WP_008324180 hypothetical protein -
CS371_RS00090 (CS371_13270) 12540..12827 + 288 WP_008324178 hypothetical protein -
CS371_RS00095 (CS371_13275) 12874..13218 + 345 WP_008324177 hypothetical protein -
CS371_RS00100 (CS371_13280) 13304..13567 + 264 WP_008324174 hypothetical protein -
CS371_RS00105 (CS371_13285) 13610..14440 + 831 WP_008324171 N-6 DNA methylase -
CS371_RS00110 (CS371_13290) 15067..15597 + 531 WP_008324170 antirestriction protein -
CS371_RS00115 (CS371_13295) 15644..16120 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
CS371_RS00120 (CS371_13300) 16552..16944 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
CS371_RS00125 (CS371_13305) 17133..17822 + 690 WP_008324166 hypothetical protein -
CS371_RS00130 (CS371_13310) 17909..18133 + 225 WP_008324165 TraY domain-containing protein -
CS371_RS00135 (CS371_13315) 18191..18541 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
CS371_RS00140 (CS371_13320) 18692..18997 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
CS371_RS00145 (CS371_13325) 19012..19578 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
CS371_RS00150 (CS371_13330) 19565..20308 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CS371_RS00155 (CS371_13335) 20405..20620 + 216 WP_101452704 hypothetical protein -
CS371_RS00160 (CS371_13340) 20642..21181 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
CS371_RS00165 (CS371_13345) 21301..21525 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CS371_RS00170 (CS371_13350) 21529..21714 + 186 WP_008324139 hypothetical protein -
CS371_RS00175 (CS371_13355) 21698..22099 + 402 WP_016479985 hypothetical protein -
CS371_RS00180 (CS371_13360) 22089..22655 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CS371_RS00185 (CS371_13365) 22648..25278 + 2631 WP_008324134 type IV secretion system protein TraC virb4
CS371_RS00190 (CS371_13370) 25275..25622 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
CS371_RS00195 (CS371_13375) 25622..26269 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CS371_RS00200 (CS371_13380) 26272..27258 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
CS371_RS00205 (CS371_13385) 27275..27904 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CS371_RS28440 (CS371_13390) 27901..30351 + 2451 WP_144236160 type IV secretion system DNA-binding domain-containing protein traN

Host bacterium

ID   6819 GenBank   NZ_CM008885
Plasmid name   pNDM_7209 Incompatibility group   IncFII
Plasmid size   87593 bp Coordinate of oriT [Strand]   16192..16294 [+]
Host baterium   Serratia marcescens strain 7209

Cargo genes

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