Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113794
Name   oriT_pNDM_12TM in_silico
Organism   Serratia marcescens strain 12TM
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM008895 (25044..25146 [+], 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_12TM
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8832 GenBank   WP_101415845
Name   traI_CS367_RS25200_pNDM_12TM 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: 189299.44 Da        Isoelectric Point: 6.0099

>WP_101415845.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
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   10246 GenBank   WP_008324134
Name   traC_CS367_RS25120_pNDM_12TM 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   10247 GenBank   WP_016479979
Name   traD_CS367_RS25195_pNDM_12TM 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: 24496..49667

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CS367_RS25010 (CS367_24945) 19593..19916 + 324 WP_008324183 hypothetical protein -
CS367_RS25015 (CS367_24950) 19978..20337 + 360 WP_015493069 hypothetical protein -
CS367_RS25020 (CS367_24955) 20964..21338 + 375 WP_008324180 hypothetical protein -
CS367_RS25025 (CS367_24960) 21392..21679 + 288 WP_008324178 hypothetical protein -
CS367_RS25030 (CS367_24965) 21726..22070 + 345 WP_008324177 hypothetical protein -
CS367_RS25035 (CS367_24970) 22156..22419 + 264 WP_008324174 hypothetical protein -
CS367_RS25040 (CS367_24975) 22462..23292 + 831 WP_008324171 N-6 DNA methylase -
CS367_RS25045 (CS367_24980) 23919..24449 + 531 WP_008324170 antirestriction protein -
CS367_RS25050 (CS367_24985) 24496..24972 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
CS367_RS25055 (CS367_24990) 25404..25796 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
CS367_RS25060 (CS367_24995) 25985..26674 + 690 WP_008324166 hypothetical protein -
CS367_RS25065 (CS367_25000) 26761..26985 + 225 WP_008324165 TraY domain-containing protein -
CS367_RS25070 (CS367_25005) 27043..27393 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
CS367_RS25075 (CS367_25010) 27544..27849 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
CS367_RS25080 (CS367_25015) 27864..28430 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
CS367_RS25085 (CS367_25020) 28417..29160 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CS367_RS25090 (CS367_25025) 29147..30541 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
CS367_RS25095 (CS367_25030) 30563..31102 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
CS367_RS25100 (CS367_25035) 31222..31446 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CS367_RS25105 (CS367_25040) 31450..31635 + 186 WP_008324139 hypothetical protein -
CS367_RS25110 (CS367_25045) 31619..32020 + 402 WP_016479985 hypothetical protein -
CS367_RS25115 (CS367_25050) 32010..32576 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CS367_RS25120 (CS367_25055) 32569..35199 + 2631 WP_008324134 type IV secretion system protein TraC virb4
CS367_RS25125 (CS367_25060) 35196..35543 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
CS367_RS25130 (CS367_25065) 35543..36190 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CS367_RS25135 (CS367_25070) 36193..37179 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
CS367_RS25140 (CS367_25075) 37196..37825 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CS367_RS25145 (CS367_25080) 37822..39675 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CS367_RS25150 (CS367_25085) 39707..39895 + 189 WP_008324128 conjugal transfer protein TrbE -
CS367_RS25155 (CS367_25090) 39926..40675 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CS367_RS25160 (CS367_25095) 40692..40940 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
CS367_RS25165 (CS367_25100) 40930..41484 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CS367_RS25170 (CS367_25105) 41477..41905 + 429 WP_008324122 hypothetical protein -
CS367_RS25175 (CS367_25110) 41892..43262 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CS367_RS25180 (CS367_25115) 43262..46084 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CS367_RS25185 (CS367_25120) 46106..46537 + 432 WP_008324118 entry exclusion protein -
CS367_RS26780 46612..46950 + 339 WP_032072912 tetratricopeptide repeat protein -
CS367_RS26785 46958..47287 + 330 WP_223856629 tetratricopeptide repeat protein -
CS367_RS25195 (CS367_25130) 47421..49667 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14229 GenBank   NZ_CM008895
Plasmid name   pNDM_12TM Incompatibility group   IncFII
Plasmid size   119046 bp Coordinate of oriT [Strand]   25044..25146 [+]
Host baterium   Serratia marcescens strain 12TM

Cargo genes

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