Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107513
Name   oriT_pNDM_12TM in_silico
Organism   Serratia marcescens strain 12TM
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MF042351 (93901..94003 [-], 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   5036 GenBank   WP_101415845
Name   traI_HTN84_RS00355_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   5248 GenBank   WP_016479979
Name   traD_HTN84_RS00360_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.



ID   5249 GenBank   WP_008324134
Name   traC_HTN84_RS00435_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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 69380..94551

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTN84_RS00360 69380..71626 - 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4
HTN84_RS00680 71760..72089 - 330 WP_223856629 hypothetical protein -
HTN84_RS00685 72097..72417 - 321 WP_227543090 tetratricopeptide repeat protein -
HTN84_RS00370 72510..72941 - 432 WP_008324118 entry exclusion protein -
HTN84_RS00375 72963..75785 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
HTN84_RS00380 75785..77155 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
HTN84_RS00385 77142..77570 - 429 WP_008324122 hypothetical protein -
HTN84_RS00390 77563..78117 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTN84_RS00395 78107..78355 - 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
HTN84_RS00400 78372..79121 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
HTN84_RS00405 79152..79340 - 189 WP_008324128 conjugal transfer protein TrbE -
HTN84_RS00410 79372..81225 - 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTN84_RS00415 81222..81851 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTN84_RS00420 81868..82854 - 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
HTN84_RS00425 82857..83504 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
HTN84_RS00430 83504..83851 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
HTN84_RS00435 83848..86478 - 2631 WP_008324134 type IV secretion system protein TraC virb4
HTN84_RS00440 86471..87037 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
HTN84_RS00445 87027..87428 - 402 WP_016479985 hypothetical protein -
HTN84_RS00450 87412..87597 - 186 WP_008324139 hypothetical protein -
HTN84_RS00455 87601..87825 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
HTN84_RS00460 87945..88484 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
HTN84_RS00465 88506..89900 - 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
HTN84_RS00470 89887..90630 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
HTN84_RS00475 90617..91183 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
HTN84_RS00480 91198..91503 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
HTN84_RS00485 91654..92004 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
HTN84_RS00490 92062..92286 - 225 WP_008324165 TraY domain-containing protein -
HTN84_RS00495 92373..93062 - 690 WP_008324166 hypothetical protein -
HTN84_RS00500 93251..93643 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
HTN84_RS00505 94075..94551 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
HTN84_RS00510 94598..95128 - 531 WP_008324170 antirestriction protein -
HTN84_RS00515 95755..96585 - 831 WP_008324171 N-6 DNA methylase -
HTN84_RS00520 96628..96891 - 264 WP_008324174 hypothetical protein -
HTN84_RS00525 96977..97321 - 345 WP_008324177 hypothetical protein -
HTN84_RS00530 97368..97655 - 288 WP_008324178 hypothetical protein -
HTN84_RS00535 97709..98083 - 375 WP_008324180 hypothetical protein -
HTN84_RS00540 98710..99069 - 360 WP_015493069 hypothetical protein -
HTN84_RS00545 99131..99454 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   7948 GenBank   NZ_MF042351
Plasmid name   pNDM_12TM Incompatibility group   IncFIB
Plasmid size   119046 bp Coordinate of oriT [Strand]   93901..94003 [-]
Host baterium   Serratia marcescens strain 12TM

Cargo genes

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