Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111827
Name   oriT_pF321-NDM in_silico
Organism   Citrobacter portucalensis strain F321
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137480 (45844..45946 [+], 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_pF321-NDM
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7666 GenBank   WP_016479978
Name   traI_R4T15_RS25075_pF321-NDM 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   8758 GenBank   WP_008324134
Name   traC_R4T15_RS24990_pF321-NDM 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   8759 GenBank   WP_075621255
Name   traD_R4T15_RS25070_pF321-NDM insolico UniProt ID   _
Length   751 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 751 a.a.        Molecular weight: 84305.01 Da        Isoelectric Point: 5.1609

>WP_075621255.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGI
SESGEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 45296..70476

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R4T15_RS24880 (R4T15_24880) 40393..40716 + 324 WP_008324183 hypothetical protein -
R4T15_RS24885 (R4T15_24885) 40778..41137 + 360 WP_015493069 hypothetical protein -
R4T15_RS24890 (R4T15_24890) 41764..42138 + 375 WP_008324180 hypothetical protein -
R4T15_RS24895 (R4T15_24895) 42192..42479 + 288 WP_008324178 hypothetical protein -
R4T15_RS24900 (R4T15_24900) 42526..42870 + 345 WP_008324177 hypothetical protein -
R4T15_RS24905 (R4T15_24905) 42956..43219 + 264 WP_008324174 hypothetical protein -
R4T15_RS24910 (R4T15_24910) 43262..44092 + 831 WP_008324171 N-6 DNA methylase -
R4T15_RS24915 (R4T15_24915) 44719..45249 + 531 WP_008324170 antirestriction protein -
R4T15_RS24920 (R4T15_24920) 45296..45772 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
R4T15_RS24925 (R4T15_24925) 46204..46596 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
R4T15_RS24930 (R4T15_24930) 46785..47474 + 690 WP_008324166 hypothetical protein -
R4T15_RS24935 (R4T15_24935) 47561..47785 + 225 WP_008324165 TraY domain-containing protein -
R4T15_RS24940 (R4T15_24940) 47843..48193 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
R4T15_RS24945 (R4T15_24945) 48344..48649 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
R4T15_RS24950 (R4T15_24950) 48664..49230 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
R4T15_RS24955 (R4T15_24955) 49217..49960 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
R4T15_RS24960 (R4T15_24960) 49947..51341 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
R4T15_RS24965 (R4T15_24965) 51363..51902 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
R4T15_RS24970 (R4T15_24970) 52022..52246 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
R4T15_RS24975 (R4T15_24975) 52250..52435 + 186 WP_008324139 hypothetical protein -
R4T15_RS24980 (R4T15_24980) 52419..52820 + 402 WP_016479985 hypothetical protein -
R4T15_RS24985 (R4T15_24985) 52810..53376 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
R4T15_RS24990 (R4T15_24990) 53369..55999 + 2631 WP_008324134 type IV secretion system protein TraC virb4
R4T15_RS24995 (R4T15_24995) 55996..56343 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
R4T15_RS25000 (R4T15_25000) 56343..56990 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
R4T15_RS25005 (R4T15_25005) 56993..57979 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
R4T15_RS25010 (R4T15_25010) 57996..58625 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
R4T15_RS25015 (R4T15_25015) 58622..60475 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
R4T15_RS25020 (R4T15_25020) 60507..60695 + 189 WP_008324128 conjugal transfer protein TrbE -
R4T15_RS25025 (R4T15_25025) 60726..61475 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
R4T15_RS25030 (R4T15_25030) 61492..61740 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
R4T15_RS25035 (R4T15_25035) 61730..62284 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
R4T15_RS25040 (R4T15_25040) 62277..62705 + 429 WP_008324122 hypothetical protein -
R4T15_RS25045 (R4T15_25045) 62692..64062 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
R4T15_RS25050 (R4T15_25050) 64062..66884 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
R4T15_RS25055 (R4T15_25055) 66906..67337 + 432 WP_008324118 entry exclusion protein -
R4T15_RS25060 (R4T15_25060) 67412..67750 + 339 WP_032072912 tetratricopeptide repeat protein -
R4T15_RS25065 (R4T15_25065) 67758..68087 + 330 WP_223856629 hypothetical protein -
R4T15_RS25070 (R4T15_25070) 68221..70476 + 2256 WP_075621255 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   12262 GenBank   NZ_CP137480
Plasmid name   pF321-NDM Incompatibility group   IncFIB
Plasmid size   110795 bp Coordinate of oriT [Strand]   45844..45946 [+]
Host baterium   Citrobacter portucalensis strain F321

Cargo genes

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