Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102954
Name   oriT_pEC4-NDM-6 in_silico
Organism   Escherichia coli strain ARL10/167 isolate EC4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KC887916 (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_pEC4-NDM-6
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2214 GenBank   WP_016479978
Name   traI_HTB16_RS00400_pEC4-NDM-6 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   1898 GenBank   WP_008324134
Name   traC_HTB16_RS00320_pEC4-NDM-6 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   1899 GenBank   WP_016479979
Name   traD_HTB16_RS00395_pEC4-NDM-6 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: 45296..70467

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTB16_RS00210 40393..40716 + 324 WP_008324183 hypothetical protein -
HTB16_RS00215 40778..41137 + 360 WP_015493069 hypothetical protein -
HTB16_RS00220 41764..42138 + 375 WP_008324180 hypothetical protein -
HTB16_RS00225 42192..42479 + 288 WP_008324178 hypothetical protein -
HTB16_RS00230 42526..42870 + 345 WP_008324177 hypothetical protein -
HTB16_RS00235 42956..43219 + 264 WP_008324174 hypothetical protein -
HTB16_RS00240 43262..44092 + 831 WP_008324171 N-6 DNA methylase -
HTB16_RS00245 44719..45249 + 531 WP_008324170 antirestriction protein -
HTB16_RS00250 45296..45772 - 477 WP_008324168 transglycosylase SLT domain-containing protein -
HTB16_RS00255 46204..46596 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
HTB16_RS00260 46785..47474 + 690 WP_008324166 hypothetical protein -
HTB16_RS00265 47561..47785 + 225 WP_008324165 TraY domain-containing protein -
HTB16_RS00270 47843..48193 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
HTB16_RS00275 48344..48649 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
HTB16_RS00280 48664..49230 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
HTB16_RS00285 49217..49960 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
HTB16_RS00290 49947..51341 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
HTB16_RS00295 51363..51902 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
HTB16_RS00300 52022..52246 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
HTB16_RS00305 52250..52435 + 186 WP_008324139 hypothetical protein -
HTB16_RS00310 52419..52820 + 402 WP_016479985 hypothetical protein -
HTB16_RS00315 52810..53376 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
HTB16_RS00320 53369..55999 + 2631 WP_008324134 type IV secretion system protein TraC virb4
HTB16_RS00325 55996..56343 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
HTB16_RS00330 56343..56990 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
HTB16_RS00335 56993..57979 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
HTB16_RS00340 57996..58625 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTB16_RS00345 58622..60475 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTB16_RS00350 60507..60695 + 189 WP_008324128 conjugal transfer protein TrbE -
HTB16_RS00355 60726..61475 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
HTB16_RS00360 61492..61740 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
HTB16_RS00365 61730..62284 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTB16_RS00370 62277..62705 + 429 WP_008324122 hypothetical protein -
HTB16_RS00375 62692..64062 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
HTB16_RS00380 64062..66884 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
HTB16_RS00385 66930..67337 + 408 WP_233406080 entry exclusion protein -
HTB16_RS00625 67430..67750 + 321 WP_227543090 tetratricopeptide repeat protein -
HTB16_RS00630 67758..68087 + 330 WP_223856629 hypothetical protein -
HTB16_RS00395 68221..70467 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3397 GenBank   NZ_KC887916
Plasmid name   pEC4-NDM-6 Incompatibility group   IncFIB
Plasmid size   110786 bp Coordinate of oriT [Strand]   45844..45946 [+]
Host baterium   Escherichia coli strain ARL10/167 isolate EC4

Cargo genes

Drug resistance gene   sul1, rmtC, blaNDM-6
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -