Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114435
Name   oriT_AR_0157|unnamed3 in_silico
Organism   Citrobacter sp. CRE-46 strain AR_0157
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP029731 (29746..29848 [+], 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_AR_0157|unnamed3
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9255 GenBank   WP_016479978
Name   traI_AN232_RS29105_AR_0157|unnamed3 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   10724 GenBank   WP_008324134
Name   traC_AN232_RS29025_AR_0157|unnamed3 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   10725 GenBank   WP_016479979
Name   traD_AN232_RS29100_AR_0157|unnamed3 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: 29198..54369

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AN232_RS28915 (AN232_28915) 24295..24618 + 324 WP_008324183 hypothetical protein -
AN232_RS28920 (AN232_28920) 24680..25039 + 360 WP_015493069 hypothetical protein -
AN232_RS28925 (AN232_28925) 25666..26040 + 375 WP_008324180 hypothetical protein -
AN232_RS28930 (AN232_28930) 26094..26381 + 288 WP_008324178 hypothetical protein -
AN232_RS28935 (AN232_28935) 26428..26772 + 345 WP_008324177 hypothetical protein -
AN232_RS28940 (AN232_28940) 26858..27121 + 264 WP_008324174 hypothetical protein -
AN232_RS28945 (AN232_28945) 27164..27994 + 831 WP_008324171 N-6 DNA methylase -
AN232_RS28950 (AN232_28950) 28621..29151 + 531 WP_008324170 antirestriction protein -
AN232_RS28955 (AN232_28955) 29198..29674 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
AN232_RS28960 (AN232_28960) 30106..30498 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
AN232_RS28965 (AN232_28965) 30687..31376 + 690 WP_008324166 hypothetical protein -
AN232_RS28970 (AN232_28970) 31463..31687 + 225 WP_008324165 TraY domain-containing protein -
AN232_RS28975 (AN232_28975) 31745..32095 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
AN232_RS28980 (AN232_28980) 32246..32551 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
AN232_RS28985 (AN232_28985) 32566..33132 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
AN232_RS28990 (AN232_28990) 33119..33862 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
AN232_RS28995 (AN232_28995) 33849..35243 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
AN232_RS29000 (AN232_29000) 35265..35804 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
AN232_RS29005 (AN232_29005) 35924..36148 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
AN232_RS29010 (AN232_29010) 36152..36337 + 186 WP_008324139 hypothetical protein -
AN232_RS29015 (AN232_29015) 36321..36722 + 402 WP_016479985 hypothetical protein -
AN232_RS29020 (AN232_29020) 36712..37278 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
AN232_RS29025 (AN232_29025) 37271..39901 + 2631 WP_008324134 type IV secretion system protein TraC virb4
AN232_RS29030 (AN232_29030) 39898..40245 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
AN232_RS29035 (AN232_29035) 40245..40892 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
AN232_RS29040 (AN232_29040) 40895..41881 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
AN232_RS29045 (AN232_29045) 41898..42527 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
AN232_RS29050 (AN232_29050) 42524..44377 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AN232_RS29055 (AN232_29055) 44409..44597 + 189 WP_008324128 conjugal transfer protein TrbE -
AN232_RS29060 (AN232_29060) 44628..45377 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
AN232_RS29065 (AN232_29065) 45394..45642 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
AN232_RS29070 (AN232_29070) 45632..46186 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AN232_RS29075 (AN232_29075) 46179..46607 + 429 WP_008324122 hypothetical protein -
AN232_RS29080 (AN232_29080) 46594..47964 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
AN232_RS29085 (AN232_29085) 47964..50786 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
AN232_RS29090 (AN232_29090) 50808..51239 + 432 WP_008324118 entry exclusion protein -
AN232_RS32225 51314..51652 + 339 WP_032072912 tetratricopeptide repeat protein -
AN232_RS32230 51660..51989 + 330 WP_223856629 tetratricopeptide repeat protein -
AN232_RS29100 (AN232_29100) 52123..54369 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   14870 GenBank   NZ_CP029731
Plasmid name   AR_0157|unnamed3 Incompatibility group   IncFII
Plasmid size   108148 bp Coordinate of oriT [Strand]   29746..29848 [+]
Host baterium   Citrobacter sp. CRE-46 strain AR_0157

Cargo genes

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