Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102875
Name   oriT_B3R3|unnamed1 in_silico
Organism   Serratia marcescens strain B3R3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013047 (78701..78750 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      19..25, 29..35  (GCAAAAT..ATTTTGC)
Location of nic site      44..45
Conserved sequence flanking the
  nic site    		  GGTGTGATGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_B3R3|unnamed1
ATTTAAATAGAAAAATCTGCAAAATACAATTTTGCGTGGGGTGTGATGCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2154 GenBank   WP_060560562
Name   traI_AR325_RS26730_B3R3|unnamed1 insolico UniProt ID   _
Length   1768 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1768 a.a.        Molecular weight: 189688.06 Da        Isoelectric Point: 6.4414

>WP_060560562.1 conjugative transfer relaxase/helicase TraI [Serratia marcescens]
MMSIGQVGPAGKAGDYYTHQDNYYVLGSMDERWVGQGAEALGLSGKVDVKDFVAVLEGKLPDGSDLTRMV
GGENKHRPGYDLTFSAPKGISVLAMLGGDKRLIAVHNHAVEVAVREVEKLASTRVMEGGVSETKLTGNLV
VALFNHDTSRDLDPQLHTHAVVANVTQHDGKWQTLSSDTVGKTGFIESVYANQVTFGQIYRHVFRQDVEA
MGYKTKTVGPHGMWEPDNMDSVIDVFSKRSHAIDAAAGPDASLKSRDMATLDTRKAKVASDPAALAVVLM
QEMKATGFDIQAYMAEAQSRTMVTPSPTLLEAGGDVLVDQAVGKAISALSDRQVNFTHNQVANKAISYLS
GEPGMLDAVRDGIDRAIEREQLIPLDKEKGVFTSDIHLLDELSVAQLSRTHLDESAVVIGAPKSDPRTGS
IPTYSDAVQQLAQHAPTMAVLSGIGGASVNRSRVAEVVELAREQGRDATVLTVDRQSQQYLQQSIHLDEG
RVVTRAALGTEALFAPNSTLVVDQAEKLTLKETVALLDGAVRNNVQLVLMDTEKRKGTGNALAVMKEAGV
PRYQFSGRQAVPAEMVSEPDKAQRFGQLAKGVVQALLEDRPAVAQVNGPADQRMLTAMIRNELKDAGLLG
REETHVATLTPVWLDSKNRGAIDTYREGMVMERWDAESQQRERFVIDRVGAQTRNLVLRNAEGEKHTLAV
KAVDKDWSLFRAGTMGVADGERLRVLGQEGRGKDALKAGTALTVVRAGAGELQVRVAGEPDATQKPADRA
LAVGSDVFSAVKVAPVYVESLGASVSSTAAVYAAVKKNELNSATLSGIARSGGHITLYSALDARKTQEKV
AQHPAYRLAGEQVKQLAGEEGLDAAIAGQKSGLFTPAQQAIHLAIPTLEGDSVAFGQARLLAGSLGFAAK
GVSMKAIQTEIEAQVKRGELLKVDVAPGVGADLLVSRASFEAEKSIIRLIADGKDSLPPLVTTSSKTHNE
DGPGQREGKVAPYLTQGQRQAVDLILNTTDRFVAIQGYAGVGKTTQVKAVLDGIAQLPESERPRVVGLAP
THRAVGEMQAAGVDAQTLASFLHDEGLKVAGGEKPDYRNTLFVVDESSMVGNSDMARAYALIAEGNGRAV
MSGDEAQLEAIAPGAPFRLAQGRSAIDMAVMKEIVRQTPELKPAVYKMIDNDVPGALDVVRAVVPANVPR
QADAWVPVQSVVEYPAKGSDDIHAAIVSDYLGRTEAARRDTLIITHLNADRHIINAGIHQERKAAGELKG
ASVNLPILETANIRDGELRKLDTWARHRDAVVLLDNTYYRMAGIDSQSRTVSLHDSEGNTRQFSPASAVR
EGVTLYNPRTIEVNVGDRMRFSKSDVERGHVANSTWTVEAIKGDVVTLSDGQQTRTVNPREQQQDRHVDL
AYAITAHGAQGASERFAITLEGVEGGREQLVNRASAYVALSRAKEHVQVYTDNETGWLNAIGKAKARTTA
HDAVLGMAPGSQKAAADLYGKAEPLAGNALGRAVLRGSQLTGDTLAHYVSPGKKYPQPHAMLPMYDANGK
PAGAWLAPLADTQGKSVGGLPTQGRVLGSDSAQFVALQGSRNNETRLAGTMQDGIRLAARYPDSGVVVRL
QGDDVPFNPQAMTGGRVWVNDETLKATARESCASDSVIKLPESPEERLQRELQTQADKLGREPNAPDPQR
LAGLNDEQLRALLVRGELRAEDVKARLPEAVMREVMGQGAALRVDAAVRQVARAPVSTRSRLQQDEQNLV
RDTHAERELNKEKTLGGD

  Protein domains


Predicted by InterproScan.

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(638-716)

AAA domain (AAA_30)

(994-1180)

TrwC relaxase (TrwC)

(10-280)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(580-632)

DNA helicase TraI (TraI_C)

(1438-1557)


  Protein structure



No available structure.




T4CP

ID   1822 GenBank   WP_060560512
Name   traC_AR325_RS26640_B3R3|unnamed1 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: 98848.74 Da        Isoelectric Point: 5.7463

>WP_060560512.1 type IV secretion system protein TraC [Serratia marcescens]
MNLLDKVTHTANSLLSALKMPDEAAAANKVLGDMNFPQLSSVLPYRDYDEESGLFINAGSIGFVLEALPL
AGANEQVVLTLESLLRTKLPRGIALSVHLMASKRVGDLVESGLRDFSWSGKDADKFNAITRAFYLMAAEG
RFSLPPGVDMPLTLRNYRVFISYCVKSKRRNKALITELENLVKVLRASLMGAKIPTESLNDEDFINVVGE
IINHDPSQLYNKRRKLDPLKDLNFQCIDNGFGMDVYPDCVKINLRDAGSKKGSVARVMNFQLEQNPEMAF
LWNTADNYGNLLYPELSIATPFIITLTLVVEEQTKTSFEANRKYIDLEKKSRTSYAKFFPGTLEEMKEWG
DLRQSLASNQTAIVSFFYNVTVFCEDNDSVALRCEQDVINSYRKNGFDLISPRFKQHWNFLACLPFMAEH
GVFQDLAMHGAVHRAKTLNVVNLMPIVADNRLAPSGLLAPTYRNQLAFIDIYSEVMRNTNYNMAVAGTSG
AGKTGLIQPMLRSVLDTGGAAWVFDMGDGYKSLCENMGGVYIDAQTLKFNPFANVKDINLSATQIANLIS
VMASPDGNLDEVHESLLEMAVKAAWLSKQKNARIDDVRDFLRDSMDEEVYRDSPTIRNRLHEMTILLDKY
CSDGTYGEFFNSDEPSLRDDVNMVVLEMGGLKNRPDLLVAVMFSLMIYIEGRMYQTSRQSKKLCVIDEGW
KLLNFKNAKAGEFIEEGYRTARRHRGAYITITQNIKDFDSDTASSAAKAAWGNSSYKIILMQDASEFKTY
LQKNPDNFTQLQQDMIGKFESAKDQWFSSFMLMVSGKVSWHRLFVDPLSRAMYSSQGQDFEFMQARREQG
VSVHDAVYELAHRNFGEEMARIERWVEENYTGRAAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(468-770)

Family of unknown function (DUF5934) (DUF5934)

(289-447)

TraC protein (TraC_F_IV)

(37-277)

  Protein structure



No available structure.



ID   1823 GenBank   WP_060560502
Name   traD_AR325_RS26715_B3R3|unnamed1 insolico UniProt ID   _
Length   732 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 732 a.a.        Molecular weight: 81690.24 Da        Isoelectric Point: 4.9642

>WP_060560502.1 type IV conjugative transfer system coupling protein TraD [Serratia marcescens]
MSFNAKDMTQGGQIAFMRLRMFTQIGNLIFYCLFIAFFLVAICTLLWRVSIQNLTNGLIYWWVWMVEGWP
SISPSETLYHLDYYGKTLTYTSKQVLLDSYVSYCGQLIWREGIFACIVAAGACVTGFVVTVWILGRQGKQ
QSEDEITGGRTLTDNPAVVANMLKRDCMASDIIIDGLPLLKNSEVKNFCAMGSVGTGKSRLYRKLMDYAR
KRGDMVIVYDKSCDFVKDYYDPQHDKILNPQDARCVAWDLWSECLTLPDFENVADILIPMGSNEDPFWQG
SARTIFVEAAYRMRNDEDRSYAKLLNTLLSIDLPRLRAYLEGTPAANLVDGKIEKTAISIRSVLTNYAKA
LRYMQGVEKLGAPFTIRDWMRGVKDNGKNGWLFLTSDSASHKALKPLISMWLSIASHSLLSMGENPDRRV
WIFADELPTLHKLPDLVSIVPEARKFGGCFVLGFQTYSQLEDIYGVKAAATLFGVLRTRFLFSVPDRVGA
EFAAGEVGEKEYRKASEQYSYGADPVRDGVSVGKDLERMQLVSYSDIQTLPDLCCYVTLPGPYPAVRLQM
VYKKVRQVAHPYEPRKMDAAADGRLVSAIEMREAETGNMDALFAATPILPAASARETADAPVSAVSTVPT
ENPDSDVPVVSAAATATGGQEAELKQKPAPGDDDAEREELPPGISGDGEVVDIAQYEAWQTQQQVMGQQA
MQRREETNINIDRHRRELAEVHHGDSEPGDEF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-124)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 78147..101568

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AR325_RS26550 (AR325_25915) 74594..75013 + 420 WP_060560525 conjugation system SOS inhibitor PsiB -
AR325_RS26555 (AR325_25910) 75010..75612 + 603 WP_194286132 plasmid SOS inhibition protein A -
AR325_RS26560 (AR325_25905) 76206..76577 + 372 WP_060560523 hypothetical protein -
AR325_RS26565 (AR325_25900) 76636..77463 + 828 WP_060560522 DUF932 domain-containing protein -
AR325_RS26570 (AR325_25895) 78147..78617 - 471 WP_060560521 transglycosylase SLT domain-containing protein virB1
AR325_RS26575 (AR325_25890) 79036..79437 + 402 WP_060560520 conjugal transfer relaxosome DNA-binding protein TraM -
AR325_RS26580 (AR325_25885) 79516..80178 + 663 WP_060560519 VUT family protein -
AR325_RS26585 (AR325_27045) 80196..80927 + 732 WP_076606846 metallophosphoesterase -
AR325_RS27205 80920..81408 - 489 WP_153303177 hypothetical protein -
AR325_RS26590 (AR325_27050) 81412..82026 - 615 WP_194286133 helix-turn-helix domain-containing protein -
AR325_RS26595 (AR325_27055) 82269..82466 + 198 WP_076606844 TraY domain-containing protein -
AR325_RS26600 (AR325_25880) 82593..82958 + 366 WP_060560518 type IV conjugative transfer system pilin TraA -
AR325_RS26605 (AR325_25875) 82970..83275 + 306 WP_042785939 type IV conjugative transfer system protein TraL traL
AR325_RS26610 (AR325_25870) 83286..83849 + 564 WP_060560517 type IV conjugative transfer system protein TraE traE
AR325_RS26615 (AR325_25865) 83839..84567 + 729 WP_060560516 type-F conjugative transfer system secretin TraK traK
AR325_RS26620 (AR325_25860) 84567..85967 + 1401 WP_060560515 F-type conjugal transfer pilus assembly protein TraB traB
AR325_RS26625 (AR325_25855) 85972..86190 + 219 WP_060560514 hypothetical protein virb4
AR325_RS26630 (AR325_25850) 86187..86573 + 387 WP_060560513 hypothetical protein -
AR325_RS26635 (AR325_25845) 86598..87137 + 540 WP_060560566 type IV conjugative transfer system lipoprotein TraV traV
AR325_RS26640 (AR325_25840) 87151..89781 + 2631 WP_060560512 type IV secretion system protein TraC virb4
AR325_RS26645 (AR325_25835) 89778..90197 + 420 WP_079007680 type-F conjugative transfer system protein TrbI -
AR325_RS26650 (AR325_25830) 90194..91126 + 933 WP_079007681 DsbA family protein -
AR325_RS26655 (AR325_25825) 91126..91761 + 636 WP_153303178 type-F conjugative transfer system protein TraW traW
AR325_RS26660 (AR325_25820) 91773..92150 + 378 WP_060560509 hypothetical protein -
AR325_RS26665 (AR325_25815) 92147..93145 + 999 WP_060560508 conjugal transfer pilus assembly protein TraU traU
AR325_RS26670 (AR325_25810) 93156..93830 + 675 WP_079007682 type-F conjugative transfer system pilin assembly protein TrbC trbC
AR325_RS26675 (AR325_25805) 93887..95731 + 1845 WP_076606855 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AR325_RS26680 (AR325_25800) 95797..96522 + 726 WP_228392606 type-F conjugative transfer system pilin assembly protein TraF traF
AR325_RS26685 (AR325_25795) 96534..96848 + 315 WP_076606843 hypothetical protein -
AR325_RS26690 (AR325_25790) 96835..97371 + 537 WP_060560506 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AR325_RS26695 (AR325_25785) 97368..98735 + 1368 WP_060560505 conjugal transfer pilus assembly protein TraH traH
AR325_RS26700 (AR325_25780) 98737..101568 + 2832 WP_060560504 conjugal transfer mating-pair stabilization protein TraG traG
AR325_RS26705 (AR325_25775) 101565..102098 + 534 WP_060560503 hypothetical protein -
AR325_RS26710 (AR325_25770) 102101..102310 + 210 WP_033641525 hypothetical protein -
AR325_RS26715 (AR325_25765) 102300..104498 + 2199 WP_060560502 type IV conjugative transfer system coupling protein TraD -
AR325_RS26720 (AR325_25760) 104534..104932 - 399 WP_060560501 tRNA(fMet)-specific endonuclease VapC -
AR325_RS26725 (AR325_25755) 104932..105159 - 228 WP_060560500 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   3318 GenBank   NZ_CP013047
Plasmid name   B3R3|unnamed1 Incompatibility group   -
Plasmid size   123171 bp Coordinate of oriT [Strand]   78701..78750 [-]
Host baterium   Serratia marcescens strain B3R3

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -