Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113730
Name   oriT_FY|p2 in_silico
Organism   Serratia marcescens strain FY
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP053380 (59074..59123 [+], 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_FY|p2
ATTTAAATAGAAAAATCTGCAAAATACAATTTTGCGTGGGGTGTGATGCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8791 GenBank   WP_171455178
Name   traI_HMJ22_RS24605_FY|p2 insolico UniProt ID   _
Length   1759 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1759 a.a.        Molecular weight: 189025.78 Da        Isoelectric Point: 5.8669

>WP_171455178.1 conjugative transfer relaxase/helicase TraI [Serratia marcescens]
MMSVWPVGPAGKAGDYYTHQDNYYVLGSMDERWVGQGAEALGLTGKVDVKDFVAVLEGKLPDGSDLTRMV
GGENKHRPGYDLTFSAPKSVSIMAMLGGDKRLIAAHNHAVEVAVREIEKMASTRVMEGGVSETKLTGNLV
VALFNHDTSRDLDPQLHTHAVVANVTQHDGKWQTLSSDTVGKTGFIENVYANQIAGGQIYRHILQREVEA
MGYETETTGPHGMWEFKRTEAVREPFSKRSHAIDAAAGPDASLKSRDMATLDTRKAKVASDPAALAVEWL
QEMKSAGFDAKAYLAEAQSRTMVTPSPTPLEAGGDALVDQAVGQAISALSDRQVNFTHNQVANKAISYLS
GEPGILDAVRDGIDRAIEREQLIPLDKEKGVFTSDIHLLDELSVAQLSRTHFDESAVVIGAPKADPRTGS
MPAYSDAVQQLAQHAPAMAVLSGLGGASVNRSRVAEVVELAREQGRDATVLTVDRQSQQYLQQSVHLDEG
RVVTLAALGSEALFAPNSTLVVDQAEKLTLKETVALLDGAVRNNVQLVLMDTEKRKGTGNALAVMKEAGV
PRYQFSGRQAVPTEVVSEPDKAQRFGQLAKGVVQALVEDRSAVAQVNGSADQRMLTAMIRDELKDTGLLG
REETHVATLTPVWLDSKNRGAIDTYREGMVMERWDAESRQRERFVIDRVGSQTRNLVLRNAEGEKHTLAV
KAVDKDWSLFRAGTMGVADGERLQVLGQEGRGKDALKAGTALTVVRAGAGELQVRVAGEPDATQKPADRA
LAVGSDVFSAVKVAPAYVESLGASVSSTAAVYAAVKKNELNSATLSGIARSGGHITLYSALDAHKTQEKV
AQHPAYRLAGEQVKQLAGEEGLDAAISGQKSGLFTPAQQAIHLAIPTLEGDSVAFGQAKLLAGSLDFAAK
GVSMEAIQTEIEAQVKRGELLKVDVAPGVGADLLVSRASFEAEKSIIRLIADGKDSMPALMSGTARNQLA
SIQSSLTQGQKESVDLILGTTDRFVAIQGYSGVGKTTQFKAVLAGIEQLPESERPRVVGLAPTHRAVGEM
QAAGVDAQTLASFLHDEGLKVASGEKPDYRNTLFVVDESSMVGNSDMARAYALIAEGNGRAVMSGDEAQL
EAIAPGAPFRLAQGRSAIDMAVMKEIVRQTPELKPAVYKMIENDVPGALDVVRTVAPANVPRQANAWVPA
KSVMELAVDIPDIHDAIVSDYLGRTEAARQDTLIITHLNADRHIINAGIHGERKAAGELKGESVSLPVLE
TANIRDGELRKLDTWARHRDAVVLLDNTYYRMADIDSQSRTVSLQDSEGNTRQFSPASAVREGVTLYNPR
TIEVNVGDRMRFSKSDVERGHVANSVWTVEAIKGDMVTLSDGQQTRTVNPREQQQDRHVDLAYAITAHGA
QGASERFAITLEGVEGGREPLVNRASAYVALSRAKEHVQVYTDNEAGWLNAIGKAKARTTAHDAVLGMAP
GSQKAAVDLYGKASSLSENALGRAVLRGSQLTGDTLAHYVSPGKKYPQPHAMLPMYDANGKPAGAWLAPL
ADTQGKSVGGLPTQGRVFGSDSAQFVALQGSRNNETRLAGTMQDGIRLAARYPDSGVVVRLQGDDVPFNP
QAMTGGRVWVNDETLKATARESGASDNVIKLPESPEERLQRELQTQADKLGREPNAPDPQRLAGLNDEQL
RALLARGELRAEDVKDRLPEAVMREVMGQDVAQRVDAAVRQVAREPVSTRSRLQQDEHNLVRDTHAEREL
NKEKTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

AAA domain (AAA_30)

(986-1171)

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

(580-632)

DNA helicase TraI (TraI_C)

(1429-1548)

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

(638-716)


  Protein structure



No available structure.




T4CP

ID   10190 GenBank   WP_171455181
Name   traD_HMJ22_RS24620_FY|p2 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: 81631.31 Da        Isoelectric Point: 5.1369

>WP_171455181.1 type IV conjugative transfer system coupling protein TraD [Serratia marcescens]
MSFNAKDMTQGGQIAFMRLRMFTQIGNLIFYCLFIAFFLVAICTLLWRVSIQNLTNGLIYWWVWMVEGWP
SISPSETLYHLDYYGKTLTYTAKQVLLDRYVSYCGQLIWREGIFACIVAAVACVTGFVVTVWILGRQGKQ
QSEDEITGGRTLTDNPAVVANMLKRDGMASDIIIDGLPLLKNSEVKNFCAMGSVGTGKSRLYRKLMDYAR
KRGDMVIVYDKSCDFVKDYYDPQHDKILNPQDARCVAWDLWSECLTLPDFENVADILIPMGSNEDPFWQG
SARTIFVEAAYRMRNDEDRSYAKLLNTLLSIDLPRLRAYLEGTPAANLVDGKIEKTAISIRSVLTNYAKA
LRYMQGVEKLGAPFTIRDWMRGVKDNGKNGWLFLTSDSASHKALKPLISMWLSIASHSLLSMGENPDRRV
WIFADEVPTLHKLPDLVSIVPEARKFGGCFVLGFQTYSQLEDIYGVKAAATLFGVLRTRFLFSVPDRVGA
EFAAGEVGEKEYRKASEQFSYGADPVRDGVSVGKDLERMQLVSYSDIQTLPDLCCYVTLPGPYPAVRLQM
VYKKVRQVAHPYEPRKLDAAADGRLVSAIEMREAETGNMDALFAATPILPAASARETADAPVSAVSKVPT
ENPASDVPVVSAATTATGGQEAELKQKPAPGDDDAEREELPPGISGDGEVVDIAQYEAWQAQQQVMGQQA
MQRREEANITIDRHRRELAEVHHGDSEPGDEF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-127)

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

(173-560)

  Protein structure



No available structure.



ID   10191 GenBank   WP_079450624
Name   traC_HMJ22_RS24700_FY|p2 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: 98864.80 Da        Isoelectric Point: 5.7461

>WP_079450624.1 type IV secretion system protein TraC [Serratia marcescens]
MNLLDKVTHTANSLLSALKMPDEAAAANKVLGDMNFPQLSSVLPYRDYDEESGLFINAGSIGFVLEALPL
AGANEQVVLTLESLLRTKLPRGIALSVHLMASKRVGDLVESGLRDFSWSGKDADKFNAITRAFYLMAAEG
RFSLPPGVDMPLTLRNYRVFISYCVKSKRRNKALITELENLVKVLRASLMGAKIPTESLNDEDFINVVGE
IINHDPSQLYNKRRKLDPLKDLNFQCIDNGFGMDVYPDCVKINLRDAGSKKGSVARVMNFQLEQNPEMAF
LWNTADNYGNLLYPELSIATPFIITLTLVVEEQTKTSFEANRKYIDLEKKSRTSYAKFFPGTLEEMKEWG
DLRQSLASNQTAIVSFFYNVTVFCEDNDSVALRCEQDVINSYRKNGFDLISPRFKQHWNFLACLPFMAEH
GVFQDLAMHGAVHRAKTLNVVNLMPIVADNRLAPSGLLAPTYRNQLAFIDIYSEVMRNTNYNMAVCGTSG
AGKTGLIQPMLRSVLDTGGAAWVFDMGDGYKSLCENMGGVYIDAQTLKFNPFANVKDINLSATQIANLIS
VMASPDGNLDEVHESLLEMAVKAAWLSKQKNARIDDVRDFLRDAMDEEVYRDSPTIRNRLHEMTILLDKY
CSDGTYGEFFNSDEPSLRDDVNMVVLEMGGLKNRPDLLVAVMFSLMIYIEGRMYQTSRQSKKLCVIDEGW
KLLNFKNAKAGEFIEEGYRTARRHRGAYITITQNIKDFDSDTASSAAKAAWGNSSYKIILMQDASEFKTY
LQKNPDNFTQLQQDMIGKFESAKDQWFSSFMLMVSGKVSWHRLFVDPLSRAMYSSQGQDFEFMQARREQG
VSVHDAVYELAHRNFGEEMARIERWVEENYTGRAAA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(37-277)

Family of unknown function (DUF5934) (DUF5934)

(289-447)

TraG P-loop domain (P-loop_TraG)

(468-770)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36280..59677

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HMJ22_RS24610 32692..32919 + 228 WP_171455179 toxin-antitoxin system antitoxin VapB -
HMJ22_RS24615 32919..33317 + 399 WP_171455180 tRNA(fMet)-specific endonuclease VapC -
HMJ22_RS24620 33353..35551 - 2199 WP_171455181 type IV conjugative transfer system coupling protein TraD -
HMJ22_RS24625 35541..35750 - 210 WP_033641525 hypothetical protein -
HMJ22_RS24630 35753..36283 - 531 WP_171455182 hypothetical protein -
HMJ22_RS24635 36280..39111 - 2832 WP_171455183 conjugal transfer mating-pair stabilization protein TraG traG
HMJ22_RS24640 39113..40480 - 1368 WP_171455184 conjugal transfer pilus assembly protein TraH traH
HMJ22_RS24645 40477..40893 - 417 WP_171455185 hypothetical protein -
HMJ22_RS24650 40886..41425 - 540 WP_171455186 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HMJ22_RS24655 41412..41726 - 315 WP_171455187 type-F conjugative transfer system pilin chaperone TraQ -
HMJ22_RS24660 41737..42462 - 726 WP_253718574 type-F conjugative transfer system pilin assembly protein TraF traF
HMJ22_RS24665 42528..44432 - 1905 WP_171455189 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HMJ22_RS24670 44578..45252 - 675 WP_253718565 type-F conjugative transfer system pilin assembly protein TrbC trbC
HMJ22_RS24675 45263..46261 - 999 WP_171455190 conjugal transfer pilus assembly protein TraU traU
HMJ22_RS24680 46258..46635 - 378 WP_171455191 hypothetical protein -
HMJ22_RS24685 46647..47285 - 639 WP_171455229 type-F conjugative transfer system protein TraW traW
HMJ22_RS24690 47282..48163 - 882 WP_171455192 DsbA family protein -
HMJ22_RS24695 48247..48666 - 420 WP_171455193 type-F conjugative transfer system protein TrbI -
HMJ22_RS24700 48663..51293 - 2631 WP_079450624 type IV secretion system protein TraC virb4
HMJ22_RS24705 51307..51846 - 540 WP_171455230 type IV conjugative transfer system lipoprotein TraV traV
HMJ22_RS24710 51871..52257 - 387 WP_171455194 hypothetical protein -
HMJ22_RS24715 52254..52472 - 219 WP_070914249 hypothetical protein virb4
HMJ22_RS24720 52469..53068 - 600 WP_171455195 hypothetical protein -
HMJ22_RS24725 53065..54459 - 1395 WP_171455196 F-type conjugal transfer pilus assembly protein TraB traB
HMJ22_RS24730 54459..55187 - 729 WP_171455197 type-F conjugative transfer system secretin TraK traK
HMJ22_RS24735 55177..55740 - 564 WP_147882578 type IV conjugative transfer system protein TraE traE
HMJ22_RS24740 55751..56056 - 306 WP_042785939 type IV conjugative transfer system protein TraL traL
HMJ22_RS24745 56068..56433 - 366 WP_070914241 type IV conjugative transfer system pilin TraA -
HMJ22_RS24750 56547..56744 - 198 WP_094141473 TraY domain-containing protein -
HMJ22_RS24755 56921..57505 + 585 WP_094141474 helix-turn-helix domain-containing protein -
HMJ22_RS24760 57496..58332 + 837 WP_171455198 queuosine precursor transporter -
HMJ22_RS24765 58402..58788 - 387 WP_171455199 conjugal transfer relaxosome DNA-binding protein TraM -
HMJ22_RS24770 59207..59677 + 471 WP_171455200 transglycosylase SLT domain-containing protein virB1
HMJ22_RS24775 59962..60258 - 297 WP_171455201 DUF5983 family protein -
HMJ22_RS24780 60360..61187 - 828 WP_171455202 DUF932 domain-containing protein -
HMJ22_RS24785 61244..61615 - 372 WP_171455203 dehydrogenase -
HMJ22_RS24790 62152..62382 - 231 WP_171455157 hypothetical protein -
HMJ22_RS24795 62339..62566 - 228 WP_171455204 hypothetical protein -
HMJ22_RS24800 62633..62920 - 288 WP_004929861 type II toxin-antitoxin system RelE/ParE family toxin -
HMJ22_RS24805 62917..63168 - 252 WP_038883487 type II toxin-antitoxin system Phd/YefM family antitoxin -
HMJ22_RS24810 63620..64345 - 726 WP_171455205 plasmid SOS inhibition protein A -

Host bacterium

ID   14165 GenBank   NZ_CP053380
Plasmid name   FY|p2 Incompatibility group   -
Plasmid size   87789 bp Coordinate of oriT [Strand]   59074..59123 [+]
Host baterium   Serratia marcescens strain FY

Cargo genes

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