Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120963
Name   oriT_pCAV1761-205 in_silico
Organism   Serratia marcescens strain CAV1761
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP029448 (1416..1465 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..13, 18..24  (GCAAAAT..ATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pCAV1761-205
AAATCTGCAAAATATTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13231 GenBank   WP_047727551
Name   traI_DKC05_RS01060_pCAV1761-205 insolico UniProt ID   A0A443VHM8
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190459.15 Da        Isoelectric Point: 5.7342

>WP_047727551.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSASNYYTDKDNYYVIGSMDERWQGKGAEALGLDGKVDKQVFTDLLKGKLPDGSDLTRMQ
DGVNKHRPGYDLTFSAPKSVSVMAMIGGDKRLIDAHNQAVTEAVKQVETLAATRVMTDGKSETVLTGNLI
VAKFNHDTNRNQEPQLHTHAVVINATQNGGKWQSLGTDTVGKTGFIENVYANQIAFGKLYREVLKPLVEK
LGYETEVTGKHGMWEMKDVPVEPFSTRSQEVREAAGPDASLKSRDVATLDTRKSKETLDPAEKMVEWVNT
LKESGFDIHSYREDADKRAAEINRAPVSPAKTDGPDISDVVTKAIAGLSDRKVQFTYADMLARTVSQLEA
KPGVFELARTGIDAAIEREQLIPLDREKGLFTSNIHVLDELSVKALSQEVQRQNHVSVTPDASVVRHAPF
SDAVSVLAQDRPAMGIVYGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDARLVGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETLSLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKESGVNTYR
WQGGNQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGVREQGVLNGIIREVLKNEGTLGAKEM
TVTTLTPVWLDSKSRGVRDYYREGMVMERWDPETRKHDRFLIDRVTASSNMLTLRDKEGERLDLKVSAVD
SQWSLFRADKLPVASGERLSVLGKIPETRLKGGESITVLNAEAGQLTVQRPGQKTTQTLAVGAGPFDGIK
VGHGWVESPGRSVSETATVFASLTQRELDNATLNQLAQSGSHIRLYSAQDAARTTEKLARHTAFSVVSEQ
LKARSGETDLDAAIALQKAGLHTPAEQVIHLSIPLLESEELTFTRPQLLATALETGGGKVPMTEIDATIQ
AQIKAGSLLNVPVAPGHGNDLLISRQTWDAEKSILTKVLEGKEAVAPLMDSVPGSLMTDLTSGQRASTRM
ILETTDRFTVVQGYAGVGKTTQLRAVTGAISLLPEATRPRVIGLGPTHRAVGEMQSAGVDAQTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADTAKALSLIAAGGGRAVLSGDTDQLQSIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIDRDVNRALATIEQITPEQVPRKDGAWVPENSVVEFTPAQEETIQK
ALNKGESVPAGQPTTLYEALVKDYADRTPEAQSQTLIITHLNDDRRVLNSLIHDARRDNGEVGREEVTLP
VLVTSNIRDGELRRLSTWTAHKGAVALVDNVYHRIGSVDKENQLITLMDGEGKERLISPREALAEGVTLY
REQEITVSQGDKMRFSKSDTERGYVANSVWEVKSVSGDSVTLSDGKTTRTLNPKADQAQQHVDLAYAITA
HGAQGASEPFAIALEGVAGGRERMASFESSYVGLSRMKQHVQLYTDNREGWIKAINHSPEKATAHDILEP
RNDRAVKTAGQLFSRARALDEAAAGRAALQQSGLARGQSPGKFISPGKKYPQPHVALPAFDKNGKDAGIW
LSPLTDNDGRLQVIGGEGRVMGNEEARFVALQNSRNGESLLAGNMGEGVRIARDNPDSGVVVRLAGDDRP
WNPEAITGGRIWADPLPNPPINDTGTDIPLPPEVLAQRAAEEALRREMERQTEQATREVSGEEKKVGEPG
ERIKEVIGDVIRGLERDRPGEEKTVLPDDPQTRRQEAAVQQVATESLQRDRLQQMERDMVRDLSREKTLG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(970-1156)

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

(634-713)

TrwC relaxase (TrwC)

(10-283)

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

(576-628)

DNA helicase TraI (TraI_C)

(1432-1552)


  Protein structure



No available structure.




T4CP

ID   15510 GenBank   WP_032736842
Name   traD_DKC05_RS01055_pCAV1761-205 insolico UniProt ID   _
Length   764 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 764 a.a.        Molecular weight: 85398.61 Da        Isoelectric Point: 5.0675

>WP_032736842.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLAPMR
DIIRSQPVYTISYYGKSLEYNAEQILADKYTIWCGEQLWTAFVFAAIVSLTICVVTFFVASWVLGRQGKL
QSEDENTGGRQLSDKPKDVARQMKRDGAASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMRGDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDQPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYNPRPKIAEGFIQRRLDTRIDERLSAQLEAREAEGSLVRALFTPDEPVSEPAEEKAGVQPEQTKPAKDS
VLPVPVKTSSMAAEGAGKTPAVPLSGAPVTRVKTVPLIRPKPAASVTGTAAAASTAAVSATAGGTEQELA
QQPVEADQDMLPAGMNEDGVIEDMQAYDAWLEGEQIQRDMQRREEVNINHSRSEQDDIEIGGNF

  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: 864..26900

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DKC05_RS00895 (DKC05_00960) 294..824 + 531 WP_047727555 antirestriction protein -
DKC05_RS00900 (DKC05_00965) 864..1271 - 408 WP_080346868 transglycosylase SLT domain-containing protein virB1
DKC05_RS00905 (DKC05_00970) 1773..2165 + 393 WP_032736874 conjugal transfer relaxosome DNA-binding protein TraM -
DKC05_RS00910 2404..3105 + 702 WP_032736872 hypothetical protein -
DKC05_RS00915 (DKC05_00980) 3190..3390 + 201 WP_060415469 TraY domain-containing protein -
DKC05_RS00920 (DKC05_00985) 3459..3827 + 369 WP_032736871 type IV conjugative transfer system pilin TraA -
DKC05_RS00925 (DKC05_00990) 3841..4146 + 306 WP_032736870 type IV conjugative transfer system protein TraL traL
DKC05_RS00930 (DKC05_00995) 4166..4732 + 567 WP_047727553 type IV conjugative transfer system protein TraE traE
DKC05_RS00935 (DKC05_01000) 4719..5453 + 735 WP_032736867 type-F conjugative transfer system secretin TraK traK
DKC05_RS00940 (DKC05_01005) 5453..6874 + 1422 WP_032736866 F-type conjugal transfer pilus assembly protein TraB traB
DKC05_RS00945 6867..7028 + 162 WP_154235504 hypothetical protein -
DKC05_RS00950 (DKC05_01010) 7048..7617 + 570 WP_042946293 type IV conjugative transfer system lipoprotein TraV traV
DKC05_RS00955 (DKC05_01015) 7729..8007 + 279 WP_032736865 hypothetical protein -
DKC05_RS28725 8092..8493 + 402 WP_032736864 hypothetical protein -
DKC05_RS00965 (DKC05_01025) 8490..8789 + 300 WP_032736863 hypothetical protein -
DKC05_RS00970 (DKC05_01030) 8876..9259 + 384 WP_042946290 hypothetical protein -
DKC05_RS00975 (DKC05_01035) 9352..11991 + 2640 WP_032736861 type IV secretion system protein TraC virb4
DKC05_RS00980 (DKC05_01040) 11991..12380 + 390 WP_032736860 type-F conjugative transfer system protein TrbI -
DKC05_RS00985 (DKC05_01045) 12377..13003 + 627 WP_042946288 type-F conjugative transfer system protein TraW traW
DKC05_RS00990 (DKC05_01050) 13047..14006 + 960 WP_088912317 conjugal transfer pilus assembly protein TraU traU
DKC05_RS00995 (DKC05_01055) 14019..14645 + 627 WP_032736857 type-F conjugative transfer system pilin assembly protein TrbC trbC
DKC05_RS01000 (DKC05_01060) 14642..16585 + 1944 WP_032736856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
DKC05_RS01005 (DKC05_01065) 16699..17310 + 612 WP_032736855 hypothetical protein -
DKC05_RS01010 (DKC05_01070) 17300..17536 + 237 WP_032736854 conjugal transfer protein TrbE -
DKC05_RS01015 (DKC05_01075) 17533..17718 + 186 WP_032736852 hypothetical protein -
DKC05_RS01020 (DKC05_01080) 17765..18091 + 327 WP_032736851 hypothetical protein -
DKC05_RS01025 (DKC05_01085) 18112..18864 + 753 WP_042946285 type-F conjugative transfer system pilin assembly protein TraF traF
DKC05_RS01030 (DKC05_01090) 18875..19111 + 237 WP_032736848 type-F conjugative transfer system pilin chaperone TraQ -
DKC05_RS01035 (DKC05_01095) 19098..19661 + 564 WP_224250969 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
DKC05_RS01040 (DKC05_01100) 19648..21018 + 1371 WP_032736846 conjugal transfer pilus assembly protein TraH traH
DKC05_RS01045 (DKC05_01105) 21018..23861 + 2844 WP_047727552 conjugal transfer mating-pair stabilization protein TraG traG
DKC05_RS01050 (DKC05_01110) 23872..24399 + 528 WP_032736843 hypothetical protein -
DKC05_RS01055 (DKC05_01115) 24606..26900 + 2295 WP_032736842 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21392 GenBank   NZ_CP029448
Plasmid name   pCAV1761-205 Incompatibility group   IncFII
Plasmid size   204825 bp Coordinate of oriT [Strand]   1416..1465 [-]
Host baterium   Serratia marcescens strain CAV1761

Cargo genes

Drug resistance gene   blaSHV-30
Virulence gene   -
Metal resistance gene   merR, merT, merP, merC, merA, merD, merE, pcoE, pcoS, pcoR, pcoD, pcoC, pcoB, pcoA, silP, silA, silB, silF, silC, silR, silS, silE, terE, terD, terC, terB, terA, terZ, terW, arsR, arsD, arsA, arsB, arsC, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -