Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118980
Name   oriT_pHS1090 in_silico
Organism   Serratia marcescens strain HS1090
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OR805036 (77516..77564 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pHS1090
AATCTGCAAAATTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12027 GenBank   WP_064291677
Name   traI_VHB52_RS00285_pHS1090 insolico UniProt ID   A0A6I4Y321
Length   1753 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1753 a.a.        Molecular weight: 190676.77 Da        Isoelectric Point: 6.3386

>WP_064291677.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGIDGKAVDKALFTELLKGKLPDGSDLTRI
QDGANKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVTEAVRQLETLAATRVMTDGKSETVLTGNL
IVAKFNHDTNRNQEPQIHTHAVVINATQNGDKWQSLGTDKIGKTGFIENVYANQIAFGKLYREAFKPLVE
KLGYETEVVGKHGMWEMKGVPVEPFSTRSQEVREAAGPDASLKSRDVAALDTRKSKDAIDPAEKMVEWMN
TLKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLE
AKDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVP
FSDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVT
GKSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTY
RWQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKD
TTITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTGSSNMLTLKDREGVRLDLKVSAV
DSQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGI
KIGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSE
QLKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVSMADIDTTI
QAQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATR
MILESTDRFTVVQGYAGVGKTTQLRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLH
DTQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLTQQR
SAADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIE
KALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITL
PVLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKANQLITLTDSEGKERYISPREASAEGVTL
YRQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAIT
AHGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKHSPEKATAHDILE
PRNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGI
WLSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDR
PWNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEP
ADRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTL
GGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-284)

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

(577-629)

AAA domain (AAA_30)

(971-1157)

DNA helicase TraI (TraI_C)

(1433-1555)

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

(635-714)


  Protein structure



No available structure.




T4CP

ID   14094 GenBank   WP_072101984
Name   traD_VHB52_RS00290_pHS1090 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 85967.95 Da        Isoelectric Point: 5.0577

>WP_072101984.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIS
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPASGPADTDSHASEQPEPVSPPA
PAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATAASTASSAGAPAAAAGGTE
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLTDEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 49649..78122

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
VHB52_RS00290 49649..51961 - 2313 WP_072101984 type IV conjugative transfer system coupling protein TraD virb4
VHB52_RS00295 52090..52779 - 690 WP_072101983 hypothetical protein -
VHB52_RS00300 52972..53703 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
VHB52_RS00305 53889..54422 - 534 WP_014343486 conjugal transfer protein TraS -
VHB52_RS00310 54425..57274 - 2850 WP_013609534 conjugal transfer mating-pair stabilization protein TraG traG
VHB52_RS00315 57274..58653 - 1380 WP_014343487 conjugal transfer pilus assembly protein TraH traH
VHB52_RS00320 58631..59074 - 444 WP_004194305 F-type conjugal transfer protein TrbF -
VHB52_RS00325 59120..59677 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
VHB52_RS00330 59649..59888 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
VHB52_RS00335 59899..60651 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
VHB52_RS00340 60672..60998 - 327 WP_004152676 hypothetical protein -
VHB52_RS00345 61011..61259 - 249 WP_004152675 hypothetical protein -
VHB52_RS00350 61237..61491 - 255 WP_004152674 conjugal transfer protein TrbE -
VHB52_RS00355 61523..63478 - 1956 WP_323145343 type-F conjugative transfer system mating-pair stabilization protein TraN traN
VHB52_RS00360 63537..64175 - 639 WP_069985712 type-F conjugative transfer system pilin assembly protein TrbC trbC
VHB52_RS00365 64188..65177 - 990 WP_160208050 conjugal transfer pilus assembly protein TraU traU
VHB52_RS00370 65174..65575 - 402 WP_004194979 hypothetical protein -
VHB52_RS00375 65610..66245 - 636 WP_029497419 type-F conjugative transfer system protein TraW traW
VHB52_RS00380 66245..66634 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
VHB52_RS00385 66634..69273 - 2640 WP_013214024 type IV secretion system protein TraC virb4
VHB52_RS00390 69345..69743 - 399 WP_023179972 hypothetical protein -
VHB52_RS00395 70122..70526 - 405 WP_004197817 hypothetical protein -
VHB52_RS00400 70593..70904 - 312 WP_029497417 hypothetical protein -
VHB52_RS00405 70905..71123 - 219 WP_004195468 hypothetical protein -
VHB52_RS00410 71446..72030 - 585 WP_032440547 type IV conjugative transfer system lipoprotein TraV traV
VHB52_RS00415 72103..73527 - 1425 WP_004194260 F-type conjugal transfer pilus assembly protein TraB traB
VHB52_RS00420 73527..74267 - 741 WP_013023821 type-F conjugative transfer system secretin TraK traK
VHB52_RS00425 74254..74820 - 567 WP_004144423 type IV conjugative transfer system protein TraE traE
VHB52_RS00430 74840..75145 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
VHB52_RS00435 75159..75527 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
VHB52_RS00440 75596..75796 - 201 WP_004194116 TraY domain-containing protein -
VHB52_RS00445 75882..76583 - 702 WP_004194113 hypothetical protein -
VHB52_RS00450 76813..77205 - 393 WP_004194114 conjugal transfer relaxosome DNA-binding protein TraM -
VHB52_RS00455 77637..78122 + 486 WP_032440470 transglycosylase SLT domain-containing protein virB1
VHB52_RS00460 78155..78484 - 330 WP_071994324 DUF5983 family protein -
VHB52_RS00465 78517..79338 - 822 WP_023287138 DUF932 domain-containing protein -
VHB52_RS00470 80168..80581 - 414 WP_069985713 type II toxin-antitoxin system HigA family antitoxin -
VHB52_RS00475 80582..80860 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
VHB52_RS00480 80850..81170 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
VHB52_RS00485 81251..81475 - 225 WP_014343499 hypothetical protein -
VHB52_RS00490 81486..81698 - 213 WP_019706020 hypothetical protein -
VHB52_RS00495 81759..82115 - 357 WP_019706019 hypothetical protein -
VHB52_RS00500 82747..83097 - 351 WP_023287104 hypothetical protein -

Host bacterium

ID   19412 GenBank   NZ_OR805036
Plasmid name   pHS1090 Incompatibility group   -
Plasmid size   104146 bp Coordinate of oriT [Strand]   77516..77564 [+]
Host baterium   Serratia marcescens strain HS1090

Cargo genes

Drug resistance gene   blaKPC-2, qnrS1
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9